item: #1 of 541 id: cord-000003-ejv2xln0 author: Crouch, Erika C title: Surfactant protein-D and pulmonary host defense date: 2000-08-25 words: 6803 flesch: 33 summary: The role of collectins in host defense Structural aspects of collectins and receptors for collectins Immunocytochemical localization of surfactant protein D (SP-D) in type II cells, Clara cells, and alveolar macrophages of rat lung Surfactant protein D: subcellular localization in nonciliated bronchiolar epithelial cells Localization and developmental expression of surfactant proteins D and A in the respiratory tract of the mouse Localiza-• tion of lung surfactant protein D (SP-D) on mucosal surfaces in human tissues This recent study was the first to systematically investigate the extrapulmonary expression of SP-D in human tissues Immunolocalization of SP-D in human secretory tissues Surfactant protein A and D expression in the porcine Eustachian tube Expression of hydrophilic surfactant proteins by mesentery cells in rat and man Mouse surfactant protein-D. cDNA cloning, characterization, and gene localization to chromosome 14 Surfactant proteins A (SP-A) and D (SP-D): levels in human amniotic fluid and localization in the fetal membranes Antiviral activity of bovine collectins against rotaviruses Recombinant SP-D carbohydrate recognition domain is a chemoattractant for human neutrophils Interactions of pulmonary Surfactant Protein D (SP-D) with human blood leukocytes Surfactant proteins A and D specifically stimulate directed actin-based responses in alveolar macrophages A (SP-A) gene targeted mice P. carinii induces selective alterations in component expression and biophysical activity of lung surfactant Interleukin-4 enhances pulmonary clearance of Pseudomonas aeruginosa Surfactant Protein-D modulates lung inflammation with respiratory syncytial virus infection in vivo Pulmonary-specific expression of SP-D corrects pulmonary lipid accumulation in SP-D gene-targeted mice • Recombinant rat surfactant-associated protein D inhibits human T lymphocyte proliferation and IL-2 production This paper was the first to describe direct, inhibitory effects of SP-D on the stimulated proliferation of blood lymphocytes Interaction of • human lung surfactant proteins A and D with mite (Dermatophagoides pteronyssinus) allergens This study was the first to suggest that interactions of SP-D with glycoconjugates on particulate allergens might influence the immune response Developmental expression of pulmonary surfactant protein D (SP-D) Modulation of surfactant protein D expression by glucocorticoids in fetal rat lung Ontogeny of surfactant apoprotein D, SP-D, in the rat lung Regulation of surfactant protein D in human fetal lung Regulation of surfactant protein D expression by glucocorticoids in vitro and in vivo Pre-and postnatal stimulation of pulmonary surfactant protein D by in vivo dexamethasone treatment of rats Surfactant proteins A • and D increase in response to intratracheal lipopolysaccharide This important paper suggests that SP-A and SP-D participate in the acute response to lung injury Brief exposure to 95% oxygen alters surfactant protein D and mRNA in adult rat alveolar and bronchiolar epithelium KGF increases SP-A and SP-D mRNA levels and secretion in cultured rat alveolar type II cells Characterization of the human Surfactant Protein D promoter: transcriptional regulation of SP-D gene expression by glucocorticoids Proximal promotor of the Surfactant Protein D (SP-D) gene: regulatory role of AP-1, forkhead box, and GT-box binding proteins Genomic organization of human surfactant protein D (SP-D). keywords: alveolar; binding; cells; domain; expression; human; interactions; lung; protein; rat; surfactant cache: cord-000003-ejv2xln0.txt plain text: cord-000003-ejv2xln0.txt item: #2 of 541 id: cord-000012-p56v8wi1 author: Bigot, Yves title: Molecular evidence for the evolution of ichnoviruses from ascoviruses by symbiogenesis date: 2008-09-18 words: 6431 flesch: 40 summary: Since parasitoid wasps are able to vector different viruses [44, 45] , this second scenario opens the exciting possibility that virus genes involved in the ichnovirus biology might correspond to a gene patchwork resulting from transfers from viruses belonging to different NCLDV and non-NCLVD families. Indeed, they match an evolutionary scenario of endosymbiogenesis during which, from a single integration event of symbiotic virus genome, viral genes were lost and/or translocated from the provirus to other chromosomal regions (Fig. 5 ). keywords: ascovirus; dna; dpav4; evolution; genes; genomes; gfiv; host; ichnovirus; origin; particles; proteins; viruses; wasp cache: cord-000012-p56v8wi1.txt plain text: cord-000012-p56v8wi1.txt item: #3 of 541 id: cord-000182-ni6iyzdn author: He, Zhisong title: Predicting Drug-Target Interaction Networks Based on Functional Groups and Biological Features date: 2010-03-11 words: 6042 flesch: 37 summary: All the detailed information for the genes and drugs listed here can be found in A guide to drug discovery: Target selection in drug discovery Predicting human safety: screening and computational approaches Assessment of chemical libraries for their druggability Review: Progress in computational approach to drug development against SARS 3D structure modeling of cytochrome P450 2C19 and its implication for personalized drug design Molecular modeling of two CYP2C19 SNPs and its implications for personalized drug design Review: Pharmacogenomics and personalized use of drugs Review: Structure of cytochrome P450s and personalized drug Structure-based maximal affinity model predicts small-molecule druggability A fast flexible docking method using an incremental construction algorithm Review: Structural bioinformatics and its impact to biomedical science Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS A probabilistic model for mining implicit 'chemical compound-gene' relations from literature Prediction of drug-target interaction networks from the integration of chemical and genomic spaces Statistical prediction of protein chemical interactions based on chemical structure and mass spectrometry data Integrating statistical predictions and experimental verifications for enhancing protein-chemical interaction predictions in virtual screening Alignment-free prediction of a drug-target complex network based on parameters of drug connectivity and protein sequence of receptors A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins Review: Prediction of HIV protease cleavage sites in proteins GPCR-CA: A cellular automaton image approach for predicting G-protein-coupled receptor functional classes GPCR-GIA: a web-server for identifying Gprotein coupled receptors and their families with grey incidence analysis Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides Using functional domain composition and support vector machines for prediction of protein subcellular location Cell-PLoc: A package of web-servers for predicting subcellular localization of proteins in various organisms Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites A sequence-coupled vector-projection model for predicting the specificity of GalNAc-transferase ProtIdent: A web server for identifying proteases and their types by fusing functional domain and sequential evolution information Prediction of protease types in a hybridization space Prediction of membrane protein types and subcellular locations Low-frequency Fourier spectrum for predicting membrane protein types MemType-2L: A Web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM Support vector machines for predicting membrane protein types by using functional domain composition Review: recent advances in developing web-servers for predicting protein attributes A k-nearest neighbor classification rule based on Dempster-Shafer theory PredAcc: prediction of solvent accessibility Prediction of protein cellular attributes using pseudo amino acid composition Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes Digital coding of amino acids based on hydrophobic index Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy Insights from modelling three-dimensional structures of the human potassium and sodium channels The structure of phospholamban pentamer reveals a channel-like architecture in membranes Mechanism of drug inhibition and drug resistance of influenza A M2 channel Structure and mechanism of the M2 proton channel of influenza A virus Prediction of G-protein-coupled receptor classes Coupling interaction between thromboxane A2 receptor and alpha-13 subunit of guanine nucleotide-binding protein LIGAND: chemical database for enzyme reactions From genomics to chemical genomics: new developments in KEGG Predicting networking couples for metabolic pathways of Evaluating the statistical significance of multiple distinct local alignments A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space Prediction of protein secondary structure content by using the concept of Chou's pseudo amino acid composition and support vector machine Use of fuzzy clustering technique and matrices to classify amino acids and its impact to Chou's pseudo amino acid composition Using the concept of Chou's pseudo amino acid composition to predict apoptosis proteins subcellular location: an approach by approximate entropy Predicting protein subcellular location using Chou's pseudo amino acid composition and improved hybrid approach The modified Mahalanobis discriminant for predicting outer membrane proteins by using Chou's pseudo amino acid composition Predicting subcellular localization of mycobacterial proteins by using Chou's pseudo amino acid composition Prediction of Subcellular Localization of Apoptosis Protein Using Chou's Pseudo Amino Acid Composition Prediction of G-protein-coupled receptor classes based on the concept of Chou's pseudo amino acid composition: an approach from discrete wavelet transform Using the augmented Chou's pseudo amino acid composition for predicting protein submitochondria locations based on auto covariance approach Predicting the cofactors of oxidoreductases based on amino acid composition distribution and Chou's amphiphilic pseudo amino acid composition Predicting lipase types by improved Chou's pseudo-amino acid composition Using Chou's amphiphilic pseudoamino acid composition and support vector machine for prediction of enzyme subfamily classes Using Chou's pseudo amino acid composition to predict subcellular localization of apoptosis proteins: an approach with immune genetic algorithm-based ensemble classifier Prediction of cell wall lytic enzymes using Chou's amphiphilic pseudo amino acid composition Medicinal chemistry and bioinformatics -current trends in drugs discovery with networks topological indices Proteomics, networks, and connectivity indices Application of pseudo amino acid composition for predicting protein subcellular location: stochastic signal processing approach Weighted-support vector machines for predicting membrane protein types based on pseudo amino acid composition SLLE for predicting membrane protein types Using pseudo amino acid composition to predict protein structural classes: approached with complexity measure factor Using pseudo amino acid composition to predict protein subcellular location: approached with Lyapunov index, Bessel function, and Chebyshev filter Using cellular automata to generate Image representation for biological sequences Using cellular automata images and pseudo amino acid composition to predict protein subcellular location Using pseudo amino acid composition to predict transmembrane regions in protein: cellular automata and Lempel-Ziv complexity Using Pseudo Amino Acid Composition to Predict Protein Structural Class: Approached by Incorporating 400 Dipeptide Components Predicting protein structural classes with pseudo amino acid composition: an approach using geometric moments of cellular automaton image Using grey dynamic modeling and pseudo amino acid composition to predict protein structural classes Predicting membrane protein type by functional domain composition and pseudo amino acid composition Hum-PLoc: A novel ensemble classifier for predicting human protein subcellular localization Large-scale plant protein subcellular location prediction Predicting membrane protein types by the LLDA algorithm Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-nearest neighbor classifiers Pseudo amino acid composition and its applications in bioinformatics, proteomics and system biology Recognition of a protein fold in the context of the Structural Classification of Proteins (SCOP) classification The classification and origins of protein folding patterns Seventy-five percent accuracy in protein secondary structure prediction Predicting protein folding types by distance functions that make allowances for amino acid interactions A fuzzy k-nearest neighbours algorithm Discriminant Analysis; Chapter 12 Multivariate analysis of variance On the generalized distance in statistics Although there are more features for target than those for drug in the original feature set, more drug features were selected, showing the important role of drugs. keywords: acid; amino; composition; drug; feature; information; interactions; prediction; protein; pseudo; sequence; set; structure; target cache: cord-000182-ni6iyzdn.txt plain text: cord-000182-ni6iyzdn.txt item: #4 of 541 id: cord-000257-ampip7od author: Bagowski, Christoph P title: The Nature of Protein Domain Evolution: Shaping the Interaction Network date: 2010-08-17 words: 4681 flesch: 35 summary: In this review, we aim to describe the basic concepts of protein domain evolution and illustrate recent developments in molecular evolution that have provided valuable new insights in the field of comparative genomics and protein interaction networks. This approach thus primarily focuses on the similarity and differences of the orthologous genes within network, and is therefore ideally suited for the study of protein domain evolution and has already revealed that species-specific parts Fig. keywords: analysis; binding; domains; evolution; expression; gene; genome; interaction; network; protein; sequence cache: cord-000257-ampip7od.txt plain text: cord-000257-ampip7od.txt item: #5 of 541 id: cord-000264-o80duxhs author: Chandramouli, Kondethimmanahalli title: Proteomics: Challenges, Techniques and Possibilities to Overcome Biological Sample Complexity date: 2009-12-08 words: 12282 flesch: 24 summary: there are numerous advantages for using SILAC-based methods compared to chemical labeling, a major drawback of SILAC is that it cannot be applied to tissue protein analysis directly. Membrane proteins constitute 30% of the typical proteome, yet their propensity to aggregate and precipitate in solution confounds their analysis [28] . keywords: affinity; analysis; approach; cell; data; electrophoresis; gel; human; identification; isotope; labeling; mass; membrane; methods; peptides; plasma; protein; proteome; proteomics; samples; separation; serum; spectrometry; technology; throughput cache: cord-000264-o80duxhs.txt plain text: cord-000264-o80duxhs.txt item: #6 of 541 id: cord-000372-wzwpyvll author: Castelló, Alfredo title: The Multifaceted Poliovirus 2A Protease: Regulation of Gene Expression by Picornavirus Proteases date: 2011-04-14 words: 16348 flesch: 40 summary: However, some of the PV proteins are able to target nuclear proteins such as transcription and splicing factors and proteins involved in nuclear-cytoplasmic trafficking. PV infection strongly impacts on hostcell protein localization, giving rise to an unusual cytoplasmic distribution of nuclear proteins [188] . keywords: cells; cleavage; complex; cytoplasm; eif4gi; export; expression; factors; host; infection; initiation; mrna; nuclear; nucleus; poliovirus; pro; protease; protein; rna; synthesis; translation; virus cache: cord-000372-wzwpyvll.txt plain text: cord-000372-wzwpyvll.txt item: #7 of 541 id: cord-000479-u87eaaj8 author: Stolf, Beatriz S. title: Protein Disulfide Isomerase and Host-Pathogen Interaction date: 2011-10-11 words: 6000 flesch: 36 summary: Here, we summarise examples of the cellular association of host PDI with different pathogens and explore the possible roles of pathogen PDIs in infection. Overall, PDI redox activity modulates the stability of the antigen peptide-MHC class I complex and further determines the transport of the complex to the plasma membrane keywords: antigen; cells; disulfide; endoplasmic; host; infection; isomerase; leishmania; oxidase; pathogen; pdi; phagocytosis; process; protein; redox; reticulum cache: cord-000479-u87eaaj8.txt plain text: cord-000479-u87eaaj8.txt item: #8 of 541 id: cord-000575-g1ob16b9 author: Xie, Xiao-li title: Protein sequence analysis based on hydropathy profile of amino acids date: 2012-01-27 words: 2183 flesch: 40 summary: In order to plot amino acid sequence, 20 amino acids in protein sequences are divided into different types, including protein sequence regarded as a word with three, four, or five different letters. A 2-D graphical representation of protein sequences based on nucleotide triplet codons A representation of DNA primary sequences by random walk A 3D graphical representation of RNA secondary structures based on chaos game representation Novel DNA sequence representation H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences 2-D graphical representation of protein sequences and its application to coronavirus phylogeny Simplification of protein sequence and alignment-free sequence analysis Analysis of similarity of DNA sequences based on 3D graphical representation Application of 2D graphical representation of DNA sequence Protein-based phylogenetic analysis by using hydropathy profile of amino acids Enzymes/non-enzymes classification model complexity based on composition, sequence, 3D and topological indices A new graphical representation and analysis of DNA sequence structure: I. Methodology and application to globin genes Two-dimensional graphical representation of DNA sequences and intron-exon discrimination in intronrich sequences Simple numerical descriptor for quantifying effect of toxic substances on DNA sequences Mathematical descriptors of DNA sequences: development and applications Molecular Evolution and Phylogenetics A probabilistic measure for alignment-free sequence comparison Condensed representation of DNA primary sequences 2-D Graphical representation of proteins based on physico-chemical properties of amino acids Characterization of 3-D sequences of proteins On a four-dimensional representation of DNA primary sequences On the characterization of DNA primary sequences by triplet of nucleic acid bases Alignment-free sequence comparison-a review A 2D graphical representation of protein sequence and its numerical characterization Analysis of similarity/dissimilarity of protein sequences Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation A protein map and its application The Z curve database: a graphic representation of genome sequences We would like to thank Dr. Jian-gang WANG (College of Animal Science and Technology, Northwest A&F University, China), Jian-zhong LUO (Department of Foreign languages, Northwest A&F University, China), Feng AN and Dr. Jun-li DU (College of Sciences, Northwest A&F University, China) for their helpful suggestions. keywords: acids; amino; protein; representation; sequence cache: cord-000575-g1ob16b9.txt plain text: cord-000575-g1ob16b9.txt item: #9 of 541 id: cord-000642-mkwpuav6 author: Moreira, Rebeca title: Transcriptomics of In Vitro Immune-Stimulated Hemocytes from the Manila Clam Ruditapes philippinarum Using High-Throughput Sequencing date: 2012-04-19 words: 6864 flesch: 41 summary: Hits to R. philippinarum sequences were represented in a Venn diagram. The discovery of new immune sequences was very productive and resulted in a large variety of contigs that may play a role in the defense mechanisms of Ruditapes philippinarum. keywords: analysis; bivalves; clam; contigs; expression; factor; genes; immune; philippinarum; proteins; recognition; response; ruditapes; sequences; species; transcriptome cache: cord-000642-mkwpuav6.txt plain text: cord-000642-mkwpuav6.txt item: #10 of 541 id: cord-000674-36jzzy77 author: Reggiori, Fulvio title: Autophagy: More Than a Nonselective Pathway date: 2012-05-15 words: 10528 flesch: 32 summary: The origin of the autophagosomal membrane Chemical modulators of autophagy as biological probes and potential therapeutics Autophagy and cytokines Vitamin D, vitamin D receptor, and macroautophagy in inflammation and infection Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes How shall i eat thee Image-based genome-wide siRNA screen identifies selective autophagy factors Structural basis of target recognition by Atg8/LC3 during selective autophagy p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy Structural basis for sorting mechanism of p62 in selective autophagy Selective autophagy mediated by autophagic adapter proteins The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy Autophagy-related protein 8 (Atg8) family interacting motif in Atg3 mediates the Atg3-Atg8 interaction and is crucial for the cytoplasm-to-vacuole targeting pathway FYCO1 is a Rab7 effector that binds to LC3 and PI3P to mediate microtubule plus end-directed vesicle transport Autophagy negatively regulates Wnt signalling by promoting Dishevelled degradation The selective acroautophagic degradation of aggregated proteins requires the PI3P-binding protein alfy Mechanism of cargo selection in the cytoplasm to vacuole targeting pathway The Cvt pathway as a model for selective autophagy Selective Autophagy Regulates Insertional Mutagenesis by the Ty1 Retrotransposon in Saccharomyces cerevisiae Autophagy in organelle homeostasis: peroxisome turnover Autophagy: molecular machinery for self-eating Cooperative binding of the cytoplasm to vacuole targeting pathway proteins, Cvt13 and Cvt20, to phosphatidylinositol 3-phosphate at the pre-autophagosomal structure is required for selective autophagy Atg21 is a phosphoinositide binding protein required for efficient lipidation and localization of Atg8 during uptake of aminopeptidase I by selective autophagy Peroxisome size provides insights into the function of autophagy-related proteins Atg32 is a mitochondrial protein that confers selectivity during mitophagy Mitochondria-anchored receptor Atg32 mediates degrada-tion of mitochondria via selective autophagy PpAtg30 tags peroxisomes for turnover by selective autophagy p62/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtin-induced cell death p62/SQSTM1 and ALFY interact to facilitate the formation of p62 bodies/ALIS and their degradation by autophagy The propeptide of Aminopeptidase 1 mediates aggregation and vesicle formation in the Cytoplasm-to-vacuole targeting pathway A Role for NBR1 in autophagosomal degradation of ubiquitinated substrates Homeostatic levels of p62 control cytoplasmic inclusion body formation in autophagy-deficient mice The adaptor protein p62/SQSTM1 targets invading bacteria to the autophagy pathway Autophagy protects against sindbis virus infection of the central nervous system Midbody ring disposal by autophagy is a post-abscission event of cytokinesis Ubiquitin signals autophagic degradation of cytosolic proteins and peroxisomes Peroxisomal dynamics Nix is critical to two distinct phases of mitophagy, reactive oxygen species-mediated autophagy induction and Parkin-ubiquitin-p62-mediated mitochondrial priming PINK1/Parkinmediated mitophagy is dependent on VDAC1 and p62/SQSTM1 Delivery of cytosolic components by autophagic adaptor protein p62 endows autophagosomes with unique antimicrobial properties p62 targeting to the autophagosome formation site requires self-oligomerization but not LC3 binding Alfy, a novel FYVE-domain-containing protein associated with protein granules and autophagic membranes Phosphorylation of the autophagy receptor optineurin restricts Salmonella growth Phosphorylation of serine 114 on Atg32 mediates mitophagy Two MAPK-signaling pathways are required for mitophagy in Saccharomyces cerevisiae Regulation of the autophagy protein LC3 by phosphorylation Protein kinase C inhibits autophagy and phosphorylates LC3 The Nterminus and Phe52 residue of LC3 recruit p62/SQSTM1 into autophagosomes Serine 403 phosphorylation of p62/SQSTM1 regulates selective autophagic clearance of ubiquitinated proteins Parkin is recruited selectively to impaired mitochondria and promotes their autophagy RNF185, a novel mitochondrial ubiquitin E3 ligase, regulates autophagy through interaction with BNIP1 The deacetylase HDAC6 regulates aggresome formation and cell viability in response to misfolded protein stress HDAC6 controls autophagosome maturation essential for ubiquitin-selective quality-control autophagy HDAC6 rescues neurodegeneration and provides an essential link between autophagy and the UPS Acetylation targets mutant huntingtin to autophagosomes for degradation Disease-causing mutations in Parkin impair mitochondrial ubiquitination, aggregation, and HDAC6-dependent mitophagy Autophagy: renovation of cells and tissues Role of FIP200 in cardiac and liver development and its regulation of TNFα and TSC-mTOR signaling pathways Promotion of tumorigenesis by heterozygous disruption of the beclin 1 autophagy gene Beclin 1, an autophagy gene essential for early embryonic development, is a haploinsufficient tumor suppressor Impairment of starvation-induced and constitutive autophagy in Atg7-deficient mice The role of autophagy during the early neonatal starvation period Atg9a controls dsDNAdriven dynamic translocation of STING and the innate immune response Loss of the autophagy protein Atg16L1 enhances endotoxin-induced IL-1β production Suppression of basal autophagy in neural cells causes neurodegenerative disease in mice Neural-specific deletion of FIP200 leads to cerebellar degeneration caused by increased neuronal death and axon degeneration Loss of autophagy in the central nervous system causes neurodegeneration in mice A recent genomewide small interfering RNA screen aimed at identifying mammalian genes required for selective autophagy found 141 candidate genes to be required for viral autophagy and 96 of those genes were also required for Parkin-mediated mitophagy [79] . keywords: atg5; autophagosome; autophagy; cargo; cell; complex; degradation; figure; formation; kinase; lc3; membrane; mice; mitochondria; mitophagy; p62; pathway; protein; role; ubiquitin cache: cord-000674-36jzzy77.txt plain text: cord-000674-36jzzy77.txt item: #11 of 541 id: cord-000708-iuo2cw23 author: Lippé, Roger title: Deciphering Novel Host–Herpesvirus Interactions by Virion Proteomics date: 2012-05-28 words: 5057 flesch: 28 summary: Proteomic analysis of cells in the early stages of herpes simplex virus type-1 infection reveals widespread changes in the host cell proteome Gene ontology: tool for the unification of biology Redistribution of microtubules and Golgi apparatus in herpes simplex virus-infected cells and their role in viral exocytosis Proteome analysis of vaccinia virus IHD-W-infected HEK 293 cells with 2-dimensional gel electrophoresis and MALDI-PSD-TOF MS of on solid phase support N-terminally sulfonated peptides Host and viral proteins in the virion of Kaposi's sarcomaassociated herpesvirus New insights into viral structure and virus-cell interactions through proteomics Identification of proteins associated with murine gammaherpesvirus 68 virions Cellular stress rather than stage of the cell cycle enhances the replication and plating efficiencies of herpes simplex virus type 1 ICP0-viruses Herpes simplex virus trans-regulatory protein ICP27 stabilizes and binds to 3 ends of labile mRNA Hijacking the translation apparatus by RNA viruses Plunder and stowaways: incorporation of cellular proteins by enveloped viruses A role for the SNARE protein syntaxin 3 in human cytomegalovirus morphogenesis Already, proteomics revealed how viruses modulate the expression of host proteins (Rassmann et al., 2006; Sun et al., 2008; Tong et al., 2008; Antrobus et al., 2009; Pastorino et al., 2009; Thanthrige-Don et al., 2009; Zandi et al., 2009; Zhang et al., 2009 Zhang et al., , 2010 Coombs et al., 2010; Emmott et al., 2010; Lu et al., 2010 Lu et al., , 2012 Munday et al., 2010; Bartel et al., 2011; Lietzen et al., 2011; Ramirez-Boo et al., 2011; Chou et al., 2012) . keywords: analysis; cell; et al; herpes; herpesviruses; host; infection; particles; proteins; type; virions; virus; viruses cache: cord-000708-iuo2cw23.txt plain text: cord-000708-iuo2cw23.txt item: #12 of 541 id: cord-000884-zq8kqf6h author: Shen, Hsin-Hui title: Reconstitution of Membrane Proteins into Model Membranes: Seeking Better Ways to Retain Protein Activities date: 2013-01-14 words: 6869 flesch: 36 summary: This review will discuss the reconstitution of membrane protein activities in four different types of model membrane—monolayers, supported lipid bilayers, liposomes and nanodiscs, comparing their advantages in membrane protein reconstitution. It is essential to find better solutions for retaining membrane protein activities for measurement and characterization in vitro. keywords: activity; atpase; bilayer; binding; interface; lipid; membrane; membrane proteins; model; nanodiscs; phospholipid; proteins; proteoliposomes; reconstitution; structure; water cache: cord-000884-zq8kqf6h.txt plain text: cord-000884-zq8kqf6h.txt item: #13 of 541 id: cord-000979-cav9n18w author: Hoppe, Sebastian title: Rapid Identification of Novel Immunodominant Proteins and Characterization of a Specific Linear Epitope of Campylobacter jejuni date: 2013-05-29 words: 10065 flesch: 45 summary: NCBI gene expression and hybridization array data repository Primer3 on the WWW for general users and for biologist programmers Geneious v5 Basic local alignment search tool Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes A hidden Markov model for predicting transmembrane helices in protein sequences A semi-empirical method for prediction of antigenic determinants on protein antigens New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and x-ray derived accessible sites The SWISS-MODEL Workspace: A web-based environment for protein structure homology modeling The SWISS-MODEL Repository and associated resources SWISS-MODEL: an automated protein homology-modeling server SWISS-MODEL and the Swiss-PdbViewer: A case-control study in FoodNet sites Typing of Campylobacter jejuni and Campylobacter coli isolated from live broilers and retail broiler meat by flaA-RFLP, MLST, PFGE and REP-PCR Rapid pulsed-field gel electrophoresis protocol for subtyping of Campylobacter jejuni Evaluation of three commercial latex agglutination tests for identification of Campylobacter spp Molecular Cloning: A Laboratory Manual, Third Edition Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray Immunogenic cross-reaction among outer membrane proteins of Gram-negative bacteria Microarray-based method for screening of immunogenic proteins from bacteria Proteinprotein interactions: analysis of a false positive GST pulldown result HaloTag: a novel protein labeling technology for cell imaging and protein analysis Validation of two ribosomal RNA removal methods for microbial metatranscriptomics Polyadenylic acid sequences in E. coli messenger RNA Identification of the gene for an Escherichia coli poly(A) polymerase A simple method to enrich mRNA from prokaryotic RNA Magnetic capturehybridization method for purification and probing of mRNA for neutral protease of Bacillus cereus Direct detection of recombinant gene expression by two genetically engineered yeasts in soil on the transcriptional and translational level Normalization of full-length-enriched cDNA Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq Ligation-independent cloning of PCR products (LIC-PCR) High efficiency transformation of E. coli by high voltage electroporation The Campylobacter jejuni/coli CjaA (cj0982c) gene encodes an N-glycosylated lipoprotein localized in the inner membrane Genetic diversity of the Campylobacter genes coding immunodominant proteins Immunogenicity and immunoprotection of recombinant PEB1 in Campylobacter-jejuni-infected mice The National Center for Biotechnology Information's Protein Clusters Database Characterization of Genetically Matched Isolates of Campylobacter jejuni Reveals that Mutations in Genes Involved in Flagellar Biosynthesis Alter the Organism's Virulence Potential Nutrient Acquisition and Metabolism by Campylobacter jejuni Identification of Campylobacter jejuni Genes Contributing to Acid Adaptation by Transcriptional Profiling and Genome-Wide Mutagenesis Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems The Protein Data Bank: A Computer-based Archival File for Macromolecular Structures The 2.0 Crystal Structure of ABC Transporter from Thermatoga maritima Toward the estimation of the absolute quality of individual protein structure models Construction and Evaluation of Normalized cDNA keywords: antibodies; antibody; antigenic; binding; campylobacter; cdna; epitope; immunodominant; incubation; jejuni; linear; min; pcr; proteins; reaction; rna; screening; sequence; specific cache: cord-000979-cav9n18w.txt plain text: cord-000979-cav9n18w.txt item: #14 of 541 id: cord-001093-5l0fthw3 author: Jin, Fan title: Ligand Clouds around Protein Clouds: A Scenario of Ligand Binding with Intrinsically Disordered Proteins date: 2013-10-03 words: 6129 flesch: 47 summary: It is clear that both the apo and the holo peptides have a rather broad conformation distribution, which is typical of disordered proteins. Dynamic modeling of human 5-lipoxygenase-inhibitor interactions helps to discover novel inhibitors Discovery of multitarget inhibitors by combining molecular docking with common pharmacophore matching Virtual screening of novel noncovalent inhibitors for SARS-CoV 3C-like proteinase Rational drug design via intrinsically disordered protein Inhibition of the p53-MDM2 interaction: targeting a proteinprotein interface In vivo activation of the p53 pathway by small-molecule antagonists of MDM2 A small molecule blocking oncogenic protein EWS-FLI1 interaction with RNA helicase A inhibits growth of Ewing's sarcoma Improved low molecular weight Myc-Max inhibitors Multiple independent binding sites for small-molecule inhibitors on the oncoprotein c-Myc Structural rationale for the coupled binding and unfolding of the c-Myc oncoprotein by small molecules Low molecular weight inhibitors of Myc-Max interaction and function X-ray structures of Myc-Max and Mad-Max recognizing DNA: Molecular bases of regulation by proto-oncogenic transcription factors Smallmolecule inhibition of c-MYC:MAX leucine zipper formation is revealed by ion mobility mass spectrometry Polyelectrostatic interactions of disordered ligands suggest a physical basis for ultrasensitivity Electrostatically accelerated coupled binding and folding of intrinsically disordered proteins Binding-induced folding of a natively unstructured transcription factor Optimizing protein-solvent force fields to feproduce intrinsic conformational preferences of model peptides Anchoring intrinsically disordered proteins to multiple targets: lessons from N-terminus of the p53 protein Energy landscape analyses of disordered histone tails reveal special organization of their conformational dynamics A free-energy landscape for coupled folding and binding of an intrinsically disordered protein in explicit solvent from detailed all-atom computations A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations Residual structures, conformational fluctuations, and electrostatic interactions in the synergistic folding of two intrinsically disordered proteins Binding of two intrinsically disordered peptides to a multi-specific protein: a combined Monte Carlo and molecular dynamics study The impact of small molecule binding on the energy landscape of the intrinsically disordered protein C-Myc Ensemble modeling of protein disordered states: Experimental restraint contributions and validation Constructing ensembles for intrinsically disordered proteins Automated prediction of 15N, 13Ca, 13Cb and 13C' chemical shifts in proteins using a density functional database Structure and dynamics of the Ab(21-30) peptide from the interplay of NMR experiments and molecular simulations Homogeneous and heterogeneous tertiary structure ensembles of amyloid-b peptides Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts Fast and accurate predictions of protein NMR chemical shifts from interatomic distances SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features A physical basis for protein secondary structure Determination of secondary structure populations in disordered states of proteins using nuclear magnetic resonance chemical shifts Intrinsically disordered proteins may escape unwanted interactions via functional misfolding MMPBSA.py: an efficient program for end-state free energy calculations Do intrinsically disordered proteins possess high specificity in protein-protein interactions Inhibitor discovery targeting the intermediate structure of beta-amyloid peptide on the conformational transition pathway: Implications in the aggregation mechanism of beta-amyloid peptide Binding energy landscape analysis helps to discriminate true hits from high-scoring decoys in virtual screening The PyMOL molecular graphics system Algorithms for highly efficient, load-balanced, and scalable molecular simulation Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility Atomic-level characterization of the ensemble of the Ab(1-42) monomer in water using unbiased molecular dynamics simulations and spectral slgorithms ACPYPE -AnteChamber PYthon Parser interfacE Fast, efficient generation of highquality atomic Charges. keywords: binding; disordered; figure; idps; interactions; ligand; myc; proteins; simulations; structure cache: cord-001093-5l0fthw3.txt plain text: cord-001093-5l0fthw3.txt item: #15 of 541 id: cord-001244-qdld7hdc author: Fan, Yue-Nong title: iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking date: 2014-03-19 words: 6509 flesch: 35 summary: A subcellular location predictor by incorporating term-frequency gene ontology into the general form of Chou's pseudo-amino acid composition Predicting protein subchloroplast locations with both single and multiple sites via three different modes of Chou's pseudo amino acid compositions Predicting membrane protein types by incorporating protein topology, domains, signal peptides, and physicochemical properties into the general form of Chou's pseudo amino acid composition A multilabel model based on Chou's pseudo-amino acid composition for identifying membrane proteins with both single and multiple functional types Genetic programming for creating Chou's pseudo amino acid based features for submitochondria localization Predicting protein submitochondria locations by combining different descriptors into the general form of Chou's pseudo amino acid composition Multi-kernel transfer learning based on Chou's PseAAC formulation for protein submitochondria localization Using the augmented Chou's pseudo amino acid composition for predicting protein submitochondria locations based on auto covariance approach Prediction of GABA(A) receptor proteins using the concept of Chou's pseudo-amino acid composition and support vector machine Using Chou's amphiphilic pseudo-amino acid composition and support vector machine for prediction of enzyme subfamily classes Predicting antibacterial peptides by the concept of Chou;s pseudo-amino acid composition and machine learning methods Supersecondary structure prediction using Chou's pseudo amino acid composition Identifying bacterial virulent proteins by fusing a set of classifiers based on variants of Chou's pseudo amino acid composition and on evolutionary information A novel feature representation method based on Chou's pseudo amino acid composition for protein structural class prediction Predicting the cofactors of oxidoreductases based on amino acid composition distribution and Chou's amphiphilic pseudo amino acid composition Prediction of metalloproteinase family based on the concept of Chou's pseudo amino acid composition using a machine learning approach SecretP: Identifying bacterial secreted proteins by fusing new features into Chou's pseudo-amino acid composition Prediction of allergenic proteins by means of the concept of Chou's pseudo amino acid composition and a machine learning approach Using Chou's pseudo amino acid composition to predict protein quaternary structure: A sequence-segmented PseAAC approach Identifying protein quaternary structural attributes by incorporating physicochemical properties into the general form of Chou's PseAAC via discrete wavelet transform Using the concept of Chou's pseudo amino acid composition for risk type prediction of human papillomaviruses Prediction of cyclin proteins using Chou's pseudo amino acid composition Discriminating outer membrane proteins with fuzzy K-nearest neighbor algorithms based on the general form of Chou's PseAAC Use of fuzzy clustering technique and matrices to classify amino acids and its impact to Chou's pseudo amino acid composition Protein remote homology detection by combining Chou's pseudo amino acid composition and profile-based protein representation Identification of colorectal cancer related genes with mRMR and shortest path in protein-protein interaction network Hepatitis C virus network based classification of hepatocellular cirrhosis and carcinoma Signal propagation in protein interaction network during colorectal cancer progression PseAAC-Builder: A cross-platform stand-alone program for generating various special Chou's pseudo-amino acid compositions Propy: A tool to generate various modes of Chou's PseAAC PseAAC: A flexible web-server for generating various kinds of protein pseudo amino acid composition The folding type of a protein is relevant to the amino acid composition An optimization approach to predicting protein structural class from amino acid composition Monte Carlo simulation studies on the prediction of protein folding types from amino acid composition Predicting protein folding types by distance functions that make allowances for amino acid interactions Monte Carlo simulation studies on the prediction of protein folding types from amino acid composition. To acquire the 3D structural information in a timely manner, one has to resort to various structural bioinformatics tools (see, e.g., [37] ), particularly the homologous modeling approach as utilized for a series of protein receptors urgently needed during the process of drug development [19, [52] keywords: acid; acid composition; amino; amino acid; approach; chou; composition; drug; pairs; prediction; protein; pseudo; pseudo amino; sequence cache: cord-001244-qdld7hdc.txt plain text: cord-001244-qdld7hdc.txt item: #16 of 541 id: cord-001435-ebl8yc92 author: Hoppe, Sebastian title: Identification of Antigenic Proteins of the Nosocomial Pathogen Klebsiella pneumoniae date: 2014-10-21 words: 9628 flesch: 46 summary: The structure of bacterial outer membrane proteins Identification and characterization of ompl as a potential vaccine candidate for immune-protection against salmonellosis in mice The unique structure of Haemophilus influenzae protein E reveals multiple binding sites for host factors Directed evaluation of enterotoxigenic Escherichia coli autotransporter proteins as putative vaccine candidates Structure of the c-terminal domain of Neisseria heparin binding antigen (nhba), one of the main antigens of a novel vaccine against Neisseria meningitidis In vivo versus in vitro protein abundance analysis of Shigella dysenteriae type 1 reveals changes in the expression of proteins involved in virulence, stress and energy metabolism Surface expression, singlechannel analysis and membrane topology of recombinant Chlamydia trachomatis major outer membrane protein Predicting transmembrane protein topology with a hidden markov model: application to complete genomes A hidden markov model for predicting transmembrane helices in protein sequences A semi-empirical method for prediction of antigenic determinants on protein antigens New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and x-ray-derived accessible sites Toward the estimation of the absolute quality of individual protein structure models The rin: an rna integrity number for assigning integrity values to rna measurements Gene expression omnibus: Protein expression, lysis, and spotting of fulllength proteins were performed as described above. keywords: a.u; alanine; antibodies; antibody; cdna; epitope; linear; min; model; pcr; peptides; pneumoniae; position; proteins; reaction; sequence; specificity cache: cord-001435-ebl8yc92.txt plain text: cord-001435-ebl8yc92.txt item: #17 of 541 id: cord-001567-3bw7jbzq author: Borlak, Jürgen title: Proteome mapping of epidermal growth factor induced hepatocellular carcinomas identifies novel cell metabolism targets and mitogen activated protein kinase signalling events date: 2015-02-25 words: 14018 flesch: 33 summary: Categorization of tumour regulated proteins based on ontology terms 82 non-redundant tumour proteins covering To, UR and DR categories were considered and analysed for Ontologies using the GeneXplain software (v.2.4.1), the biological pathways tools Reactome (http://www.REACTOME.org) and KEGG (http://www.genome.jp/kegg) and WikiPathways (http://wikipathways.org). It is designed to find master regulatory molecules upstream of an input list of regulated tumour proteins. keywords: acid; cancer; carcinoma; cell; disease; egf; egfr; expression; figure; file; gene; growth; hcc; human; liver; master; metabolism; mice; min; network; pathway; proteins; receptor; regulation; serum; signalling; specific; study; table; transgenic; tumour cache: cord-001567-3bw7jbzq.txt plain text: cord-001567-3bw7jbzq.txt item: #18 of 541 id: cord-001726-d7iwkatn author: Henry, Kevin A. title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold date: 2015-08-04 words: 10454 flesch: 13 summary: Filamentous bacteriophage: biology, phage display and nanotechnology applications Antigen-specific therapy of EAE via intranasal delivery of filamentous phage displaying a myelin immunodominant epitope Expression of a 28-kilodalton glutathione S-transferase antigen of Schistosoma mansoni on the surface of filamentous phages and evaluation of its vaccine potential Structural requirements for the activity of the MirB ferrisiderophore transporter of Aspergillus fumigatus Chemically linked phage idiotype vaccination in the murine B cell lymphoma 1 model Phage idiotype vaccination: first phase I/II clinical trial in patients with multiple myeloma Phage display selection of peptides that affect prostate carcinoma cells attachment and invasion A helper phage to improve single-chain antibody presentation in phage display Metagenomic analysis of viruses in reclaimed water Assessing the diversity and specificity of two freshwater viral communities through metagenomics Recombinant expression and neutralizing activity of an MHC class II binding epitope of toxic shock syndrome toxin-1 Epitope-specific antibody response to IgE by mimotope immunization Some physical-chemical and biological properties of the rod-shaped coliphage M13 Generation and characterization of phage-GnRH chemical conjugates for potential use in cat and dog immunocontraception Phage display allows identification of zona pellucida-binding peptides with species-specific properties: novel approach for development of contraceptive vaccines for wildlife Infective and inactivated filamentous phage as carriers for immunogenic peptides Vaccination with filamentous bacteriophages targeting DEC-205 induces DC maturation and potent anti-tumor T-cell responses in the absence of adjuvants The use of filamentous bacteriophage fd to deliver HLA-A2-restricted peptides and to induce strong antitumor CTL responses Selection of HIV-specific immunogenic epitopes by screening random peptide libraries with HIV-1-positive sera Application of bacteriophages for detection of foodborne pathogens Searching for peptide ligands with an epitope library De novo selection of high-affinity antibodies from synthetic Fab libraries displayed on phage as pIX fusion proteins High copy display of large proteins on phage for functional selections Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface Effect of DNA copy number on genetic stability of phage-displayed peptides Hydroxyapatite chromatography of phage-display virions Phage display Libraries of peptides and proteins displayed on filamentous phage Generation of anti-β-amyloid antibodies via phage display technology towards Alzheimer's disease vaccination Filamentous bacteriophage as a novel therapeutic tool for Alzheimer's disease treatment Comparison of phage pVIII and KLH as vector in inducing the production of cytokines in C57BL/6J mice Bacteriophage therapy Viruses in the sea Soon thereafter, filamentous phage were discovered that do not use F-pili for entry (If and Ike; Meynell and Lawn, 1968; Khatoon et al., 1972) , and over time the list of known filamentous phage has expanded to over 60 members (Fauquet et al., 2005) , including temperate and Gram-positivetropic species. keywords: antibodies; antibody; antigen; applications; bacteriophage; cell; coat; coli; display; epitope; et al; evolution; immunization; libraries; m13; mice; peptide; phage; phage display; protein; pviii; responses; specific; surface; system; tumor; type; virus cache: cord-001726-d7iwkatn.txt plain text: cord-001726-d7iwkatn.txt item: #19 of 541 id: cord-001835-0s7ok4uw author: None title: Abstracts of the 29th Annual Symposium of The Protein Society date: 2015-10-01 words: 138771 flesch: 38 summary: In conclusion, the analysis of hydropathic environments strongly suggests that the orientation of a residue in a three-dimensional structure is a direct consequence of its hydropathic environment, which leads us to propose a new paradigm, interaction homology, as a key factor in protein structure. In computer simulation modeling of protein structure in a solvent medium, explicit, implicit, effectivemedium, approaches are often adopted to incorporate the effects of solvation. keywords: acid; activation; activity; addition; affinity; amino; amyloid; analysis; antibodies; antibody; antigen; approach; assay; assembly; associated; bacterial; binding; biology; bonds; cancer; catalytic; cell; cellular; chain; changes; characterization; chemical; chemistry; coli; complex; computational; concentration; conditions; conformation; conserved; control; core; cross; crystal; crystal structure; data; department; determine; development; dimer; disease; disordered; disordered proteins; dna; docking; domain; drug; effect; energy; enzyme; essential; experiments; expression; factors; family; fluorescence; fluorescent protein; formation; forms; fragments; free; functions; gene; group; helix; human; hydrogen; hydrophobic; important; increase; inhibitors; institute; key; kinetic; level; ligand; light; like; lipid; loop; low; major; mass; mechanism; membrane protein; method; model; modification; molecular; molecules; motif; mutant; mutations; n protein; native; nature; new; nmr; non; novel; number; oligomers; order; pathways; peptide; potential; prediction; presence; present; process; processes; properties; protease; protein; protein aggregation; protein association; protein complexes; protein concentration; protein data; protein degradation; protein design; protein domain; protein dynamics; protein engineering; protein evolution; protein expression; protein families; protein folding; protein function; protein interactions; protein interface; protein kinases; protein molecules; protein production; protein sequences; protein stability; protein structure; protein surface; protein tyrosine; provide; range; ray; reaction; receptor; recognition; recombinant; region; regulation; research; residues; response; results; rna; role; self; sequence; set; shows; signal; signaling; simulations; site; size; solution; species; specific; specificity; spectroscopy; stability; state; step; structural; studies; study; substrate; subunit; surface; synthetic; system; target; target protein; tau protein; techniques; temperature; terminal; time; transcription; transfer; transition; transmembrane; type protein; understanding; unfolding; university; use; variants; virus; vitro; wild; work; yeast cache: cord-001835-0s7ok4uw.txt plain text: cord-001835-0s7ok4uw.txt item: #20 of 541 id: cord-001866-s5otdtwq author: Mandal, Nakul title: Proteomic Analysis of the Vitreous following Experimental Retinal Detachment in Rabbits date: 2015-11-18 words: 4583 flesch: 33 summary: Recent trends in the management of rhegmatogenous retinal detachment Pathogenesis of rhegmatogenous retinal detachment: predisposing anatomy and cell biology The epidemiology and socioeconomic associations of retinal detachment in Scotland: a two-year prospective population-based study Cellular effects of detachment and reattachment on the neural retina and the retinal pigment epithelium Epithelial-mesenchymal transition and proliferation of retinal pigment epithelial cells initiated upon loss of cell-cell contact A novel strategy to develop therapeutic approaches to prevent proliferative vitreoretinopathy Ocular proteomics with emphasis on two-dimensional gel electrophoresis and mass spectrometry Proteomics of uveal melanomas suggests HSP-27 as a possible surrogate marker of chromosome 3 loss Proteomic analysis of human vitreous associated with idiopathic epiretinal membrane Analytical platforms in vitreoretinal proteomics Dye-free porcine model of experimental branch retinal vein occlusion: a suitable approach for retinal proteomics Protein changes in the retina following experimental retinal detachment in rabbits Proteome profiling of vitreoretinal diseases by cluster analysis Vitreous proteomic analysis of proliferative vitreoretinopathy Elucidation of the pathogenic mechanism of rhegmatogenous retinal detachment with proliferative vitreoretinopathy by proteomic analysis Proteomic analyses of the vitreous humour Translational vitreous proteomics Improved silver staining protocols for high sensitivity protein identification using matrix-assisted laser desorption/ionization-time of flight analysis Components of the fibrinolytic system in the vitreous body in patients with vitreoretinal disorders Proteome analysis of human vitreous proteins Role of albumin as a fatty acid carrier for biosynthesis of lens lipids Shifting the paradigm of the blood-aqueous barrier Blood-aqueous barrier breakdown associated with rhegmatogenous retinal detachment Risk factors for proliferative vitreoretinopathy Levels of pentosidine in the vitreous of eyes with proliferative diabetic retinopathy, proliferative vitreoretinopathy and retinal detachment Elevation of vitreous leptin in diabetic retinopathy and retinal detachment Immunoglobulins in paired specimens of vitreous and subretinal fluids from patients with rhegmatogenous retinal detachment Experimental retinal detachment. In each case three micrograms of vitreous sample protein was separated on Novex 10-20% gradient Tris-Glycine polyacrylamide gels (Invitrogen Corporation, Carlsbad, CA) and subsequently transferred to nitrocellulose Hybond-C Extra membranes (GE Healthcare). keywords: albumin; antiproteinase; collagen; detachment; mass; peroxiredoxin; protein; spots; vitreous cache: cord-001866-s5otdtwq.txt plain text: cord-001866-s5otdtwq.txt item: #21 of 541 id: cord-001898-ntqyjqqk author: Huang, Chih-Wei title: Lys-315 at the Interfaces of Diagonal Subunits of δ-Crystallin Plays a Critical Role in the Reversibility of Folding and Subunit Assembly date: 2016-01-05 words: 6589 flesch: 43 summary: However, the urea dissociated monomers of K315A mutant protein in GdmCl were reversible folding through a multiple steps mechanism as measured by tryptophan and ANS fluorescence. As shown in Fig 2A, the dramatic changes in the signal for the first transition were due to subunit dissociation as reported previously, with the GdmCl concentrations for half transition ([D] 1/2 ) at 1 ± 0.05 and 0.5 ± 0.01 M for wildtype and K315A mutant protein, respectively [28] . keywords: conformation; crystallin; fig; gdmcl; k315a; monomeric; monomers; mutant; protein; type; urea cache: cord-001898-ntqyjqqk.txt plain text: cord-001898-ntqyjqqk.txt item: #22 of 541 id: cord-002100-dt5zvebj author: He, Yonghua title: Transgenic Soybean Production of Bioactive Human Epidermal Growth Factor (EGF) date: 2016-06-17 words: 6802 flesch: 39 summary: Genistein enhances relaxation of the spontaneously hypertensive rat aorta by transactivation of epidermal growth factor receptor following binding to membrane estrogen receptors-α and activation of G protein-coupled, endothelial nitric acid synthase-dependent pathway Genistein increases epidermal growth factor receptor signaling and promotes tumor progression in advanced human prostate cancer The production of recombinant pharmaceutical proteins in plants Sowing the seeds of success: pharmaceutical proteins from plants Recombinant Pharmaceuticals from Plants: The Plant Endomembrane System as Bioreactor Commercialization of biopharmaceutical and bioindustrial proteins from plants Efficacy of a food plant-based oral cholera toxin β subunit vaccine Oral immunization with hepatitis β surface antigen expressed in transgenic plants Immunogenicity of recombinant LT-B delivered orally to humans in transgenic corn Expression of hepatitis B surface antigen (HBsAg) gene in transgenic banana (Musa Sp) Severe acute respiratory syndrome (SARS) S protein production in plants: development of recombinant vaccine Expression and immunogenicity of an Escherichia coli K99 fimbriae subunit antigen in soybean Protein expression systems: why soybean seeds? in Soybean-Molecular Aspects of Breeding Cosuppression of the α-subunits of β-conglycinin in transgenic soybean seeds induces the formation of endoplasmic reticulum-derived protein bodies Silencing of soybean seed storage proteins results in a rebalanced protein composition preserving seed protein content without major collateral changes in the metabolome and transcriptome Reduction of protease inhibitor activity by expression of a mutant Bowman-Birk gene in soybean seed Epidermal growth factor augments adaptation following small bowel resection: optimal dosage, route, and timing of administration Expression of functional recombinant human growth hormone in transgenic soybean seeds Processing and localization of bovine β-casein expressed in transgenic soybean seeds under control of a soybean lectin expression cassette Embryo-specific silencing of a transporter reduces phytic acid content of maize and soybean seeds Metabolically engineered oilseed crops with enhanced seed tocopherol An alternative to fish oils: metabolic engineering of oilseed crops to produce omega 3 long chain polyunsaturated fatty acids Correct targeting of proinsulin in protein storage vacuoles of transgenic soybean seeds High-level expression of basic fibroblast growth factor in transgenic soybean seeds and characterization of its biological activity Expression of correctly processed human growth hormone in seeds of transgenic tobacco plants Genistein analogues: effects on epidermal growth factor receptor tyrosine kinase and on stress-activated pathways Increased sulfur amino acids in soybean plants overexpressing the maize 15 kD zein protein Enhanced levels of methionine and cysteine in transgenic alfalfa (Medicago sativa L.) plants over-expressing the Arabidopsis cystathionine γ-synthase gene Transgenic soybean plants overexpressing O-acetylserine sulfhydrylase accumulate enhanced levels of cysteine and Bowman-Birk protease inhibitor in seeds Effects of proteome rebalancing and sulfur nutrition on the accumulation of methionine Dry seeds from two successive generations of PCR positive plants were analyzed by ELISA for the expression of EGF protein until all 7 lines were confirmed to be homozygous. keywords: cells; control; egf; egfr; expression; factor; growth; hegf; human; lines; milk; protein; seeds; soybean; soymilk; sulfur; transgenic cache: cord-002100-dt5zvebj.txt plain text: cord-002100-dt5zvebj.txt item: #23 of 541 id: cord-002179-v8lpw4r7 author: Viktorovskaya, Olga V. title: Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements date: 2016-08-24 words: 8043 flesch: 41 summary: [13] exploited a cross-linking label-free MS approach to identify DENV RNA associating proteins in cell culture by cross-linking the RNA to the proteins using short wavelength UV light and isolating DENV RNA bound proteins by anti-sense DNA affinity capture [74] . The overall down-regulation of RNA binding proteins appears to be driven by changes in cytoplasmic and mitochondrial ribosomal subunits, and proteins involved in RNA degradation and processing (S5 Fig). keywords: amplification; analysis; binding; cells; cross; dengue; denv; factors; fig; hnrnp; host; infection; proteins; qtux; replication; rna; virus cache: cord-002179-v8lpw4r7.txt plain text: cord-002179-v8lpw4r7.txt item: #24 of 541 id: cord-002711-b7mlt19n author: Jacomin, Anne-Claire title: iLIR@viral: A web resource for LIR motif-containing proteins in viruses date: 2017-08-14 words: 4467 flesch: 41 summary: Here, we have developed the iLIR@viral database (http://ilir.uk/virus/) as a freely accessible web resource listing all the putative canonical LIR motifs identified in viral proteins. We have developed a database, iLIR@viral (http://ilir.uk/ virus/), that organizes information on the presence of LIR motifs in viral proteins. keywords: atg8; autophagy; family; lc3; lir; motifs; proteins; virus; viruses; wxxl; xlir cache: cord-002711-b7mlt19n.txt plain text: cord-002711-b7mlt19n.txt item: #25 of 541 id: cord-002739-7t1o19kn author: Yu, Xiaobo title: Multiplexed Nucleic Acid Programmable Protein Arrays date: 2017-09-20 words: 6462 flesch: 43 summary: [22] , DNA array to protein array (DAPA) Printing protein arrays from DNA arrays Next-generation high-density self-assembling functional protein arrays Self-assembling protein microarrays Mapping transcription factor interactome networks using HaloTag protein arrays Protein chip fabrication by capture of nascent polypeptides Copper-catalyzed azide-alkyne cycloaddition (click chemistry)-based detection of global pathogen-host AMPylation on self-assembled human protein microarrays Cell-free protein expression and functional assay in nanowell chip format Mycobacterial membrane vesicles administered systemically in mice induce a protective immune response to surface compartments of Mycobacterium tuberculosis Host-pathogen interaction profiling using self-assembling human protein arrays Cytoscape: a software environment for integrated models of biomolecular interaction networks Mapping transcription factor interactome networks using HaloTag protein arrays Autoantibody signature for the serologic detection of ovarian cancer Dynamic antibody responses to the Mycobacterium tuberculosis proteome Systematic identification of interactions between host cell proteins and E7 oncoproteins from diverse human papillomaviruses Functional studies of E7 proteins from different HPV types Adenovirus E1A, simian virus 40 tumor antigen, and human papillomavirus E7 protein share the capacity to disrupt the interaction between transcription factor E2F and the retinoblastoma gene product Antiviral antibody profiling by high-density protein arrays A contra capture protein array platform for studying post-translationally modified auto-antigenomes Exploration of panviral proteome: high-throughput cloning and functional implications in virus-host interactions Serological autoantibody profiling of type 1 diabetes by protein arrays Mycobacterium tuberculosis proteome microarray for global studies of protein function and immunogenicity The identification of phosphoglycerate kinase-1 and histone H4 autoantibodies in pancreatic cancer patient serum using a natural protein microarray Development of natural protein microarrays for diagnosing cancer based on an antibody response to tumor antigens We thank for Dr. Mark Atkinson (University of Florida) for providing sera samples. keywords: antibody; arrays; cell; figure; human; microarrays; nappa; number; plasmids; protein; signal; slide; spot cache: cord-002739-7t1o19kn.txt plain text: cord-002739-7t1o19kn.txt item: #26 of 541 id: cord-002835-qaogpxy9 author: Too, Issac Horng Khit title: Prohibitin plays a critical role in Enterovirus 71 neuropathogenesis date: 2018-01-11 words: 8624 flesch: 43 summary: Incubation of Roc-A with virus prior to NSC-34 cell infection (co-treatment) did not result in any significant reduction in viral titer (S4a Fig) . Meta-analysis with previously published proteomics studies in neuroblastoma or muscle cell lines revealed minimal overlapping which suggests unique host-pathogen interactions in NSC-34 cells. keywords: analysis; anti; assay; cells; control; enterovirus; ev71; fig; host; infection; intracellular; mitochondria; nsc-34; phb; prohibitin; protein; replication; roc; role; virus cache: cord-002835-qaogpxy9.txt plain text: cord-002835-qaogpxy9.txt item: #27 of 541 id: cord-002842-4evbeijx author: Pandey, Rajan Kumar title: Novel Immunoinformatics Approaches to Design Multi-epitope Subunit Vaccine for Malaria by Investigating Anopheles Salivary Protein date: 2018-01-18 words: 5777 flesch: 41 summary: To enhance the stability of vaccine protein, disulfide engineering was performed in a region of high mobility. The molecular weight of vaccine protein was found to be 58 kDa which will favor the antigenicity of the vaccine construct 23 . keywords: cell; construct; ctl; epitopes; model; prediction; protein; response; salivary; sequence; server; structure; subunit; subunit vaccine; vaccine cache: cord-002842-4evbeijx.txt plain text: cord-002842-4evbeijx.txt item: #28 of 541 id: cord-002967-yy3bennu author: Penna, Fabio title: Modulating Metabolism to Improve Cancer-Induced Muscle Wasting date: 2018-01-29 words: 6782 flesch: 30 summary: prognosis Targeting obesity and cachexia: identification of the GFRAL receptor-MIC-1/GDF15 pathway Novel targeted therapies for cancer cachexia Coming back: autophagy in cachexia Increased muscle proteasome activity correlates with disease severity in gastric cancer patients Precachexia in patients with stages I-III non-small cell lung cancer: systemic inflammation and functional impairment without activation of skeletal muscle ubiquitin proteasome system Autophagic-lysosomal pathway is the main proteolytic system modified in the skeletal muscle of esophageal cancer patients In vivo analysis of autophagy in response to nutrient starvation using transgenic mice expressing a fluorescent autophagosome marker Guidelines for the use and interpretation of assays for monitoring autophagy Autophagic degradation contributes to muscle wasting in cancer cachexia Aerobic exercise and pharmacological treatments counteract cachexia by modulating autophagy in colon cancer Autophagy is induced in the skeletal muscle of cachectic cancer patients The calpain system Muscle wasting associated with cancer cachexia is linked to an important activation of the atpdependent ubiquitin-mediated proteolysis Anticytokine treatment prevents the increase in the activity of ATPubiquitin-and Ca 2+ -dependent proteolytic systems in the muscle of tumour-bearing rats Interference with Ca 2+ -dependent proteolysis does not alter the course of muscle wasting in experimental cancer cachexia CALPAIN activity is increased in skeletal muscle from gastric cancer patients with no or minimal weight loss Role of inflammation in muscle homeostasis and myogenesis Anti-cytokine strategies for the treatment of cancer-related anorexia and cachexia NF-κB-mediated Pax7 dysregulation in the muscle microenvironment promotes cancer cachexia Nuclear transcription factor κB activation and protein turnover adaptations in skeletal muscle of patients with progressive stages of lung cancer cachexia Targeting of Fn14 prevents cancer-induced cachexia and prolongs survival BMP signaling controls muscle mass The role of E3 ubiquitin-ligases MuRF-1 and MAFbx in loss of skeletal muscle mass Effect of the specific proteasome inhibitor bortezomib on cancer-related muscle wasting MG132-mediated inhibition of the ubiquitin-proteasome pathway ameliorates cancer cachexia Severe acute respiratory syndrome coronavirus replication is severely impaired by MG132 due to proteasome-independent inhibition of m-calpain Activation of the ATP-ubiquitin-proteasome pathway in skeletal muscle of cachectic rats bearing a hepatoma Increased ATPubiquitin-dependent proteolysis in skeletal muscles of tumor-bearing rats Calpain inhibitors ameliorate muscle wasting in a cachectic mouse model bearing CT26 colorectal adenocarcinoma Anticachectic effects of formoterol Phase I/II trial of formoterol fumarate combined with megestrol acetate in cachectic patients with advanced malignancy Tumor necrosis factor-alpha mediates changes in tissue protein turnover in a rat cancer cachexia model Protein synthesis in muscle measured in vivo in cachectic patients with cancer Attenuation of resting but not load-mediated protein synthesis in prostate cancer patients on androgen deprivation Effects of oral meal feeding on whole body protein breakdown and protein synthesis in cachectic pancreatic cancer patients Protein anabolic resistance in cancer IGF-1 is downregulated in experimental cancer cachexia Muscle atrophy in experimental cancer cachexia: is the IGF-1 signaling pathway involved? Cancer cachexia and diabetes: similarities in metabolic alterations and possible treatment Central tenet of cancer cachexia therapy: do patients with advanced cancer have exploitable anabolic potential? Normal protein anabolic response to hyperaminoacidemia in insulinresistant patients with lung cancer cachexia Muscle protein synthesis in cancer patients can be stimulated with a specially formulated medical food High anabolic potential of essential amino acid mixtures in advanced nonsmall cell lung cancer Current Opinion in Clinical Nutrition and Metabolic Care Anamorelin hydrochloride in the treatment of cancer anorexia-cachexia syndrome: design, development, and potential place in therapy Anamorelin (ONO-7643) in Japanese patients with non-small cell lung cancer and cachexia: results of a randomized phase 2 trial Anamorelin in patients with non-small-cell lung cancer and cachexia (ROMANA 1 and ROMANA 2): results from two randomised, double-blind, phase 3 trials Amino acid uptake in skeletal muscle of rats bearing the Yoshida AH-130 ascites hepatoma Tumour growth results in changes in placental amino acid transport in the rat: a tumour necrosis factor α-mediated effect Cancer cachexia, malnutrition, and tissue protein turnover in experimental animals Hypothesis: muscular glutamine deficiency in sepsis-a necessary step for a hibernation-like state? Enhanced leucine oxidation in rats bearing an ascites hepatoma (Yoshida AH-130) and its reversal by clenbuterol The energy state of tumor-bearing rats Effect of branched-chain amino acids on muscle atrophy in cancer cachexia Leucine-rich diet alters the 1 H-NMR based metabolomic profile without changing the Walker-256 tumour mass in rats Branchedchain amino acids: the best compromise to achieve anabolism? Cancer-induced muscle wasting: latest findings in prevention and treatment Comparison of the anticatabolic effects of leucine and Caβ-hydroxy-β-methylbutyrate in experimental models of cancer cachexia Reversal of cancer-related wasting using oral supplementation with a combination of β-hydroxy-βmethylbutyrate, arginine, and glutamine Supplementation with a combination of beta-hydroxy-beta-methylbutyrate (HMB), arginine, and glutamine is safe and could improve hematological parameters A randomized, doubleblind, placebo-controlled trial of a β-hydroxyl β-methyl butyrate, glutamine, and arginine mixture for the treatment of cancer cachexia (RTOG 0122) Glutamine supplementation in cancer patients L-Glutamine supplementation promotes an improved energetic balance in Walker-256 tumor-bearing rats Lipid mobilization in cachexia: mechanisms and mediators Muscle UCP-3 mRNA levels are elevated in weight loss associated with gastrointestinal adenocarcinoma in humans Mitochondrial and sarcoplasmic reticulum abnormalities in cancer cachexia: altered energetic efficiency? Combination of exercise training and erythropoietin prevents cancer-induced muscle alterations Cancer cachexia is associated with a decrease in skeletal muscle mitochondrial oxidative capacities without alteration of ATP production efficiency Skeletal muscle mitochondrial uncoupling in a murine cancer cachexia model Disrupted skeletal muscle mitochondrial dynamics, mitophagy, and biogenesis during cancer cachexia: a role for inflammation Antioxidant supplementation accelerates cachexia development by promoting tumor growth in C26 tumorbearing mice IL-6 regulation on skeletal muscle mitochondrial remodeling during cancer cachexia in the Apc Min/+ mouse Combined approach to counteract experimental cancer cachexia: eicosapentaenoic acid and training exercise Altered mitochondrial quality control signaling in muscle of old gastric cancer patients with cachexia Mitochondrial biogenesis and fragmentation as regulators of muscle protein degradation The OPA1-dependent mitochondrial cristae remodeling pathway controls atrophic, apoptotic, and ischemic tissue damage Modulation of autophagy and ubiquitinproteasome pathways during ultra-endurance running Skeletal muscle PGC-1β signaling is sufficient to drive an endurance exercise phenotype and to counteract components of detraining in mice Regulatory circuitry of TWEAK-Fn14 system and PGC-1α in skeletal muscle atrophy program A PGC-1α isoform induced by resistance training regulates skeletal muscle hypertrophy Increase in muscle mitochondrial biogenesis does not prevent muscle loss but increased tumor size in a mouse model of acute cancer-induced cachexia The therapeutic potential of skeletal muscle plasticity in Duchenne muscular dystrophy: phenotypic modifiers as pharmacologic targets AMPK and PPARδ agonists are exercise mimetics AMPK activation stimulates autophagy and ameliorates muscular dystrophy in the mdx mouse diaphragm Effects of pharmacological interventions on muscle protein synthesis and breakdown in recovery from burns Effects of the antidiabetic drugs on the age-related atrophy and sarcopenia associated with diabetes type II Metformin treatment modulates the tumour-induced wasting effects in muscle protein metabolism minimising the cachexia in tumour-bearing rats AMP-activated protein kinase-deficient mice are resistant to the metabolic effects of resveratrol Calorie restriction-like effects of 30 days of resveratrol supplementation on energy metabolism and metabolic profile in obese humans An AMP-activated protein kinase-stabilizing peptide ameliorates adipose tissue wasting in cancer cachexia in mice Mammalian sirtuins: biological insights and disease relevance PGC-1α, SIRT1 and AMPK, an energy sensing network that controls energy expenditure SIRT1 protein, by blocking the activities of transcription factors FoxO1 and FoxO3, inhibits muscle atrophy and promotes muscle growth The multifaceted functions of sirtuins in cancer Metabolic control of muscle mitochondrial function and fatty acid oxidation through SIRT1/PGC-1α A pilot randomized, placebo controlled, double blind phase I trial of the novel SIRT1 activator SRT2104 in elderly volunteers A novel sirtuin 2 (SIRT2) inhibitor with p53-dependent pro-apoptotic activity in non-small cell lung cancer Cardiovascular effects of a novel SIRT1 activator, SRT2104, in otherwise healthy cigarette smokers SRT2104 extends survival of male mice on a standard diet and preserves bone and muscle mass Glutamine supplementation was reported to attenuate muscle protein wasting in cancer patients [68] , as well as to improve the energy balance in rats bearing the Walker 256 tumor [69] . keywords: acid; cachexia; cancer; energy; exercise; mass; metabolism; mice; muscle; patients; protein; synthesis; tumor; wasting cache: cord-002967-yy3bennu.txt plain text: cord-002967-yy3bennu.txt item: #29 of 541 id: cord-002973-bkr4ndl2 author: Seifi, Morteza title: Accurate prediction of functional, structural, and stability changes in PITX2 mutations using in silico bioinformatics algorithms date: 2018-04-17 words: 5066 flesch: 35 summary: We used two parallel prediction methods to investigate the possible effects on PITX2 protein structure and stability of missense variants. To assess the performance of eight different stability predictor programs (DUET, SDM, mCSM, I-Mutant3.0, MUpro, iPTREE-STAB, CUPSAT, and iStable) in predicting the effect of missense mutations on PITX2 protein stability, the change in protein stability (ΔΔG) were computed for all 24 PITX2 homeodomain variants (15 functionally characterised and 9 functionally uncharacterised mutations) (Table 7) . keywords: amino; missense; modeling; mutations; pitx2; programs; protein; stability; structure; variants cache: cord-002973-bkr4ndl2.txt plain text: cord-002973-bkr4ndl2.txt item: #30 of 541 id: cord-003020-q69f57el author: Farhadi, Tayebeh title: Computer-aided design of amino acid-based therapeutics: a review date: 2018-05-14 words: 8674 flesch: 36 summary: Designing proteins and peptides Molecular engineering: an approach to the development of general capabilities for molecular manipulation X-ray versus NMR structures as templates for computational protein design High-resolution protein design with backbone freedom Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design Backbone flexibility in computational protein design De novo computational design of retro-aldol enzymes One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions Search and sampling in structural bioinformatics The dead-end elimination theorem and its use in protein side-chain positioning Application of a self-consistent mean field theory to predict protein sidechains conformation and estimate their conformational entropy Design of protein-interaction specificity gives selective bZIP-binding peptides Computational methods for protein design and protein sequence variability: biased Monte Carlo and replica exchange Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm Side-chain and backbone flexibility in protein core design Dead-end elimination with a polarizable force field repacks PCNA structures Improved prediction of protein side-chain conformations with SCWRL4 Trading accuracy for speed: a quantitative comparison of search algorithms in protein sequence design Using self-consistent fields to bias Monte Carlo methods with applications to designing and sampling protein sequences Computational design and characterization of a monomeric helical dinuclear metalloprotein Statistical theory of combinatorial libraries of folding proteins: energetic discrimination of a target structure Achieving stability and conformational specificity in designed proteins via binary patterning Photophysics of a fluorescent non-natural amino acid: p-cyanophenylalanine An expanded eukaryotic genetic code A solvated rotamer approach to modeling watermediated hydrogen bonds at protein-protein interfaces Rotamer libraries in the 21st century Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library Potential energy functions for protein design De novo design of foldable proteins with smooth folding funnel: automated negative design and experimental verification Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions Structure by design: from single proteins and their building blocks to nanostructures Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor Using α-helical coiled coils to design nanostructured metalloporphyrin arrays Kemp elimination catalysts by computational enzyme design De novo design of a βαβ motif High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design Design of a novel globular protein fold with atomic-level accuracy Novel peptide-specific quantitative structure activity relationship (QSAR) analysis applied to collagen IV peptides with antiangiogenic activity Development of an informatics platform for therapeutic protein and peptide analytics Two-level QSAR network (2L-QSAR) for peptide inhibitor design based on amino acid properties and sequence positions Recent development of peptide drugs and advance on theory and methodology of peptide inhibitor design Predicting the affinity of epitope-peptides with class I MHC molecule HLA-A*0201: an application of amino acid-based peptide prediction A brief overview of antimicrobial peptides containing unnatural amino acids and ligand-based approaches for peptide ligands Machine learning assisted design of highly active peptides for drug discovery PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides In silico predictions of 3D structures of linear and cyclic peptides with natural and nonproteinogenic residues Long-timescale molecular dynamics simulations of protein structure and function How fastfolding proteins fold Bond distances in polypeptide backbones depend on the local conformation Identification of tetrapeptides from a mixture based positional scanning library that can restore nM full agonist function of the L106P, I69T, I102S, A219V, C271Y, and C271R human melanocortin-4 polymorphic receptors (hMC4Rs) Protein design seeks to identify the properties of amino acid sequences that fold to predetermined structures with desirable structural and functional characteristics. keywords: acid; amino; amino acid; approach; binding; design; development; docking; drug; energy; interactions; methods; novel; peptide; peptidomimetics; protein; sequence; structure; therapeutics cache: cord-003020-q69f57el.txt plain text: cord-003020-q69f57el.txt item: #31 of 541 id: cord-003070-6oca1mrm author: Shen, Wen-Jun title: RPiRLS: Quantitative Predictions of RNA Interacting with Any Protein of Known Sequence date: 2018-02-28 words: 5485 flesch: 51 summary: As the number of available RNA-protein binding experimental data has increased rapidly due to high-throughput sequencing methods, it is now possible to measure and understand RNA-protein interactions by computational methods. RNA-protein interactions (RPIs) have a critical influence on post-transcriptional gene regulation [1] [2] keywords: acid; data; interactions; method; pairs; protein; rna; rpirls; set; template cache: cord-003070-6oca1mrm.txt plain text: cord-003070-6oca1mrm.txt item: #32 of 541 id: cord-003144-nqkw5v3w author: Qu, Zehui title: Label‐Free Quantitative Proteomic Analysis of Differentially Expressed Membrane Proteins of Pulmonary Alveolar Macrophages Infected with Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus and Its Attenuated Strain date: 2017-11-24 words: 5533 flesch: 47 summary: Cluster of differentiation CD163, vimentin (VIM), and nmII as well as detected proteins are assessed together by string analysis, which elucidated a potentially different infection mechanism. Receptor proteins involved in PRRSV entry are in Figure 9 To better understand the characteristics of pathway-like regions, the GenomRNAi database was analyzed to annotate detected proteins. keywords: abundance; binding; cell; control; expression; group; infection; pams; proteins; prrsv; signaling; strain; virus cache: cord-003144-nqkw5v3w.txt plain text: cord-003144-nqkw5v3w.txt item: #33 of 541 id: cord-003297-fewy8y4a author: Wang, Ming-Yang title: A Comprehensive In Silico Method to Study the QSTR of the Aconitine Alkaloids for Designing Novel Drugs date: 2018-09-18 words: 9161 flesch: 41 summary: key: cord-003297-fewy8y4a authors: Wang, Ming-Yang; Liang, Jing-Wei; Mohamed Olounfeh, Kamara; Sun, Qi; Zhao, Nan; Meng, Fan-Hao title: A Comprehensive In Silico Method to Study the QSTR of the Aconitine Alkaloids for Designing Novel Drugs date: 2018-09-18 journal: Molecules DOI: 10.3390/molecules23092385 sha: doc_id: 3297 cord_uid: fewy8y4a A combined in silico method was developed to predict potential protein targets that are involved in cardiotoxicity induced by aconitine alkaloids and to study the quantitative structure–toxicity relationship (QSTR) of these compounds. Hence, PPI networks with protein targets related to aconitine alkaloid cardiotoxicity must enable us to find the most relevant protein for aconitine toxicity and to understand the mechanism at the network level. keywords: aconitine; aconitine alkaloids; alkaloids; analysis; binding; cardiotoxicity; centrality; channel; compounds; figure; network; potential; ppi; proteins; sodium; structure; study; toxicity; values cache: cord-003297-fewy8y4a.txt plain text: cord-003297-fewy8y4a.txt item: #34 of 541 id: cord-003435-ke0az7nf author: Schlake, Thomas title: mRNA as novel technology for passive immunotherapy date: 2018-10-17 words: 15222 flesch: 37 summary: Dual targeting strategies with bispecific antibodies Diabodies: small bivalent and bispecific antibody fragments Single-chain mono-and bispecific antibody derivatives with novel biological properties and antitumour activity from a COS cell transient expression system Immunotherapeutic perspective for bispecific antibodies Antibody pharmacokinetics and pharmacodynamics Elimination mechanisms of therapeutic monoclonal antibodies Bispecific antibodies rise again Clinical use of blinatumomab for B-cell acute lymphoblastic leukemia in adults Tailoring structure-function and pharmacokinetic properties of single-chain Fv proteins by site-specific PEGylation Strategies to extend plasma half-lives of recombinant antibodies Properties, production, and applications of camelid single-domain antibody fragments Transmigration of beta amyloid specific heavy chain antibody fragments across the in vitro blood-brain barrier Protective effect of different anti-rabies virus VHH constructs against rabies disease in mice Post-exposure treatment with anti-rabies VHH and vaccine significantly improves protection of mice from lethal rabies infection A mAb recognizing a surface antigen of Mycobacterium tuberculosis enhances host survival Antibodies to a cell surface histone-like protein protect against Histoplasma capsulatum Monoclonal antibodies for prophylactic and therapeutic use against viral infections Single-chain fragment variable passive immunotherapies for neurodegenerative diseases Human respiratory syncytial virus and other viral infections in infants receiving palivizumab Bezlotoxumab (Zinplava) for prevention of recurrent Clostridium difficile infection Depletion of B cells in vivo by a chimeric mouse human monoclonal antibody to CD20 Rituximab, an anti-cd20 monoclonal antibody: history and mechanism of action Targeted therapy with the T-cell-engaging antibody blinatumomab of chemotherapy-refractory minimal residual disease in B-lineage acute lymphoblastic leukemia patients results in high response rate and prolonged leukemia-free survival Blinatumomab: a bispecific T cell engager (BiTE) antibody against CD19/CD3 for refractory acute lymphoid leukemia Alternative molecular formats and therapeutic applications for bispecific antibodies Adoptive T-cell immunotherapy T-cell therapy: options for infectious diseases Cancer regression in patients after transfer of genetically engineered lymphocytes Chimeric antigen receptor-and TCR-modified T cells enter main street and wall street Adoptive cell transfer as personalized immunotherapy for human cancer Gene therapy with human and mouse T-cell receptors mediates cancer regression and targets normal tissues expressing cognate antigen Tumor regression in patients with metastatic synovial cell sarcoma and melanoma using genetically engineered lymphocytes reactive with NY-ESO-1 T cells targeting carcinoembryonic antigen can mediate regression of metastatic colorectal cancer but induce severe transient colitis Adoptive transfer of T-cell immunity: gene transfer with MHC-restricted receptors Transgenic TCR expression: comparison of single chain with full-length receptor constructs for T-cell function Independent association of T cell receptor beta and gamma chains with CD3 in the same cell Surface expression of only gamma delta and/or alpha beta T cell receptor heterodimers by cells with four (alpha, beta, gamma, delta) functional receptor chains Alpha beta T cell receptor transfer to gamma delta T cells generates functional effector cells without mixed TCR dimers in vivo TALENmediated editing of endogenous T-cell receptors facilitates efficient reprogramming of T lymphocytes by lentiviral gene transfer Optimizing T-cell receptor gene therapy for hematologic malignancies Expression of immunoglobulin-T-cell receptor chimeric molecules as functional receptors with antibody-type specificity The T-body approach: potential for cancer immunotherapy The basic principles of chimeric antigen receptor design Specific activation and targeting of cytotoxic lymphocytes through chimeric single chains consisting of antibody-binding domains and the gamma or zeta subunits of the immunoglobulin and T-cell receptors Chimeric antigen receptors for T cell immunotherapy: current understanding and future directions Structural design of engineered costimulation determines tumor rejection kinetics and persistence of CAR T cells Chimeric antigen receptors modified T-cells for cancer therapy Adoptive T cell transfer for cancer immunotherapy in the era of synthetic biology Adoptive immunotherapy for cancer: harnessing the T cell response Chimeric antigen receptor T cells for sustained remissions in leukemia CD19 CAR-T cells of defined CD4 + :CD8 + composition in adult B cell ALL patients T cells expressing CD19 chimeric antigen receptors for acute lymphoblastic leukaemia in children and young adults: a phase 1 dose-escalation trial Chimeric antigen receptor-modified T cells for the treatment of solid tumors: defining the challenges and next steps State-of-the-art gene-based therapies: the road ahead Going viral: chimeric antigen receptor T-cell therapy for hematological malignancies Case report of a serious adverse event following the administration of T cells transduced with a chimeric antigen receptor recognizing ERBB2 Treatment of metastatic renal cell carcinoma with autologous T-lymphocytes genetically retargeted against carbonic anhydrase IX: first clinical experience Treatment of metastatic renal cell carcinoma with CAIX CAR-engineered T cells: clinical evaluation and management of on-target toxicity B-cell depletion and remissions of malignancy along with cytokineassociated toxicity in a clinical trial of anti-CD19 chimericantigen-receptor-transduced T cells Clinical development of CAR T cells-challenges and opportunities in translating innovative treatment concepts Current concepts in the diagnosis and management of cytokine release syndrome Preventing and exploiting the oncogenic potential of integrating gene vectors Gene therapy. To this end, T cells can be equipped with an additional T-cell receptor (TCR) or a chimeric antigen receptor (CAR) keywords: administration; antibodies; antibody; antigen; cancer; cap; cells; delivery; efficacy; encoding; expression; gene; human; immunotherapy; mice; mrna; protein; receptor; serum; studies; t cells; therapeutic; transfer; treatment; tumor; use; virus; vivo cache: cord-003435-ke0az7nf.txt plain text: cord-003435-ke0az7nf.txt item: #35 of 541 id: cord-003761-ikni2acz author: Li, Zengbin title: Biological Function and Application of Picornaviral 2B Protein: A New Target for Antiviral Drug Development date: 2019-06-04 words: 6439 flesch: 34 summary: In this review, we mainly summarize recent research data on the viroporin or viroporin-like activity of 2B proteins, which affects the biological function of the membrane, regulates cell death, and affects the host immune response. In addition, the 2B protein exhibits a viroporin or viroporin-like activity, and thus, targeted drugs against viroporin could potentially target 2B protein as a novel strategy to treat or prevent picornavirus infections. keywords: activity; disease; fmdv; foot; host; membrane; mouth; protein; replication; viroporin; virus cache: cord-003761-ikni2acz.txt plain text: cord-003761-ikni2acz.txt item: #36 of 541 id: cord-003817-k3m72uxw author: Braun, Elisabeth title: Furin‐mediated protein processing in infectious diseases and cancer date: 2019-08-05 words: 9081 flesch: 34 summary: 63, 64 MARV and human pathogenic Ebolavirus species harbour canonical furin cleavage sites (R-X-K/R-R↓). Several approaches, including incorporation of D-instead of L-amino acids, have been applied to increase the stability and hence efficacy of furin inhibitors. keywords: activation; activity; cell; cleavage; env; example; expression; furin; glycoprotein; human; influenza; inhibitors; processing; proprotein; proteases; protein; proteolytic; site; target; virus; viruses cache: cord-003817-k3m72uxw.txt plain text: cord-003817-k3m72uxw.txt item: #37 of 541 id: cord-004181-exbs3tz7 author: Pumchan, Ansaya title: Novel Chimeric Multiepitope Vaccine for Streptococcosis Disease in Nile Tilapia (Oreochromis niloticus Linn.) date: 2020-01-17 words: 5774 flesch: 35 summary: Interestingly, the designed chimeric multiepitope DNA vaccine and protein vaccine exhibited effective prevention in Nile tilapia against S. agalactiae, with efficacy similar to that of the whole-cell inactivated vaccine. Herein, the comparative efficacy of both the 45F2 and 42E2 DNA and recombinant protein vaccines indicated that the DNA vaccine provided a higher efficacy than the recombinant protein vaccine. keywords: 42e2; agalactiae; analysis; cell; chimeric; dna; epitopes; expression; fish; multiepitope; protein; serotype; structure; tilapia; vaccine cache: cord-004181-exbs3tz7.txt plain text: cord-004181-exbs3tz7.txt item: #38 of 541 id: cord-004400-li1sc47z author: Ma, Jingjiao title: Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus date: 2020-02-24 words: 4865 flesch: 40 summary: To detect the IFN-β antagonistic ability of NS1 proteins, 293T cells were transfected with the indicated NS1 expression plasmids (0.2 μg/well) together with a plasmid expressing firefly luciferase under the control of the IFN-β promoter (pGL-IFN-β-LUC, 0.2 μg/well), the Renilla luciferase expressing plasmid pRL-TK (0.07 μg/ well), and the IFN-β stimulator poly(I:C) (0.2 μg/well) or a plasmid expressing the active caspase recruitment domain (CARD) of RIG-I (pcDNA-RIG-I 0.2 μg/well), pcDNA-MAVS (0.2 μg/well), pcDNA-TBK1 (0.2 μg/well) or pcDNA-IRF3 (0.2 μg/well) as described previously [34] . This result indicated that the deacetylation-mimic K108R substitution retained NS1 protein in the cytoplasm of infected cells, suggesting that the acetylated K108 residue is important for the nuclear localization of the NS1 protein ( Figures 5A-C ). keywords: 108r; acetylation; cells; ifn; influenza; k108; ns1; ns1 protein; protein; virus; wsn cache: cord-004400-li1sc47z.txt plain text: cord-004400-li1sc47z.txt item: #39 of 541 id: cord-004435-l66ost6q author: Oli, Angus Nnamdi title: Immunoinformatics and Vaccine Development: An Overview date: 2020-02-26 words: 8948 flesch: 30 summary: mSphere An overview of bioinformatics tools for epitope prediction: implications on vaccine development Bioinformatics tools for identifying class I-restricted epitopes In silico-accelerated identification of conserved and immunogenic variola/vaccinia T-cell epitopes NHLBI-AbDesigner: an online tool for design of peptide-directed antibodies iVAX: an integrated toolkit for the selection and optimization of antigens and the design of epitope-driven vaccines From genome to vaccine: in silico predictions, ex vivo verification Designing string-of-beads vaccines with optimal spacers HIV vaccine development by computer assisted design: the GAIA vaccine NERVE: new Enhanced reverse vaccinology environment Jennerpredict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions Genome-wide prediction of vaccine target of human herpes simplex viruses using Vaxign RV VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology PanRV: pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome Understanding Emerging and Re-Emerging Infectious Diseases. Current conventional vaccines came empirically when there were vague or no knowledge of vaccine immune system activation. keywords: antigenic; antigens; approach; cell; data; design; development; diseases; epitope; hla; host; human; immune; immunoinformatics; infection; pathogens; protein; responses; system; vaccine; virus cache: cord-004435-l66ost6q.txt plain text: cord-004435-l66ost6q.txt item: #40 of 541 id: cord-004534-jqm1hxps author: None title: Abstract date: 2009-06-09 words: 139178 flesch: 39 summary: This simple model illustrates how differential detergent selectivity for faces and strong constraints coming from purely environmental features could influence transmembrane helix packing, membrane protein structure and assembly. Imaging of mobile stable lipid rafts in the live cell plasma membrane M. Brameshuber 1 , J. Weghuber 1 , V. Ruprecht 1 , H. Stockinger 2 , G. J. Schuetz 1 1 Johannes Kepler University Linz, Austria, 2 Medical University of Vienna, Austria The organization of the cellular plasma membrane at a nanoscopic length scale is believed to affect the association of distinct sets of membrane proteins for the regulation of multiple signaling pathways. keywords: acid; actin; activation; activity; addition; affinity; afm; aggregates; aggregation; amyloid; analysis; applications; approach; assembly; atomic; atp; behavior; bilayer; binding; biological; biology; biophysics; brain; calcium; cancer; cell; cell membrane; cell surface; center; chain; changes; channel; characterization; charge; chemical; chemistry; cholesterol; combination; complex; complexes; concentration; conditions; confocal; conformational; constant; contrast; control; correlation; cross; current; data; decrease; delivery; density; department; design; detection; development; diffusion; disease; distribution; dna; domain; drug; dynamics; effect; electron; emission; energy; environment; enzyme; excitation; experiments; expression; fibrils; field; flow; fluorescence; fluorescence microscopy; fluorescent protein; force; force microscopy; formation; france; free; fret; function; gene; genova; germany; group; growth; helix; human; imaging; increase; influence; institute; intensity; interaction; intracellular; italy; key; kinetics; laser; length; level; lifetime; ligand; light; lipid; lipid membranes; liposomes; living; measurements; mechanism; membrane; membrane protein; membrane surface; method; microscopy; model; model membrane; molecular; molecules; muscle; mutant; nanoparticles; neuronal; neurons; new; non; novel; number; order; parameters; particles; peptide; phase; physical; physics; plasma membrane; pore; potential; presence; present; probe; process; processes; properties; protein; protein complexes; protein dynamics; protein interactions; protein structure; range; rate; ray; reaction; receptor; region; release; report; research; residues; resolution; response; results; rna; role; sample; scanning; scattering; sciences; second; self; sequence; signal; simulations; site; size; solvent; species; specific; spectroscopy; stability; state; step; structure; studies; study; surface; system; target; techniques; temperature; terminal; time; transfer; transition; transmembrane; transport; treatment; type; understanding; unfolding; university; use; vesicles; virus; vitro; vivo; water; work cache: cord-004534-jqm1hxps.txt plain text: cord-004534-jqm1hxps.txt item: #41 of 541 id: cord-004584-bcw90f5b author: None title: Abstracts: 8th EBSA European Biophysics Congress, August 23rd–27th 2011, Budapest, Hungary date: 2011-08-06 words: 106959 flesch: 38 summary: to that of cell proteins (amide II band at *1550 cm -1 ) Membrane proteins and peptides are acting in an environment rich in other proteins or peptides. keywords: acid; actin; activation; activity; affinity; aggregation; amino; amyloid; analysis; applications; approach; assembly; associated; atomic; bilayer; binding; biological; cancer; cell; cell membrane; cell surface; chain; changes; channel; charge; chemical; cholesterol; complex; complexes; composition; compounds; concentration; conditions; conformational; control; correlation; data; delivery; detection; development; diffusion; distribution; dna; domain; drug; dynamics; effect; electron; energy; environment; enzyme; experiments; expression; fast; field; fluorescence; force; formation; free; function; fusion; gene; group; human; hydrophobic; imaging; increase; influence; institute; interaction; key; kinetics; laser; level; ligand; light; lipid; lipid membranes; liposomes; living; magnetic; major; measurements; mechanism; membrane; membrane binding; membrane interaction; membrane protein; membrane structure; membrane surface; method; microscopy; model; model membrane; molecular; molecules; nanoparticles; native; network; new; nmr; non; novel; number; order; organization; parameters; peptide; phase; plasma membrane; potential; presence; processes; properties; protein; protein complex; protein dynamics; protein interactions; protein structure; proton; range; rate; ray; reaction; receptor; region; regulation; research; residues; resolution; response; results; role; scattering; self; signal; simulations; sites; size; species; specific; spectra; spectroscopy; stability; state; structure; studies; study; substrate; surface; system; techniques; temperature; terminal; time; transfer; transition; transport; type; understanding; university; use; vesicles; vitro; vivo; water; work cache: cord-004584-bcw90f5b.txt plain text: cord-004584-bcw90f5b.txt item: #42 of 541 id: cord-004672-0lf5j8lo author: Anderson, Kevin title: Structural and physiological properties of mengovirus: Avirulent, hemagglutination-defective mutants express altered alpha (1 D) proteins and are adsorption-defective date: 1987 words: 5717 flesch: 53 summary: These data suggest that arrangement of structural proteins on the surface of mutant eapsids did not differ from that of wild-type. Differenees were deteeted among the alpha (1 D) structural proteins of the wild-type and mutant viruses. keywords: alpha; cells; mutant; proteins; species; type; virus; viruses cache: cord-004672-0lf5j8lo.txt plain text: cord-004672-0lf5j8lo.txt item: #43 of 541 id: cord-004673-c8qcjve9 author: Faaberg, K. S. title: Membrane association of the C-terminal half of the open reading frame 1a protein of lactate dehydrogenase-elevating virus date: 1996 words: 4659 flesch: 49 summary: The primary findings concerning the A69 and 183-1 proteins were that they are, as predicted by their hydrophobicity profiles, integral membrane proteins and that they are not N-glycosylated. encoding ORF 1a protein segments encompassing transmembrane segments 5 to 11 and its amphipathic C-terminal end as well as the N-terminal 80 amino acids of the downstream ORF 1b protein were transcribed and the transcripts in vitro translated in the absence and presence of microsomal membranes. keywords: fig; membranes; orf; presence; products; protein; segments; terminal cache: cord-004673-c8qcjve9.txt plain text: cord-004673-c8qcjve9.txt item: #44 of 541 id: cord-004719-3stcx0dd author: Mushegian, A. R. title: Cell-to-cell movement of plant viruses: Insights from amino acid sequence comparisons of movement proteins and from analogies with cellular transport systems date: 1993 words: 6347 flesch: 38 summary: Also, as binding of movement proteins to RNA is thought not to be sequence-specific [14, 17] , it could be anticipated that the majority of movement protein will bind to cellular RNAs, which in the case of TMV infection are in excess over virus RNAs at the time when 30 kD protein is transiently expressed [18] . All the proteins containing the conserved motifs shown in Fig. 1 should be considered a single vast, and highly diverged superfamily of plant virus movement proteins. keywords: acid; amino; cell; mosaic; movement; movement proteins; plant; proteins; rna; sequence; virus; viruses cache: cord-004719-3stcx0dd.txt plain text: cord-004719-3stcx0dd.txt item: #45 of 541 id: cord-004879-pgyzluwp author: None title: Programmed cell death date: 1994 words: 81833 flesch: 47 summary: 8cl-2(z is a mitochondrial or perinuclear-associated oncoprotein that prolongs the life span of a variety of cell types by interfering with programmed cell death. Single and repetitive uptake and release of CPZ were measured in each cell type after individual exposure or exposure in any combination of cell types: In 2 hour competitive uptake studies fibreblasts reached 1.7 and 2.6 times the concentrations of C6-and ROC-cells, :respectively. keywords: acid; activation; activity; addition; adult; amino; analysis; animals; antibodies; binding; brain; calcium; cdna; cell lines; cells; changes; cloned; complex; concentrations; conditions; contrast; control; cultures; current; data; days; decrease; development; different; differentiation; dna; domain; early; effects; end; enzyme; epithelial; experiments; expression; extracts; factor; family; fold; form; formation; function; fusion; gene; gene expression; growth; homology; hormone; human; increase; induction; infected; inhibition; institut; interaction; intracellular; kda; kinase; levels; major; mammalian; mechanisms; medium; membrane; mice; molecular; mouse; mrna; muscle; mutant; nerve; neuronal; neurons; new; non; nuclear; nucleus; number; order; pathway; phosphorylation; play; positive; potential; presence; present; process; production; promoter; properties; protein; protein expression; rat; rate; rats; reaction; receptor; recombinant; recombination; region; regulation; release; replication; response; results; rna; role; sequence; signal; sites; species; specific; stage; stimulation; structure; studies; study; subunit; surface; synthesis; system; t cells; target; terminal; time; tissue; tnf; transcription; treatment; tumor; type; university; virus; vitro; vivo; yeast cache: cord-004879-pgyzluwp.txt plain text: cord-004879-pgyzluwp.txt item: #46 of 541 id: cord-004948-ad3i9wgj author: None title: 7th International Congress on Amino Acids and Proteins : Vienna, Austria, August 6–10, 2001 date: 2001 words: 73789 flesch: 41 summary: After the performic acid oxidation and the 6 M HCl hydrolysis of the protein, OPA/TATG (o-phthaldialdehyde/tetra-O-acetyl-1-thio--D-glucopiranoside) precolumn derivatisation method was used, and the enantiomers of sulphur containing amino acids were separated by RP-HPLC (LiChrosphere 100 RP-18e, 125 ϫ 4 mm, 5 µm column, Merck-Hitachi LaChrom HPLC). The dominant ones are water, ethanol, glycerol, sugars, organic acids, and various ions, while amino acids are present at much lower concentration. keywords: acids; activation; activities; activity; addition; administration; amino acid; analysis; animals; antagonists; apoptosis; approach; arginine; binding; biological; blood; brain; cancer; cell; chain; changes; clinical; complex; compounds; concentration; conditions; content; control; cysteine; data; decrease; department; derivatives; development; disease; dna; dopa; effect; enzyme; ethanol; experiments; expression; following; formation; free; function; gaba; gel; gene; glucose; glutamate; glutamine; group; growth; human; identification; increase; inhibition; institute; leucine; levels; liver; lysine; mass; mechanism; membrane; metabolism; methionine; method; mice; model; molecular; mrna; new; nmda; non; number; patients; peptide; plasma; polyamines; present; production; properties; proteins; rats; reaction; receptor; reduced; release; research; response; results; role; samples; sequence; stress; structure; studies; study; substrate; synthesis; system; taurine; time; tissue; transport; treatment; tumor; type; university; uptake; vitamin; vitro; vivo cache: cord-004948-ad3i9wgj.txt plain text: cord-004948-ad3i9wgj.txt item: #47 of 541 id: cord-005034-wyipzwo4 author: Gleeson, Paul A. title: Targeting of proteins to the Golgi apparatus date: 1994 words: 6551 flesch: 45 summary: There are a number of distinct groups of Golgi membrane proteins, including glycosyltransferases, recyclingtrans-Golgi network proteins, peripheral membrane proteins, receptors and viral glycoproteins. Interestingly no soluble resident Golgi proteins have been identified within the lumen of the Golgi apparatus, which probably indicates that the mechanisms for retaining proteins to this organelle are restricted to membraneassociated proteins. keywords: apparatus; domain; glycosyltransferases; golgi; golgi localization; localization; membrane; proteins; retention; transmembrane cache: cord-005034-wyipzwo4.txt plain text: cord-005034-wyipzwo4.txt item: #48 of 541 id: cord-005145-1l87fdmi author: Marquet-Blouin, E. title: Neutralizing immunogenicity of transgenic carrot (Daucus carota L.)-derived measles virus hemagglutinin date: 2003 words: 5652 flesch: 42 summary: Efficacy of a food plant based cholera toxin B subunit vaccine A plant-based cholera toxin B subunit-insulin fusion protein protects against the development of autoimmune diabetes Analysis of the N-glycosylation of recombinant glycoproteins produced in transgenic plants Binary Agrobacterium vectors for plant transformation Immunosorbent assay based on recombinant hemagglutinin protein produced in a high-efficiency mammalian expression system for surveillance of measles immunity A simplified immunoassay based on measles virus recombinant hemagglutinin protein for testing the immune status of vaccinees Transgenic plants as a potential source of an oral vaccine against Helicobacter pylori Oral immunization by transgenic plants Protective immune response to foot-and-mouth disease virus with VP1 expressed in transgenic plants Measles virus fusion protein-and hemagglutinin-transfected cell lines are sensitive tool for the detection of specific antibodies by FACS-measured immunofluorescence assay Enhanced antigenicity of a four-contact-residue epitope of the measles virus hemagglutinin protein by phage display libraries: evidence of a helical structure in the putative active site Detection, biosynthesis and some functions of glycans N-linked to plant secreted proteins A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity Antibodies to a new linear site at the topographical or functional interface between the haemagglutinin and fusion proteins protect against measles encephalitis Correlation between epitopes on hemagglutinin of measles virus and biological activities: passive protection by monoclonal antibodies is related to their hemagglutination inhibiting activity Expression of immunogenic glycoprotein S polypeptides from transmissible gastroenteritis coronavirus in transgenic plants Oral immunization with a recombinant bacterial antigen produced in transgenic plants Transformation and regeneration of carrot Foreign gene expression in plants Role of individual cysteine residues in the processing and antigenicity of measles virus hemagglutinin protein Role of N-linked oligosaccharide chains in the processing and the antigenicity of the measles virus haemagglutinin protein Plant-derived measles virus hemagglutinin protein induces neutralizing antibodies in mice Preparation of RNA from cotton leaves and pollen A plant-derived edible vaccine against hepatitis B virus Oral immunization with hepatitis B surface antigen expressed in transgenic plants Immunization of mice with recombinant gp41 in a systemic prime/mucosal boost protocol induces HIV-1-specific serum IgG and secretary IgA antibodies Expression of hepatitis B surface antigen in transgenic plants Expression of Norwalk virus capsid protein in transgenic tobacco and potato and its oral immunogenicity in mice Monospecific antibody to the haemagglutinin of measles virus Expression of the rabies virus glycoprotein in transgenic tomatoes Antibodies to measles, mumps, and rubella in UK children 4 years after vaccination with different MMR vaccines Immunization against rabies with plant-derived antigen Modeling the impact of subclinical measles transmission in vaccinated populations with waning immunity Cholera toxin B stimulates systemic neutralizing antibodies after intranasal co-immunization with measles virus Human membrane cofactor protein (CD46) acts as a cellular receptor for measles virus Identification of DNA sequences required for activity of a plant promoter: the CaMV 35S promoter Expression in plants of two bacterial antibiotic resistance genes after protoplast transformation with a new plant expression vector Nuclear transport of plant potyviral proteins Production of hepatitis B surface antigen in transgenic plants for oral immunization Oral immunization in mice with transgenic tomato fruit expressing respiratory syncytial virus-F protein induces a systemic immune response Promoters for pregenomic RNA of banana streak badnavirus are active for transgene expression in monocot and dicot plants Immunogenicity in humans of a recombinant bacterial antigen delivered in a transgenic potato Human immune responses to a novel norwalk virus vaccine delivered in transgenic potatoes Immunogenicity of transgenic plant-derived hepatitis B surface antigen A rapid method for transformation of carrot (Daucus carota L.) by using direct somatic embryogenesis Synthesis of the membrane fusion and hemagglutinin proteins of measles virus, using a novel baculovirus vector containing the β-galactosidase gene Induction of a protective antibody response to foot and mouth disease virus in mice following oral or parental immunization with alfalfa transgenic plants expressing the viral structural protein VP1 Measles virus: both hemagglutinin and fusion glycoproteins are requiered for fusion Protection against measles virus encephalitis by monoclonal antibodies binding to a cystein loop domain of the H protein mimicked by peptides which are not recognized by maternal antibodies We are grateful to Richard Wagner and his team (IBMP) for taking care of the transgenic carrots. These results demonstrate that transgenic carrot plants can be used as an efficient expression system to produce highly immunogenic viral antigens. keywords: antibodies; cells; dna; et al; expression; measles; membrane; plants; protein; transgenic; virus cache: cord-005145-1l87fdmi.txt plain text: cord-005145-1l87fdmi.txt item: #49 of 541 id: cord-006229-7yoilsho author: None title: Abstracts of the 82(nd) Annual Meeting of the German Society for Experimental and Clinical Pharmacology and Toxicology (DGPT) and the 18(th) Annual Meeting of the Network Clinical Pharmacology Germany (VKliPha) in cooperation with the Arbeitsgemeinschaft für Angewandte Humanpharmakologie e.V. (AGAH) date: 2016-02-06 words: 134020 flesch: 40 summary: Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cell carcinoma (RCC) and is characterized by a metabolic shift towards enhanced aerobic glycolysis and hence, increased lactate production. Further studies will be performed to clarify whether silver ions and/or silver nanoparticles could affect the specific N-acetylation of arylamines in human cells. keywords: acid; activation; activity; addition; agents; agonist; aim; analysis; animal; anti; approach; assay; assessment; background; barrier; binding; blood; body; brain; camp; cancer; cancer cells; cardiac; cell death; cell line; cells; cgmp; changes; channels; chemical; chronic; clinical; complex; compounds; concentrations; conclusion; conditions; contrast; control; culture; current; damage; data; days; death; development; differences; different; differentiation; disease; dna; dose; drug; e.g.; effects; endothelial; enzyme; experiments; exposure; expression; factor; fibroblasts; findings; flow; fold; food; formation; fret; function; g protein; gene; germany; group; growth; health; heart; human; impact; increase; induction; inflammation; influence; inhibition; inhibitors; insulin; interaction; intracellular; kidney; levels; line; liver; loss; low; lung; mcpd; mechanisms; membrane; metabolism; metabolites; methods; mice; migration; model; mouse; mrna; nanoparticles; neurons; new; non; novel; number; oct1; order; p<0.05; parameters; pathways; patients; phosphorylation; plasma; platelet; potential; presence; present; primary; processes; products; proliferation; properties; protein; protein expression; rats; receptor; receptor activation; reduced; reduction; regulation; release; research; resistance; response; results; risk; role; samples; set; signaling; skin; small; specific; stimulation; stress; studies; study; substances; system; target; test; testing; therapy; time; tissue; total; toxicity; transcription; treatment; tumor; type; uptake; vitro; vivo; vs.; weight cache: cord-006229-7yoilsho.txt plain text: cord-006229-7yoilsho.txt item: #50 of 541 id: cord-006230-xta38e7j author: None title: Deutsche Gesellschaft für Experimentelle und Klinische Pharmakologie und Toxikologie e.V. date: 2012-02-22 words: 136000 flesch: 40 summary: In in-vitro studies on rat and canine mast cells and human mast cell leukemia cells HMC1.2 BZ at micromolar concentrations inhibited mediator release which appeared to be related to an inhibition of the intracellular cAMP pathway. Previous work showed that mouse cells lacking the immediate-early gene c-fos are hypersensitive to ultraviolet (UVC) light. keywords: acid; activation; activity; acute; addition; adducts; agonist; aim; analysis; animals; anti; apoptosis; approach; assay; assessment; binding; blood; brain; calcium; camp; cancer; cancer cells; cardiac; cell line; cells; cellular; cgmp; changes; channels; chronic; clinical; complex; compounds; concentration; conclusion; conditions; contrast; control; current; damage; data; days; death; decrease; deficient; development; differences; differentiation; disease; dna; dose; drug; e.g.; effects; endothelial; enzyme; evidence; experiments; exposure; expression; factor; failure; family; fibroblasts; findings; fold; food; formation; function; für; g protein; gene; gene expression; germany; glucose; growth; health; heart; human; hypertrophy; increase; induction; inflammation; inhibition; inhibitors; institut; insulin; interaction; intracellular; kidney; kinase; leads; levels; like; line; liver; loss; low; lung; macrophages; mechanisms; membrane; methods; mice; model; mouse; mrna; muscle cells; mutations; nanoparticles; ndpk; non; novel; number; pain; pathway; patients; pcr; pharmakologie; phosphorylation; plasma; potential; presence; present; pressure; primary; processes; production; products; proliferation; promoter; properties; protein; protein expression; pulmonary; rats; receptor; reduced; regulation; release; response; results; risk; rkip; role; ros; samples; selective; signaling; site; skin; smooth; specific; stimulation; stress; studies; study; substances; subunits; synthesis; system; t cells; target; test; tested; therapy; time; tissue; toxicity; toxikologie; toxin; transcription; transport; treatment; tumor; tumor cells; type; universität; uptake; values; vascular; vitro; vivo; water cache: cord-006230-xta38e7j.txt plain text: cord-006230-xta38e7j.txt item: #51 of 541 id: cord-006331-s2qf98lj author: Spiridonova, V. A. title: Molecular recognition elements: DNA/RNA-aptamers to proteins date: 2010-05-23 words: 7145 flesch: 57 summary: Now convincing evidence exists that aptamers are a new effective group of therapeutics, which may represent The scheme illustrating the SELEX method for preparation of DNA and RNA aptamers. The range of disso ciation constants characterizing binding of DNA and RNA aptamers to their protein targets varies from nanomolar to subnanomolar levels. keywords: activity; aptamer; binding; cells; complex; control; dna; hiv; human; library; molecules; protein; rna; rounds; selection; thrombin cache: cord-006331-s2qf98lj.txt plain text: cord-006331-s2qf98lj.txt item: #52 of 541 id: cord-006636-xgikbdns author: Ühlein, E. title: Übersicht Über neue ernährungswissenschaftliche Publikationen date: 1964-02-01 words: 31083 flesch: 47 summary: im Liehte der mathematisehen Analyse der Bestimmungen der Fleischbcschau yon Schweinefleisch mSglieh? zur Bestimmung der Gesamtjodzahl yon keywords: 1963; absorption; abstr; acid; acid composition; acid metabolism; activity; amino; amino acid; analysis; arch; auf; beef; bei; bei der; bestimmung; blood; body; calcium; carbohydrate; changes; chemical; chick; children; cholesterol; comparison; composition; content; corn; cows; dairy; deficiency; den; der; des; determination; development; die; diet; digestibility; effect; egg; energy; ern; evaluation; excretion; factors; fat; fats; fatty; fed; feeding; feeds; fiber; fish; flour; food; fruit; glucose; growth; hrung; human; influence; intake; iron; lebensmittel; levels; lipids; liver; low; magnesium; malnutrition; meat; metabolism; method; milch; milk; nitrogen; nutrient; nutrition; nutritive; oil; performance; phosphorus; pigs; plant; plasma; potassium; poultry; production; products; protein; quality; r. s.; rats; relation; relationship; requirements; residues; response; s. s.; serum; sheep; sodium; storage; studies; study; temperature; tissue; und; untersuchungen; use; utilization; value; van; vitamin; water; wheat; wirkung; wiss; yon; zinc; zum; zur cache: cord-006636-xgikbdns.txt plain text: cord-006636-xgikbdns.txt item: #53 of 541 id: cord-006860-a3b8hyyr author: None title: 40th Annual Meeting of the GTH (Gesellschaft für Thrombose- und Hämostaseforschung) date: 1996 words: 90772 flesch: 46 summary: The data show that children with low risk did in part receive higher doses of heparin and/or AT III concentrate than did high risk patients, whereas plasma therapy was adjusted to severity of eoagnlopathy. Inhibitor testing was done on patients plasma samples using the Bethesda method. keywords: activation; activity; acute; addition; age; agents; aggregation; analysis; antibodies; anticoagulant; anticoagulation; antigen; antithrombin; apc; aptt; assay; binding; bleeding; blood; blood coagulation; blood samples; cases; cells; children; clinical; clotting; coagulation; coagulation factor; complex; complications; concentrations; conclusion; contrast; control; coronary; correlation; count; data; day; days; deficiency; diagnosis; disease; dose; effect; elevated; endothelial; events; expression; factor; factor v; factor viii; family; fibrin; fibrinogen; formation; group; heparin; hirudin; hours; human; incidence; increase; influence; infusion; inhibitor; inr; laboratory; levels; low; mean; median; method; months; mutation; normal; order; parameters; patients; period; phase; plasma; plasma samples; plasminogen; platelet; platelet activation; platelet factor; present; products; protein; protein c; prothrombin; pts; range; reagent; receptor; reduced; release; resistance; response; results; risk; risk factor; role; samples; specific; studies; study; surface; surgery; system; test; therapy; thrombin; thrombosis; time; tissue; total; treatment; type; use; values; vascular; vein; venous; viii; vwf; weight; years cache: cord-006860-a3b8hyyr.txt plain text: cord-006860-a3b8hyyr.txt item: #54 of 541 id: cord-007092-ukqvhzws author: Themsakul, Sirintra title: Secretion of M2e:HBc fusion protein by Lactobacillus casei using Cwh signal peptide date: 2016-09-08 words: 3337 flesch: 45 summary: To determine whether the three selected SPs (i.e. CwhSP, SurASP and SP6565) could drive heterologous protein secretion in L. casei, an ESV based on each of these was constructed. For this reason, homologous SPs are thought to drive protein secretion more efficiently than heterologous SPs (Mathiesen et al. 2008) . keywords: casei; gfpuv; hbc; m2e; plc; protein; secretion; sps cache: cord-007092-ukqvhzws.txt plain text: cord-007092-ukqvhzws.txt item: #55 of 541 id: cord-007208-wnkjdg6y author: Li, Sheng-Hsiang title: Demonstration of a Glycoprotein Derived From the Ceacam10 Gene in Mouse Seminal Vesicle Secretions(1) date: 2005-09-01 words: 5646 flesch: 52 summary: The role of the seminal vesicles, coagulating glands and prostate glands on the fertility and fecundity of mice Effects of seminal vesicle removal on fertility and uterine sperm motility in the house mouse The androgendependent mouse seminal vesicle secretory protein IV: characterization and complementary deoxyribonucleic acid cloning A novel heat-labile phospholipid-binding protein, SVS VII, in mouse seminal vesicle as a sperm motility enhancer Developmental profile of a caltrin-like protease inhibitor, P12, in mouse seminal vesicle and characterization of its binding sites on sperm surface Seminal vesicle autoantigen, a novel phospholipid-binding protein secreted from luminal epithelium of mouse seminal vesicle, exhibits the ability to suppress mouse sperm motility A seminal vesicle autoantigen of mouse is able to suppress sperm capacitation-related events stimulated by serum albumin The cea10 gene encodes a secreted member of the murine carcinoembryonic antigen family and is expressed in the placenta, gastrointestinal tract and bone marrow Enzymatic deglycosylation of asparagine-linked glycans: purification, properties, and specificity of oligosaccharide-cleaving enzymes from Flavobacterium meningosepticum Measurement of protein using bicinchoninic acid Various forms of mouse lactoferrins: purification and characterization Cleavage of structural proteins during the assembly of the head of bacteriophage T4 Molecular Cloning. 5PW column (Waters, Milford, MA); Vydac 218TP54 C 18 column (Separations Group, Hesperia, CA); AminoLink coupling gel, bicinchoninic protein assay kit (Pierce, Rockford, IL); testosterone propionate, nitroblue tetrazolium, 5-bromo-4-chloro-3-indolyl phosphate (BCIP), PMSF, periodic acid Schiff reagent, and silanated glass slides (Sigma Chemical Co., St Louis, MO); cDNA integrity kit, alkaline phosphataseconjugated streptavidin, and biotin-conjugated goat anti-rabbit immunoglobulin G (IgG; Kirkegaard & Perry Laboratories, Gaithersburg, MD); rhodamine-conjugated goat anti-rabbit IgG (Zymed Laboratories, San Francisco, CA); Nuclear Fast Red (Vector Laboratories, Burlingame, CA); enhanced chemiluminescent substrate and [␣- 32 A) Fractionation of soluble mouse SVS proteins by ion exchange chromatography on a DEAE-Sephacel column. keywords: ceacam10; column; fig; mice; min; motility; mouse; peak; protein; rna; solution; sperm; vesicle cache: cord-007208-wnkjdg6y.txt plain text: cord-007208-wnkjdg6y.txt item: #56 of 541 id: cord-007211-prygoc0q author: Segawa, Hiroaki title: The Roles of Individual Cysteine Residues of Sendai Virus Fusion Protein in Intracellular Transport(1) date: 1998-06-17 words: 5961 flesch: 46 summary: Cell Surface Transport of Cysteine Mutant F Proteins-To examine the expression of cysteine mutant F proteins in the cells and their transport to the cell surface, the cells were fixed with acetone or paraformaldehyde and examined by indirect immunofluorescence staining using anti-F antiserum. This indicates that cysteine mutant F proteins were efficiently expressed in these cells. keywords: cells; cysteine; disulfide; expression; f proteins; mutant; protein; psrd; surface; virus cache: cord-007211-prygoc0q.txt plain text: cord-007211-prygoc0q.txt item: #57 of 541 id: cord-007648-tm0hn0hz author: Mockett, A.P.Adrian title: Envelope proteins of avian infectious bronchitis virus: Purification and biological properties date: 2002-12-20 words: 2219 flesch: 52 summary: Three different antigens were used for the EI,ISAs: spike protein, membrane protein and IB virus. The advantages of purifying viral proteins using affinity chromatography with monoclonal antibodies are discussed. keywords: antibodies; membrane; proteins; spike; virus cache: cord-007648-tm0hn0hz.txt plain text: cord-007648-tm0hn0hz.txt item: #58 of 541 id: cord-007755-o2r8ktie author: Kokoszka, Malgorzata E. title: Mapping Protein–Protein Interactions with Phage-Displayed Combinatorial Peptide Libraries and Alanine Scanning date: 2014-10-20 words: 2927 flesch: 52 summary: A general workfl ow diagram for isolating and characterizing the peptide ligands to protein domains or fragments using phage display methods. Also, decreasing the amount of used target can facilitate isolation of higher affi nity clones. keywords: binding; cbk1; dna; ligands; peptide; phage; protein; target cache: cord-007755-o2r8ktie.txt plain text: cord-007755-o2r8ktie.txt item: #59 of 541 id: cord-008293-5cwb5g3h author: Shaw, Shyh-Yu title: Analogous amino acid sequences in myelin proteolipid and viral proteins date: 1986-10-27 words: 1581 flesch: 41 summary: When comparing myelin proteins with viral proteins, it is difficult to make a compelling case for homology, since the similarities fall off after a few residues. * To whom correspondence should be addressed Abbreviations: MBP, myelin basic protein; EAE, experimental allergic encephalomyelitis; CNS, central nervous system; MLV, murine leukemia virus; AIDS, acquired immune deficiency syndrome; HTLV-III/LAV, human T-lymphotropic retrovirus The most abundant protein of CNS myelin is myelin proteolipid protein, which is embedded in the myelin membrane. keywords: mbp; myelin; proteins; proteolipid cache: cord-008293-5cwb5g3h.txt plain text: cord-008293-5cwb5g3h.txt item: #60 of 541 id: cord-008556-oetrdm8g author: Kozak, Marilyn title: Regulation of Protein Synthesis in Virus-Infected Animal Cells date: 2008-03-01 words: 23992 flesch: 40 summary: On the regulation of protein synthesis in vaccinia virus infected cells A joint product of the genes gag and pol of avian sarcoma virus: A possible precursor of reverse transcriptase Post-translational regulation of the 54K cellular tumor antigen in normal and transformed cells The influence of the host cell on the inhibition of virus protein synthesis in cells doubly infected with VSV and mengovirus Sequence studies of several alphavirus genomic RNAs in the region containing the start of the subgenomic RNA Characterization of a ts mutant of vaccinia virus 25,422-426. The replication of picornaviruses Expression from an internal AUG codon of herpes simplex thymidine kinase gene inserted in a retrovirus vector The number of ribosomes on SV40 late 16s mRNA is determined in part by the nucleotide sequence of its leader Complete nucleotide sequence of alfalfa mosaic virus RNA 3 Sequence analysis of hepatitis A virus cDNA coding for capsid proteins and RNA polymerase Direct mapping of adeno-associated virus capsid proteins B and C: A possible ACG initiation codon Structure of the FMDV translation initiation site and of the structural proteins UAG readthrough during TMV RNA translation: Isolation and sequence of two tRNAsTyr with suppressor activity from tobacco plants The molecular basis for differential translation of TMV RNA in tobacco and wheat germ Measles virus P gene codes for two proteins Inhibition of HeLa cell protein synthesis during adenovirus infection Regulatory mutants of polyoma virus defective in DNA replication and the synthesis of early proteins Solubilization of a protein synthesis inhibitor from vaccinia virions Codon selection in yeast Translational interference a t overlapping reading frames in prokaryotic mRNA Effect of the tripartite leader on synthesis of a nonviral protein in an adenovirus 5 recombinant Poliovirus mutant that does not selectively inhibit host cell protein synthesis Two small RNAs encoded by Epstein-Barr virus can functionally substitute for the virus-associated RNAs in the lytic growth of adenovirus 5 Construction and analysis of additional adenovirus substitution mutants confirm the complementation of VAI RNA function by two small RNAs encoded by Epstein-Barr virus Structural requirements of adenovirus VAI RNA for its translation enhancement function Differential inhibition of host cell RNA synthesis in several picornavirus-infected cell lines Effect of viral infection on host protein synthesis and mRNA association with the cytoplasmic cytoskeletal structure Intermolecular duplexes formed from polyadenylated vaccinia virus RNA keywords: adenovirus; aug; binding; cap; cells; codon; et al; gene; host; host mrnas; host protein; host translation; infection; influenza; inhibition; initiation; late; mechanism; mrnas; poliovirus; protein; protein synthesis; reovirus; ribosomes; sequence; shutoff; site; synthesis; translation; upstream; vaccinia; viral; virus; virus mrnas cache: cord-008556-oetrdm8g.txt plain text: cord-008556-oetrdm8g.txt item: #61 of 541 id: cord-008777-i2reanan author: None title: ECB12: 12th European Congess on Biotechnology date: 2005-07-19 words: 151661 flesch: 40 summary: During the process development for protein production, short time to market and the demand for cheap processes dominate today's process development. Interdependence of the impact of methanol and oxygen supply on protein production with recombinant Pichia pastoris N.K. Khatri, F. Hoffmann Martin-Luther-University Halle-Wittenberg, Institute for Biotechnology, Halle D-06120, Germany. keywords: acid; acid production; activities; activity; addition; adsorption; affinity; aim; alternative; amino; analysis; animal; ankara; antibody; application; applied; approach; assay; bacillus; bacteria; batch; bed; binding; biology; biomass; bioreactor; biosynthesis; biotechnology; capacity; carbon; case; cell; cell growth; cerevisiae; changes; chemical; chitosan; chromatography; coli; column; complex; composition; compounds; concentration; conditions; control; conversion; cost; cultivation; culture; data; days; degradation; denmark; department; design; development; differences; different; disease; dna; e.g.; effect; efficiency; energy; engineering; environmental; enzymatic; enzyme; enzyme activity; enzyme production; ethanol; ethanol production; experiments; expression; extract; factors; fed; fermentation; fermentation process; flow; flux; food; formation; function; gel; gene; gene expression; genome; glucose; group; growth; health; high; host; human; hydrolysis; identification; increase; induction; industrial; industry; influence; institute; interest; intracellular; knowledge; laboratory; level; limited; line; lipase; liquid; mail; mass; maximum; media; medium; metabolic; metabolites; method; microbial; microorganisms; milk; model; molecular; molecules; natural; network; new; niger; nitrogen; non; novel; number; oil; operation; optimization; order; oxygen; parameters; pathway; pcr; peptide; performance; phase; phosphate; plant; plasmid; potential; presence; present; procedure; process; processes; produce; production; production process; productivity; products; project; properties; protein; protein expression; protein production; purification; quality; range; rate; reaction; recombinant; regulation; removal; research; response; resulting; results; role; samples; scale; science; screening; separation; sequence; signal; source; species; specific; stability; state; step; strains; stress; structure; studies; study; substrate; sucrose; sugar; surface; synthesis; system; target; technical; technique; temperature; therapy; time; total; transfer; treatment; turkey; type; university; use; value; vitro; water; weight; work; yeast; yield cache: cord-008777-i2reanan.txt plain text: cord-008777-i2reanan.txt item: #62 of 541 id: cord-009614-lbjesv8y author: Durmuş Tekir, Saliha D. title: Systems biology of pathogen‐host interaction: Networks of protein‐protein interaction within pathogens and pathogen‐human interactions in the post‐genomic era date: 2012-11-29 words: 7119 flesch: 36 summary: In this review, the efforts to systematic determination and analysis of protein interaction networks underlying infection pathogenesis are summarized (mainly in a chronological order) to present the current picture of the research on infectious diseases. In the light of these advances, the initial steps towards complete understanding of infection mechanisms through protein interactions have been recently published. keywords: analysis; data; genome; host; human; infection; interactions; map; network; pathogen; phi; ppi; proteins; scale; virus cache: cord-009614-lbjesv8y.txt plain text: cord-009614-lbjesv8y.txt item: #63 of 541 id: cord-009636-5kddituy author: Shirbaghaee, Zeinab title: Different applications of virus‐like particles in biology and medicine: Vaccination and delivery systems date: 2015-12-22 words: 8739 flesch: 47 summary: 25, 157 Different experiments have been concentrated on HPV VLP vaccination in mouse and human models including: (a) activation of immature human DCs by chimeric HPV16 VLPs, (b) determination of systemic cytokine pattern elicited by HPV L1 VLPs, (c) identification of gene expression signatures in HPV16 L1 VLP-induced human PBMCs, (d) generation of potent and prolonged neutralizing L1 antibodies using a single intramuscular (IM) mice injection with recombinant adenoassociated virus encoding HPV16 L1 protein (rAAV-16L1), (e) augmentation of immunogenicity of HPV L1 DNA vaccines using genetic linkage to a chemokine and secretory signal peptide sequences, (f) potent stimulation of systemic and mucosal immune responses to VLP vaccines using the encapsulation of a genetic cytokine adjuvant (e.g., IL-2), (g) improvement of HPV16 VLP immunogenicity by linkage to the modified adjuvant, and m) nasal immunization of mice with HPV16 VLPs. The potential of VLPs to target DCs is a main advantage of VLP vaccines, for activating the innate and adaptive immune responses. keywords: addition; antigen; cells; chimeric; delivery; expression; hpv; mice; particles; protein; recombinant; responses; specific; studies; surface; systems; vaccine; virus; vlps cache: cord-009636-5kddituy.txt plain text: cord-009636-5kddituy.txt item: #64 of 541 id: cord-009792-e2vvi8qo author: Pandit, SB title: Structural and Functional Characterization of Gene Products Encoded in the Human Genome by Homology Detection date: 2008-01-03 words: 5213 flesch: 35 summary: A considerable number of human proteins are characterized by short lengths, although they match significantly with protein domain families which are typically much longer. With a view to enhance structural information present in human genome, we have used structural information as in PALI profiles that is generated using structure-dependent sequence alignments of a large number of protein domain families, since the incorporation of 3-D structural information could aid in effective detection of remotely related proteins. keywords: database; domain; families; family; genome; human; pfam; proteins; sequence; superfamilies cache: cord-009792-e2vvi8qo.txt plain text: cord-009792-e2vvi8qo.txt item: #65 of 541 id: cord-009959-erh8ggh3 author: BENTLEY, WILLIAM E. title: Development of an Efficient Bioprocess for Poultry Vaccines Using High‐density Insect Cell Culture date: 2006-12-17 words: 5810 flesch: 41 summary: Structural and growth characteristics of infectious bursal disease virus Maternally derived antibody-effect on susceptibility of chicks to infectious bursal disease Genomic structure of the large RNA segment of infectious bursal disease virus Infectious bursal disease virus structural proteins expressed in a baculovirus recombinant confer protection in chickens Insect cell culture technology in baculovirus expression systems Expression of foreign genes in insects using baculovirus vectors Baculovirus as vectors for foreign gene expression in insect cells Baculovirus expression vectors: A laboratory manual Large-scale insect cell culture for recombinant protein production Production of (recombinant) baculoviruses in insect-cell bioreactors Optimization of protein-production by the baculorivus expression vector system in shake flasks Assessment of virus production and chloramphenicol-acety I-transferase expression by insect cells in serum-free and serum-supplemented media using a temperature-sensitive baculovirus Optimization of the production of full-length rCD4 in baculovirus-infected Sf9 cells High-level recombinant protein production in bioreactors using the baculovirus insect cell expression system A two-stage bioreactor system for the production of recombinant proteins using a genetically engineered baculovirus/insect cell system Culture of insect cells in a helical ribbon impeller bioreactor Expression of epoxide hydrolase in insect cells: a focus on the infected cell Quantification of cell culture factors affecting recombinant protein yields in baculovirus-infected insect cells Effects of oxygen on recombinant protein production by suspension cultures of Spodoptera fiugiperda (Sf-9) insect cells Effects of oxygen/glucose/glutamine feeding on insect cell baculovirus protein expression: A study on epoxide hydroxylase production Interaction of hepatic microsomal epoxide hydrolase derived from a recombinant baculovirus expression system with an azarene oxide and an aziridine substrate analogue Escherichia coli and Sulrnonella typhirnuriurn cellular and molecular biology Coordinated regulation of a set of genes by glucose and calcium ionophores in mammalian cells Alterations in proteases, protease inhibitors and ecdysone levels: a profile of stress in insects Effect of developmental derangements on the proteolytic and protease-inhibitory activities in Galleria rnellonella (insecta) Ecdysteroids increase the yield of recombinant protein produced in baculovirus insect cell expression system Production of recombinant sarcotoxin IA in Bonbyx rnori cells Kinetic analysis of protease activity, recombinant protein production, and metabolites of infected Sf-9 cells under different DO levels Factors influencing recombinant protein yields in an insect cell-baculovirus expression system: multiplicity of infection and intracellular protein degradation A kinetic analysis of hybridoma growth and metabolism in batch and continuous suspension culture: effect of nutrient concentration, dilution rate, and pH A structured kinetic modeling framework for the dynamic hybridoma growth and monoclonial antibody production in continuous suspension culture A model for baculovirus production with continuous insect cell cultures Continuoue production of baculovirus in a cascade of insect-cell reactors Continuous p-galactosidase production with a recombinant baculovirus insect-cell system in bioreactors A structured dynamic model for the baculovirus infection process in insect-cell reactor configurations A continuous process for the production of baculovirus using insect-cell cultures A continuous flow bioreactor system for the production of recombinant proteins using the insect cell-baculovirus expression system Continuous insect cell (Sf-9) culture with aeration through sparging in a novel low-volume bioreactor Scale-up of insect cell cultures: Protective effects of pluronic F-68 Response of mammalian cells to controlled growth rates in steady-state continuous culture The baculovirus-integrated retrotransposon TED encodes gag and pol proteins that assemble into virus-like particles with reverse transcriptase Development of baculovirus triple and quadruple expression vectors: co-expression of three or four bluetongue virus proteins and the synthesis of bluetongue virus-like particles in insect cells Three-dimensional reconstruction of baculovirus expressed bluetongue virus core-like particles by cryo-electron microscopy Synthesis of bluetongue virus (BTV) corelike particles by a recombinant baculovirus expressing the two major structural core proteins of BTV Analyses of the requirements for the synthesis of virus-like particles by feline immunodeficiency virus gag using baculovirus vectors Assembly and release of HIV-1 precursor Pr55eg virus-like particles from recombinant baculovirus-infected insect cells Synthesis of immunogenic, but non-infectious, poliovirus particles in insect cells by a baculovirus expression vector Canine parvovirus empty capsids produced by expression in a baculovirus vector: use in analysis of viral properties and immunization Crystallization of virus-like particles assembled from flock house virus coat protein expressed in a baculovirus system Cell-surface expression and purification of human CD4 produced in baculovirus-infected insect cells 17D yellow fever vaccine virus envelope protein expressed by recombinant baculovirus is antigenically indistinguishable from authentic viral protein The use of feline herpesvirus and baculovirus as vaccine vectors for the gag and env genes of feline leukemia virus keywords: activity; baculovirus; cell; culture; density; expression; glucose; infection; insect; oxygen; production; protein; rate; system cache: cord-009959-erh8ggh3.txt plain text: cord-009959-erh8ggh3.txt item: #66 of 541 id: cord-010260-8lnpujip author: Anthonsen, Henrik W. title: The blind watchmaker and rational protein engineering date: 1994-08-31 words: 17358 flesch: 42 summary: A practical approach The modelling of electrostatic interactions in the function of globular proteins Electrostatic interactions in globular proteins: Calculation of the pH dependence of the redox potential of cytochrome C55 I Extracting information on folding from the amino acid sequence: Consensus regions with preferred conformation in homologous proteins Prediction of protein secondary structure at better than 70% accuracy Secondary structure prediction of all-helical proteins in two states PHD -An automatic mail server for protein secondary structure prediction Progress in protein structure prediction? Predicting protein secondary structure with a nearest-neighbor algorithm Database of homologyderived protein structures and the structural meaning of sequence alignment An winexpensive, versatile sample illuminator for photo-CIDNP on any NMR spectrometer Pancreatic lipases: Evolutionary intermediates in a positional change of catalytic carboxylates? key: cord-010260-8lnpujip authors: Anthonsen, Henrik W.; Baptista, António; Drabløs, Finn; Martel, Paulo; Petersen, Steffen B. title: The blind watchmaker and rational protein engineering date: 1994-08-31 journal: J Biotechnol DOI: 10.1016/0168-1656(94)90152-x sha: doc_id: 10260 cord_uid: 8lnpujip In the present review some scientific areas of key importance for protein engineering are discussed, such as problems involved in deducting protein sequence from DNA sequence (due to posttranscriptional editing, splicing and posttranslational modifications), modelling of protein structures by homology, NMR of large proteins (including probing the molecular surface with relaxation agents), simulation of protein structures by molecular dynamics and simulation of electrostatic effects in proteins (including pH-dependent effects). keywords: acid; alignment; amino; approach; cases; charge; data; engineering; et al; fig; gene; information; interactions; methods; modelling; nmr; number; potential; prediction; protein; protein engineering; protein sequence; protein structure; relaxation; residues; resonance; sequence; site; solution; solvent; structure; use cache: cord-010260-8lnpujip.txt plain text: cord-010260-8lnpujip.txt item: #67 of 541 id: cord-010604-3d37o05y author: Rein, Theo title: Post-translational modifications and stress adaptation: the paradigm of FKBP51 date: 2020-04-29 words: 4345 flesch: 34 summary: The E3 ubiquitin-protein ligase complex members TRAF3 and TRAF6 also were discovered as FKBP51 associating proteins, with currently unknown consequences for their enzymatic activity [81] . Known associations include de-ubiquitinases, ubiquitinases, protein kinases and protein phosphatases (first box, writers and erasers of PTMs are grouped according to the type of their biochemical activity). keywords: activity; effect; fk506; fkbp51; kinase; phosphorylation; protein; ptms; receptor; signaling; stress; ubiquitination cache: cord-010604-3d37o05y.txt plain text: cord-010604-3d37o05y.txt item: #68 of 541 id: cord-010681-tmpxs9og author: Dondapati, Srujan Kumar title: Cell-Free Protein Synthesis: A Promising Option for Future Drug Development date: 2020-03-20 words: 10693 flesch: 31 summary: Recent advances in development of cell-free protein synthesis systems for fast and efficient production of recombinant proteins Effects of ATP regeneration systems on the yields and solubilities of cell-free synthesized proteins Combining in vitro folding with cell free protein synthesis for membrane protein expression Membrane protein production in Escherichia coli cell-free lysates Reconstitution and functional characterization of ion channels from nanodiscs in lipid bilayers Challenges in the development of functional assays of membrane proteins A comprehensive map of molecular drug targets A cell-free translocation system using extracts of cultured insect cells to yield functional membrane proteins In vitro synthesis of a major facilitator transporter for specific active transport across droplet interface bilayers Functional reconstitution of cell-free synthesized purified Kv channels The sensorless pore module of voltage-gated K + channel family 7 embodies the target site for the anticonvulsant retigabine Cell free expression and functional reconstitution of eukaryotic drug transporters Coupled cell-free synthesis and lipid vesicle insertion of a functional oligomeric channel A general scheme of CF protein production is depicted in Fig. keywords: antibody; cell; cf systems; cfps; cho; coli; development; drug; eukaryotic; expression; human; like; lysates; membrane; mps; production; protein; reaction; synthesis; systems; translation; yields cache: cord-010681-tmpxs9og.txt plain text: cord-010681-tmpxs9og.txt item: #69 of 541 id: cord-010776-ura14oci author: Hosseini, Elahe Seyed title: Optimization and One-Step Purification of Recombinant V Antigen Production from Yersinia pestis date: 2020-01-02 words: 3403 flesch: 44 summary: The purpose of this study was to develop an efficient and inexpensive method for the useful production of recombinant protein V antigen, an important virulence factor for Yersinia pestis. The enhancement of recombinant protein production and subsequently, the purification of the target protein, the effects of temperature on the induction (15, 20, and 25 °C), media (Terrific Broth or TB, contains tryptone 1.2%, yeast extract 2.4%, and glycerol 0.5%; Supper Broth or SB which contains tryptone 3%, yeast extract 2%, MOPS 1%, and Glucose 2%; and 32Y which contains tryptone 0.8%, yeast extract 3.2%, and NaCl 0.58% in 10 mM Tris-HCl, pH 7.6), and inducer concentration (0.05, 0.1 and 0.15 mM) were investigated using the Taguchi statistical method [20] ( Table 1) . keywords: antigen; expression; int; method; plague; production; protein; purification; recombinant cache: cord-010776-ura14oci.txt plain text: cord-010776-ura14oci.txt item: #70 of 541 id: cord-010938-12igesqw author: Patra, Prasanta title: Epitope-Based Vaccine Designing of Nocardia asteroides Targeting the Virulence Factor Mce-Family Protein by Immunoinformatics Approach date: 2019-08-21 words: 4631 flesch: 39 summary: The virulence factor of Mce family protein found to be responsible for the virulency of N. asteroides and pathogenicity expression. Vaccine design VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines Efficient unbound docking of rigid molecules Murine polymorphonuclear neutrophils produce interferon-γ in response to pulmonary infection with Nocardia asteroides Nocardia asteroides cerebral abscess in immunocompetent hosts: report of three cases and review of surgical recommendations Exploiting the Burkholderia pseudomallei acute phase antigen BPSL2765 for structure-based epitope discovery/design in structural vaccinology Protein-protein binding site identification by enumerating the configurations Identification of immunodominant B-cell epitope regions of reticulocyte binding proteins in Plasmodium vivax by protein microarray based immunoscreening Nocardia infection in lung transplant recipients Identification of B-cell Epitope of Leishmania donovani and its application in diagnosis of visceral leishmaniasis Prediction of B-cell epitopes in listeriolysin O, a cholesterol dependent cytolysin secreted by listeria monocytogenes The Phyre2 web portal for protein modeling, prediction and analysis Epitopebased peptide vaccine design and target site depiction against Ebola viruses: an immunoinformatics study Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes Understanding rifampicin resistance in tuberculosis through a computational approach Prediction of MHC-peptide binding: a systematic and comprehensive overview PRO-CHECK: a program to check the stereochemical quality of protein structures PROCHECK: validation of protein-structure coordinates Detection of peptide-binding sites on protein surfaces: the first step toward the modeling and targeting of peptidemediated interactions Structure of the Vδ domain of a human γδ T-cell antigen receptor Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research Clinical experience with linezolid for the treatment of Nocardia infection ProPred analysis and experimental evaluation of promiscuous T-cell epitopes of three major secreted antigens of Mycobacterium tuberculosis Identification of putative vaccine candidates against Helicobacter pylori exploiting exoproteome and secretome: a reverse vaccinology based approach Exploration of freely available web-interfaces for comparative homology modelling of microbial proteins Influenza vaccination and reduction in hospitalizations for cardiac disease and stroke among the elderly Reverse-vaccinology strategy for designing T-cell epitope candidates for Staphylococcus aureus endocarditis vaccine Soil-acquired cutaneous nocardiosis on the forearm of a healthy male contracted in a swamp in rural eastern Virginia UCSF Chimera-a visualization system for exploratory research and analysis Porter: a new, accurate server for protein secondary structure prediction Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles Schmidek and sweet: operative neurosurgical techniques 2-volume set: indications, methods and results In silico identification of catalytic residues in azobenzene reductase from Bacillus subtilis and its docking studies with azo dyes Homology modeling, model and software evaluation: three related resources COFACTOR: an accurate comparative algorithm for structure-based protein function annotation Prediction of continuous B-cell epitopes in an antigen using recurrent neural network Membrane association and epitope recognition by HIV-1 neutralizing anti-gp41 2F5 and 4E10 antibodies Nocardiosis: review of clinical and laboratory experience Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking PatchDock and SymmDock: servers for rigid and symmetric docking Pleuroplumonary Nocardiosis in an Immunocompetent Host EGF domain II of protein Pb28 from Plasmodium berghei interacts with monoclonal transmission blocking antibody 13.1 ProPred: prediction of HLA-DR binding sites ProPred1: prediction of promiscuous MHC Class-I binding sites A hidden Markov model for predicting transmembrane helices in protein sequences Design of novel multi-epitope vaccines against severe acute respiratory syndrome validated through multistage molecular interaction and dynamics Computer-aided biotechnology: from immuno-informatics to reverse vaccinology ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins VADAR: a web server for quantitative evaluation of protein structure quality Nocardiosis: updates and clinical overview Epitope mapping of two immunodominant domains of gp41, the transmembrane protein of human immunodeficiency virus type 1, using ten human monoclonal antibodies Immunogenicity prediction by VaxiJen: a ten year overview keywords: cell; epitopes; factor; family; mce; prediction; protein; server; vaccine; virulence cache: cord-010938-12igesqw.txt plain text: cord-010938-12igesqw.txt item: #71 of 541 id: cord-011012-5mev3otu author: Rathore, Abhishek Singh title: Production and immunogenicity of Fubc subunit protein redesigned from DENV envelope protein date: 2020-03-30 words: 6735 flesch: 42 summary: It was observed by ELISA that Fubc fusion protein elicited higher serum IgG antibody response either in the presence or in absence of Freund’s adjuvant in comparison to the immune response of Fu and bc peptides separately. In this study, an alignment of the domain II amino acid sequences of DENV1-4 envelope proteins spanning residues from 61 to 120 was used to find optimum conserved sequence for the development of Fubc fusion protein (Fig. 1a) . keywords: adjuvant; dengue; denv; envelope; et al; fig; fubc; fusion; immune; loop; protein; response; vaccine; virus cache: cord-011012-5mev3otu.txt plain text: cord-011012-5mev3otu.txt item: #72 of 541 id: cord-011184-ohdukhqt author: Patil, Shital P. title: Plant-Derived Bioactive Peptides: A Treatment to Cure Diabetes date: 2019-07-22 words: 7642 flesch: 37 summary: Plant peptides are still under exploration and few bioactive peptides are reported from soy, wheat, etc (Hartmann and Meisel 2007) . Plant peptides targeting glucose transporters are less explored. keywords: blood; diabetes; drug; enzyme; et al; glucose; inhibition; inhibitors; insulin; peptides; plant; protein; study; treatment; type; vitro; vivo cache: cord-011184-ohdukhqt.txt plain text: cord-011184-ohdukhqt.txt item: #73 of 541 id: cord-011602-hzqayt3n author: Chen, Jianlin title: Targeting Intrinsically Disordered Proteins through Dynamic Interactions date: 2020-05-11 words: 7796 flesch: 32 summary: Targeting intrinsically disordered transcription factors Intrinsically disordered proteins are potential drug targets Intrinsically disordered proteins and novel strategies for drug discovery How to design a drug for the disordered proteins Targeting disordered proteins with small molecules using entropy Biomolecules 2020 Druggability of Intrinsically Disordered Proteins Targeting protein-protein interactions (PPIs) of transcription factors: Challenges of intrinsically disordered proteins (IDPs) and regions (IDRs) Targeting intrinsically disordered proteins in rational drug discovery Recent insights into the development of therapeutics against coronavirus diseases by targeting N protein pE-DB: A database of structural ensembles of intrinsically disordered and of unfolded proteins Intrinsically disordered proteins in cellular signalling and regulation Intrinsically Disordered Proteins Studied by NMR Spectroscopy Structural interpretation of paramagnetic relaxation enhancement-derived distances for disordered protein states Principles of protein structural ensemble determination A critical assessment of methods to recover information from averaged data Improved structural characterizations of the drkN SH3 domain unfolded state suggest a compact ensemble with native-like and non-native structure NMR Characterization of Long-Range Order in Intrinsically Disordered Proteins Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain Recovering a Representative Conformational Ensemble from Underdetermined Macromolecular Structural Data Atomistic Ensemble Modeling and Small-Angle Neutron Scattering of Intrinsically Disordered Protein Complexes: Applied to Minichromosome Maintenance Protein Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS) Combined Monte Carlo/torsion-angle molecular dynamics for ensemble modeling of proteins, nucleic acids and carbohydrates Conformational propensities of intrinsically disordered proteins from NMR chemical shifts Modeling intrinsically disordered proteins with bayesian statistics Conformational space of flexible biological macromolecules from average data Biomolecules 2020 Simulations of disordered proteins and systems with conformational heterogeneity A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: Evidence from molecular simulations Net charge per residue modulates conformational ensembles of intrinsically disordered proteins Atomistic details of the disordered states of KID and pKID. In this review, we will first summarize important recent advances in physics-based de novo simulations of disordered protein ensembles, including Graphic Processing Unit (GPU) computing, enhanced sampling, and re-balanced protein force fields, and then focus on emerging examples that suggest the exciting possibility of targeting IDPs by directly modulating the disordered ensembles through dynamic and transient interactions. keywords: binding; disordered; ensembles; field; force; idps; interactions; molecules; p53; protein; sampling; simulations; structure; targeting cache: cord-011602-hzqayt3n.txt plain text: cord-011602-hzqayt3n.txt item: #74 of 541 id: cord-012682-7goljir4 author: Yuan, Meng title: N-myristoylation: from cell biology to translational medicine date: 2020-03-18 words: 7201 flesch: 33 summary: Protein lipidation in cell signaling and diseases: function, regulation, and therapeutic opportunities Protein lipidation SIRT2 and lysine fatty acylation regulate the transforming activity of K-Ras4a HDAC11 regulates type I interferon signaling through defatty-acylation of SHMT2 Protein lysine acylation and cysteine succination by intermediates of energy metabolism Protein myristoylation in health and disease Cholesterol sensitivity of endogenous and myristoylated Akt Myristoylated Naked2 antagonizes Wnt-beta-catenin activity by degrading Dishevelled-1 at the plasma membrane Myristoylation of the dual-specificity phosphatase c-JUN N-terminal kinase (JNK) stimulatory phosphatase 1 is necessary for its activation of JNK signaling and apoptosis Inhibition of enterovirus VP4 myristoylation is a potential antiviral strategy for hand, foot and mouth disease N-Terminal region of the catalytic domain of human Nmyristoyltransferase 1 acts as an inhibitory module HIV-1 production is specifically associated with human NMT1 long form in human Human N-myristoyltransferase amino-terminal domain involved in targeting the enzyme to the ribosomal subcellular fraction Fatty acids regulate germline Sex determination through ACS-4-dependent myristoylation Comparison of myristoyl-CoA: protein N-myristoyltransferases from three pathogenic fungi: Cryptococcus neoformans, Histoplasma capsulatum, and Candida albicans Two N-myristoyltransferase isozymes play unique roles in protein myristoylation, proliferation, and apoptosis Efficient demyristoylase activity of SIRT2 revealed by kinetic and structural studies SIRT6 regulates Ras-related protein R-Ras2 by lysine defatty-acylation Nmyristoyltransferase 1 is essential in early mouse development Protein kinase C coordinates histone H3 phosphorylation and acetylation Molecular determinants of the myristoyl-electrostatic switch of MARCKS Structural basis for activation of ARF GTPase: mechanisms of guanine nucleotide exchange and GTP-myristoyl switching Structure and membrane interaction of myristoylated ARF1 Sequestration of the membranetargeting myristoyl group of recoverin in the calcium-free state Myristoylation-dependent N-terminal cleavage of the myristoylated alanine-rich C kinase substrate (MARCKS) by cellular extracts A myristoyl/phosphoserine switch controls cAMP-dependent protein kinase association to membranes C-terminal 15 kDa fragment of cytoskeletal actin is posttranslationally N-myristoylated upon caspase-mediated cleavage and targeted to mitochondria N-Terminally myristoylated ras proteins require palmitoylation or a polybasic domain for plasmamembrane localization Membrane localization of a rice calcium-dependent protein kinase (CDPK) is mediated by myristoylation and palmitoylation Myristoylationdependent palmitoylation of the receptor tyrosine kinase adaptor FRS2alpha G proteinmembrane interactions I: Galphai1 myristoyl and palmitoyl modifications in protein-lipid interactions and its implications in membrane microdomain localization Identification and characterization of protein N-myristoylation occurring on four human mitochondrial proteins, SAMM50, TOMM40, MIC19, and MIC25 Role of N-myristoylation in stability and subcellular localization of the CLPABP protein Mouse Stbd1 is N-myristoylated and affects ER-mitochondria association and mitochondrial morphology Multiple modification and protein interaction signals drive the Ring finger protein 11 (RNF11) E3 ligase to the endosomal compartment N-Myristoylation of the Rpt2 subunit of the yeast 26S proteasome is implicated in the subcellular compartment-specific protein quality control system Aggregation of lipid-anchored full-length H-Ras in lipid bilayers: simulations with the MARTINI force field A dimerization function in the intrinsically disordered N-terminal region of Src A myristoyl-binding site in the SH3 domain modulates c-Src membrane anchoring Crystal structure of a myristoylated CAP-23/NAP-22 N-terminal domain complexed with Ca2+/calmodulin A myristoyl switch regulates membrane binding of HIV-1 Gag Myristoylation drives dimerization of matrix protein from mouse mammary tumor virus The myristoylation of TRIF-related adaptor molecule is essential for Toll-like receptor 4 signal transduction Heme oxygenase 2 binds myristate to regulate retrovirus assembly and TLR4 signaling A glycine-specific Ndegron pathway mediates the quality control of protein N-myristoylation Myristoylation and membrane binding regulate c-Src stability and kinase activity ABA inhibits myristoylation and induces shuttling of the RGLG1 E3 ligase to promote nuclear degradation of PP2CA A novel interaction between N-myristoylation and the 26S proteasome during cell morphogenesis A myristoyl/phosphotyrosine switch regulates c-Abl beta-Subunit myristoylation is the gatekeeper for initiating metabolic stress sensing by AMPactivated protein kinase (AMPK) N-myristoyltransferase deficiency impairs activation of kinase AMPK and promotes synovial tissue inflammation Exploring protein myristoylation in Toxoplasma gondii Liberated PKA Catalytic subunits associate with the membrane via myristoylation to preferentially phosphorylate membrane substrates Myristoylated alanine-rich C-kinase substrate effector domain phosphorylation regulates the growth and radiation sensitization of glioblastoma Phosphorylation of human N-myristoyltransferase by N-myristoylated SRC family tyrosine kinase members Potential role of N-myristoyltransferase in cancer Rapid detection, discovery, and identification of post-translationally myristoylated proteins during apoptosis using a bio-orthogonal azidomyristate analog Myristic acid increases the activity of dihydroceramide Delta 4-desaturase 1 through its Nterminal myristoylation Monounsaturated fatty acid modification of Wnt protein: Its role in Wnt secretion Myristoylation of human LanC-like Protein 2 (LANCL2) is essential for the interaction with the plasma membrane and the increase in cellular sensitivity to adriamycin Effects of L-histidine and its structural analogues on human N-myristoyltransferase activity and importance of EEVEH amino acid sequence for enzyme activity Expression and activity of N-myristoyltransferase in lung inflammation of cattle and its role in neutrophil apoptosis Deficiency of N-myristoylation reveals calcineurin activity as regulator of IFN-gammaproducing gamma delta T cells Myristoylation: an important protein modification in the immune response N-myristoylation of AMPK controls T cell inflammatory function The residue at position 5 of the N-terminal region of Src and Fyn modulates their myristoylation, palmitoylation, and membrane interactions VHY, a novel myristoylated testis-restricted dual specificity protein phosphatase related to VHX Novel analogs of D-e-MAPP and B13. keywords: activity; addition; apoptosis; binding; cancer; cell; group; inhibitors; kinase; lipid; membrane; myristoylation; nmt; nmt1; nmt2; protein; src cache: cord-012682-7goljir4.txt plain text: cord-012682-7goljir4.txt item: #75 of 541 id: cord-012878-j9vndxgg author: Tremblay, Reynald title: High-yield expression of recombinant soybean agglutinin in plants using transient and stable systems date: 2010-06-18 words: 6390 flesch: 41 summary: Although a protein band with a molecular mass expected for the monomer of SBA protein was seen on western blot, no analysis or characterization of the recombinant protein itself was performed; it was merely used as a marker for gene expression. Figure 4b shows that binding of ConA occurs only in the untreated samples, with no binding to any of the PNGase F treated SBA proteins, suggesting that plant-derived rSBA contains high-mannose type glycans, similar to native SBA. Plant-derived rSBA was further investigated in simulated gastric and simulated intestinal fluid (SGF and SIF) to assess its stability in the digestive system. keywords: benthamiana; cells; expression; native; plant; production; protein; purification; recombinant; rsba; sba; soybean cache: cord-012878-j9vndxgg.txt plain text: cord-012878-j9vndxgg.txt item: #76 of 541 id: cord-013046-r6dtiu97 author: Liu, Bin title: Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection date: 2014-02-15 words: 6948 flesch: 43 summary: However, this number is only about one-sixth of 539 616, the number of protein sequences held in the UniProtKB/Swiss-Prot database (Wu et al., 2006) . The most straightforward approach to generate the kernels was based on the features extracted from protein sequences. keywords: acid; amino; detection; et al; frequency; homology; kernel; methods; performance; profile; protein; sequence; svm cache: cord-013046-r6dtiu97.txt plain text: cord-013046-r6dtiu97.txt item: #77 of 541 id: cord-013178-li1x1m25 author: Hung, Ling-Chu title: The Monoclonal Antibody Recognized the Open Reading Frame Protein in Porcine Circovirus Type 2-Infected Peripheral Blood Mononuclear Cells date: 2020-08-29 words: 9845 flesch: 55 summary: This study found non-vaccinated suckers had the highest of PCV2 proteins in blood at one week of age. The data show that 3–5% of PBMCs were positive for ORF3 protein or p53 protein. keywords: anti; capsid; circovirus; figure; igg; mab; orf3; orf3 protein; p53; pbmcs; pcv2; peptide; porcine; protein; study; type cache: cord-013178-li1x1m25.txt plain text: cord-013178-li1x1m25.txt item: #78 of 541 id: cord-013315-plptulfb author: Tilocca, Bruno title: Immunoinformatic-Based Prediction of Candidate Epitopes for the Diagnosis and Control of Paratuberculosis (Johne’s Disease) date: 2020-08-27 words: 6837 flesch: 36 summary: The list of epitope sequences was further analyzed through the Basic Local Alignment Search Tool for protein sequences (pBLAST) The list of epitope sequences was further analyzed through the Basic Local Alignment Search Tool for protein sequences (pBLAST) keywords: avium; binding; class; disease; epitopes; map; mhc; mycobacterium; paratuberculosis; peptides; prediction; protein; sequences cache: cord-013315-plptulfb.txt plain text: cord-013315-plptulfb.txt item: #79 of 541 id: cord-013348-lsksys56 author: Goto, Keiko title: Development of Monoclonal Antibodies and Antigen-Capture ELISA for Human Parechovirus Type 3 date: 2020-09-19 words: 4782 flesch: 45 summary: Epitope mapping showed that these mAbs recognized three distinct domains in HPeV3 VP0. Recently, Chen et al. generated polyclonal antibodies for HPeV3 VP0, and proposed an immunofluorescence-based diagnostic assay [27] . keywords: antigen; detection; elisa; figure; hpev3; human; mabs; parechovirus; protein; system; vp0 cache: cord-013348-lsksys56.txt plain text: cord-013348-lsksys56.txt item: #80 of 541 id: cord-014368-4nasrbs6 author: None title: Gene Chip for Viral Discovery date: 2003-11-17 words: 10009 flesch: 47 summary: This finding has important practical implications for spinal-cord patients-if different cells can perform the same functions, then surgeons have far more flexibility in how and where they can introduce electrodes or other functional enhancements into the brain. Presenting results from a series of long-term studies in monkeys, they demonstrate that the same set of brain cells can control two distinct movements, the reaching and grasping of a robotic arm. keywords: biology; brain; cell; control; development; dna; expression; function; genes; genome; growth; motor; pathways; proteins; receptor; researchers; sequence; signaling; system; text cache: cord-014368-4nasrbs6.txt plain text: cord-014368-4nasrbs6.txt item: #81 of 541 id: cord-014462-11ggaqf1 author: None title: Abstracts of the Papers Presented in the XIX National Conference of Indian Virological Society, “Recent Trends in Viral Disease Problems and Management”, on 18–20 March, 2010, at S.V. University, Tirupati, Andhra Pradesh date: 2011-04-21 words: 35463 flesch: 47 summary: The following virus isolates have been used in the analysis: GTPV-Uttarkashi, P60, vaccine virus; GTPV Mukteswar, P10, Challenge virus; GTPV (Akola), GTPV Bareilly/00, GTPV Ladakh/01 and GTPV Sambalpur/82, field isolates and SPPV Srinagar, P40; SPPV Ranipet, P50; SPPV-RF, P50, vaccine viruses and SPPV Makdhoom/07, SPPV CIRG/08, SPPV Pune/08, SPPV Bareilly, SPPV 183/03 and SPPV 125/02, field isolates. Present paper discusses about virus disease of quarantine importance affecting ornamental and fruit plants such as Chrysanthimum, Dahlia, Dianthus, Rosabengalensis, Cattleya, Cymbidium, Dendrobium, Lilium, Citrus, Vitis etc. keywords: acid; analysis; animals; antibodies; antigen; assay; cases; cells; cloned; control; crop; curl; dengue; detection; development; disease; dna; elisa; expression; field; food; gene; host; india; infection; isolates; leaf; management; methods; molecular; mosaic; mosaic virus; nucleotide; pathogens; patients; pcr; plant; positive; present; primers; production; protein; region; resistance; response; results; rna; samples; sequence; specific; study; symptoms; time; tomato; total; vaccine; vector; viral; virus; virus infection; viruses; world; yellow cache: cord-014462-11ggaqf1.txt plain text: cord-014462-11ggaqf1.txt item: #82 of 541 id: cord-014597-66vd2mdu author: None title: Abstracts from the 25th European Society for Animal Cell Technology Meeting: Cell Technologies for Innovative Therapies: Lausanne, Switzerland. 14-17 May 2017 date: 2018-03-15 words: 50744 flesch: 43 summary: [3] ) -Error frequency does not invalidate use of direct observation methods for cell cloning -Single cell seen by both scientists is highly likely to be monoclonal -During method development, strategies established to control potential sources of error ( Table 1 ) Use of a contemporaneous visualisation approach, a strict control strategy, and a suitable statistical model (which takes into account potential errors) results in: -The CACC method being at least as robust as the LDC method -The CACC method being a reliable, single-step method for cloning to achieve a high P(monoclonality) The main feature of our CI-SCREEN technology is the ability to combine the advantage of cell linesthe unlimited cell supplywith the advantage of primary cellsthe physiological relevance. keywords: addition; analysis; antibodies; antibody; approach; background; batch; bioreactor; cell; cell clones; cell culture; cell density; cell growth; cell line; cho; cho cell; clones; concentration; conditions; control; cultivation; cultures; data; day; development; experiments; expression; fed; feed; fig; fold; free; gene; glucose; glycosylation; high; human; increase; integration; levels; lines; mab; media; medium; method; model; number; parameters; performance; perfusion; phase; platform; process; process development; processes; production; productivity; protein; protein production; quality; rate; results; scale; selection; specific; study; system; table; target; therapeutic; time; titer; transfection; use; vector; viability; virus cache: cord-014597-66vd2mdu.txt plain text: cord-014597-66vd2mdu.txt item: #83 of 541 id: cord-014661-mrh2pbi6 author: Dumitrascu, Georgiana R. title: Critical physiological and pathological functions of Forkhead Box O tumor suppressors date: 2013-12-31 words: 9254 flesch: 30 summary: The advances in understating the mechanism of FOXOs regulation of stem cells, cancer stem cells and how non-coding RNAs are regulated and regulate the function of FOXO genes/protein are presented. Similarities between stem cells and cancer stem cells were best described in the hematopoietic system, where similar surface markes and signal transduction patterns were described between the hematopoietic stem cells and leukemia-initiating cells 121 . keywords: activation; akt; apoptosis; cancer; cell; cycle; dna; expression; factors; family; forkhead; foxo; foxo proteins; foxo transcription; genes; proliferation; proteins; role; stem; transcription cache: cord-014661-mrh2pbi6.txt plain text: cord-014661-mrh2pbi6.txt item: #84 of 541 id: cord-014685-ihh30q6f author: None title: Posters P788 - P999 date: 2005-09-21 words: 38408 flesch: 42 summary: 12 physical property parameters of protein structure were chosen to construct a 12-dimension physical property space. These systems have proven to be also valuable as membrane mimetic structures, as promising matrices for controlled-release and delivery of proteins, vitamins and small drugs in pharmacological applications, and they offer a 3D lipid matrix for successful crystallization of membrane proteins which do not easily crystallize in bulk solution. keywords: activity; aggregation; analysis; beta; binding; cells; changes; complex; complexes; concentration; conformational; data; delivery; dna; domain; drug; dynamics; effect; energy; experiments; folding; function; human; institute; interaction; light; lipid; loop; mechanism; membrane; membrane protein; method; model; molecular; native; new; nmr; order; peptide; phase; potential; presence; process; properties; protein; protein structure; region; residues; results; rna; rst; sequence; signi; site; solution; speci; stability; state; step; structure; studies; study; surface; system; temperature; terminal; time; transition; transport; type; unfolding; university; uorescence; water; work cache: cord-014685-ihh30q6f.txt plain text: cord-014685-ihh30q6f.txt item: #85 of 541 id: cord-014852-6friw2ek author: Chumakov, S. P. title: Organization and regulation of nucleocytoplasmic transport date: 2010-04-24 words: 9165 flesch: 47 summary: For instance, affinity of the IFi16 NLS for nuclear proteins increases as a result of phosphorylation by the CK 2 kinase. Develop ment Cloning and characterization of hSRP1 gamma, a tissue specific nuclear transport factor Evidence for distinct substrate specificities of importin alpha family members in nuclear protein import Sim ple kinetic relationships and nonspecific competition govern nuclear import rates in vivo. keywords: binding; cell; complex; cytoplasm; export; importin; karyopherin; nes; nls; npc; nuclear; nucleus; nup; nup proteins; pore; proteins; rangtp; structure; transport cache: cord-014852-6friw2ek.txt plain text: cord-014852-6friw2ek.txt item: #86 of 541 id: cord-014864-0d682m0n author: None title: Biomedical vignette date: 2008-10-26 words: 2993 flesch: 29 summary: Interactions between M protein and other structural proteins of severe acute respiratory syndrome coronavirus The study by Hsieh et al. Connective tissue growth factor: a cysteine-rich mitogen secreted by human vascular endothelial cells is related to the SRC-induced immediate early gene product CEF-10 NOV (nephroblastoma overexpressed) and the CCN family of genes: structural and functional issues Connective tissue growth factor (CTGF) and cancer progression CGcgh: a tool for molecular karyotyping using DNA microarray-based comparative genomic hybridization (array-CGH) A computational screen for C/D box snoRNAs in the human genomic region associated with Prader-Willi and Angelman syndromes Interactions between M protein and other structural proteins of severe, acute respiratory syndrome-associated coronavirus Severe acute respiratory syndrome coronavirus nucleocapsid protein confers ability to efficiently produce virus-like particles when substituted for the human immunodeficiency virus nucleocapsid domain Iron dictates the virulence of Pseudomonas aeruginosa in urinary tract infections Synaptic mechanisms that shape visual signaling at the inner retina Glycinergic synaptic inputs to bipolar cells in the salamander retina Glycine input induces the synaptic facilitation in salamander rod photoreceptors Nicotine enhancement of fast excitatory synaptic transmission in CNS by presynaptic receptors Laboratory evaluation of antiepileptic drugs. keywords: alcohol; benzyl; bone; cells; cgmp; human; neurons; protein; study cache: cord-014864-0d682m0n.txt plain text: cord-014864-0d682m0n.txt item: #87 of 541 id: cord-014901-d9szap94 author: Permyakova, N. V. title: State of research in the field of the creation of plant vaccines for veterinary use date: 2015-01-04 words: 8092 flesch: 34 summary: as a feedstuff additive Expression of hemagglutinin protein of rinderpest virus in transgenic tobacco and immunogenicity of plant derived protein in a mouse model Systemic and oral immunogenicity of hemagglutinin protein of rinderpest virus expressed by transgenic peanut plants in a mouse model Expression of hemagglutinin protein of rinderpest virus in trans genic pigeon pea Oral immunogenicity of the plant derived spike protein from swine transmissible gastroenteritis coronavirus Cloning and sequence analysis of the Korean strain of spike gene of porcine epidemic diarrhea virus and expression of its neutraliz ing epitope in plants Successful oral prime immunization with VP60 from rabbit haemorrhagic disease virus pro duced in transgenic plants using different fusion strate gies Mucosal and sys temic immunization elicited by Newcastle disease virus (NDV) transgenic plants as antigens Expres sion of the fusion glycoprotein of Newcastle disease virus in transgenic rice and its immunogenicity in mice Expression of immunogenic S1 glycoprotein of infectious bronchitis virus in trans genic potatoes Transient expression of the ectodomain of matrix protein 2 (M2e) of avian RUSSIAN Immunization with plant expressed hemagglutinin protects chickens from lethal highly pathogenic avian influenza virus H5N1 challenge infection Immunogenicity study of plant made oral subunit vaccine against porcine reproductive and res piratory syndrome virus (PRRSV) Expression of the rabies virus glycoprotein in transgenic tomatoes Immunization against rabies with plant derived antigen Development of an edible rabies vaccine in maize using the Vnukovo strain Induction of a protective immune response to rabies virus in sheep after oral immunization with transgenic maize, expressing the rabies virus glycoprotein Expression of the rabies virus nucleoprotein in plants at high levels and evaluation of immune responses in mice Expression of rabies virus G pro tein in carrots (Daucus carota) Such com panies as SemBioSys Genetics Inc. (Calgary, Can ada), Medicago Inc. (Quebec, Canada), Protalix Bio Therapeutics (Karmiel, Israel), and ORF Genetics (Iceland) proved the possibility of quick establishing of the production of purified plant proteins, which are quite competitive in today's market. keywords: antigen; cells; development; disease; expression; gene; genome; immunization; plant; plant cells; plant vaccines; production; protein; response; system; target; transgenic; use; vaccines; virus cache: cord-014901-d9szap94.txt plain text: cord-014901-d9szap94.txt item: #88 of 541 id: cord-016095-jop2rx61 author: Vignais, Pierre V. title: Challenges for Experimentation on Living Beings at the Dawn of the 21(st) Century date: 2010-06-08 words: 42858 flesch: 42 summary: Nevertheless, research on such cells is mandatory if we wish to move on to a regenerative medicine that aims to be a new frontier in the art of healing. In Man, such cells could be directed by differentiation towards stable cell lines creating well-defined tissues and organs (liver, muscle…) that could be used in regenerative medicine. keywords: animal; atp; beings; biology; case; cells; century; chapter; cloning; dna; domain; enzyme; example; experiments; fact; figure; gene; genome; human; information; life; living; means; medicine; messenger; metabolic; method; molecular; molecules; neurons; non; order; plant; present; progress; proteins; research; rise; rnas; science; sequence; species; stem; stem cells; study; subject; synthesis; techniques; technology; time; type; use; way; years cache: cord-016095-jop2rx61.txt plain text: cord-016095-jop2rx61.txt item: #89 of 541 id: cord-016126-i7z0tdrk author: Dangi, Mehak title: Advanced In Silico Tools for Designing of Antigenic Epitope as Potential Vaccine Candidates Against Coronavirus date: 2018-10-14 words: 3226 flesch: 42 summary: It is basically an empirical method to hunt antigenic proteins. All these limitations are conquered by reverse vaccinology approach utilizing genome sequence information which ultimately is translated into proteins. keywords: approach; epitopes; host; prediction; proteins; vaccine; vaccinology cache: cord-016126-i7z0tdrk.txt plain text: cord-016126-i7z0tdrk.txt item: #90 of 541 id: cord-016419-v1f6dx3e author: Gupta, Varsha title: Production of Recombinant Pharmaceutical Proteins date: 2016-10-23 words: 9655 flesch: 48 summary: The gene is transcribed under the control of powerful polyhedron promoter with high yields (~30 % of total cell protein). Any kind of impairment in protein production, such as production of mutated protein, or misfolded protein, leads to disruption of the pathway controlled by that protein. keywords: blood; cell; coli; expression; factor; form; gene; glycosylation; growth; hormone; host; human; insulin; mammalian; modifi; production; promoter; protein; recombinant; scale; system cache: cord-016419-v1f6dx3e.txt plain text: cord-016419-v1f6dx3e.txt item: #91 of 541 id: cord-016442-3su3x6ed author: Aiking, Harry title: Transition Feasibility and Implications for Stakeholders date: 2006 words: 8271 flesch: 46 summary: The analysis of long-term changes indicated that there is a favourable socio-cultural context for decisions that make consumers and producers less dependent on meat proteins. That is, a shift in the Western diet from meat proteins to plant-derived protein products appears to be (1) environmentally more sustainable than present trends, (2) technologically feasible, and (3) socially desirable. keywords: consumer; crops; energy; food; meat; npfs; plant; production; products; profetas; protein; research; transition cache: cord-016442-3su3x6ed.txt plain text: cord-016442-3su3x6ed.txt item: #92 of 541 id: cord-016448-7imgztwe author: Frishman, D. title: Protein-protein interactions: analysis and prediction date: 2009-10-01 words: 18357 flesch: 31 summary: These insights arise from the integration of functional information, dynamic data and protein interaction networks. The roles of intrinsic disorder in protein interaction networks Profile hidden Markov models Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: a comparison with crystallography Protein interaction maps for complete genomes based on gene fusion events A novel genetic system to detect protein-protein interactions iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions Pfam: clans, web tools and services Pharmaceuticals: a new grammar for drug discovery A genomic approach of the hepatitis C virus generates a protein interaction map Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes Glide: a new approach for rapid, accurate docking and scoring. keywords: analysis; approach; binding; complexes; cytoscape; data; database; disease; docking; domain; domain interactions; drug; et al; evidence; fig; gene; human; information; interaction data; interactions; ligand; methods; network; nodes; number; pairs; prediction; protein; protein interactions; sequence; similarity; structure; types cache: cord-016448-7imgztwe.txt plain text: cord-016448-7imgztwe.txt item: #93 of 541 id: cord-016594-lj0us1dq author: Flower, Darren R. title: Identification of Candidate Vaccine Antigens In Silico date: 2012-09-28 words: 12575 flesch: 33 summary: A long, naturally presented immunodominant epitope from NY-ESO-1 tumor antigen: implications for cancer vaccine design Identification and characterization of pathogenicity and other genomic islands using base composition analyses A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands CpGcluster: a distance-based algorithm for CpG-island detection CpGIF: an algorithm for the identification of CpG islands Identifying CpG islands by different computational techniques CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes Evaluation of genomic island predictors using a comparative genomics approach IslandPath: aiding detection of genomic islands in prokaryotes Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models A computational approach for identifying pathogenicity islands in prokaryotic genomes Resolving the structural features of genomic islands: a machine learning approach Detection of genomic islands via segmental genome heterogeneity Prediction of pathogenicity islands in enterohemorrhagic Escherichia coli O157:H7 using genomic barcodes IslandViewer: an integrated interface for computational identification and visualization of genomic islands Towards pathogenomics: a web-based resource for pathogenicity islands Identification and characterization of a novel family of pneumococcal proteins that are protective against sepsis Functional genomics of pathogenic bacteria SYFPEITHI: database for searching and Tcell epitope prediction SYFPEITHI: database for MHC ligands and peptide motifs HIV sequence databases MHCBN 4.0: a database of MHC/TAP binding peptides and T-cell epitopes MHCBN: a comprehensive database of MHC binding and non-binding peptides EPIMHC: a curated database of MHCbinding peptides for customized computational vaccinology AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data JenPep: a novel computational information resource for immunobiology and vaccinology JenPep: a database of quantitative functional peptide data for immunology The immune epitope database 2.0 AntigenDB: an immunoinformatics database of pathogen antigens VIOLIN: vaccine investigation and online information network Epitopic peptides with low similarity to the host proteome: towards biological therapies without side effects Peptimmunology: immunogenic peptides and sequence redundancy Primer: mechanisms of immunologic tolerance Recent advances in immune modulation Cutting edge: contributions of apoptosis and anergy to systemic T cell tolerance Discriminating antigen and non-antigen using proteome dissimilarity III: tumour and parasite antigens Discriminating antigen and non-antigen using proteome dissimilarity II: viral and fungal antigens Discriminating antigen and non-antigen using proteome dissimilarity: bacterial antigens Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Single proteins might have dual but related functions in intracellular and extracellular microenvironments Locating proteins in the cell using TargetP, SignalP and related tools Improved prediction of signal peptides: SignalP 3.0 A comprehensive assessment of N-terminal signal peptides prediction methods WoLF PSORT: protein localization predictor Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization Predicting protein subcellular locations using hierarchical ensemble of Bayesian classifiers based on Markov chains SubLoc: a server/client suite for protein subcellular location based on SOAP Gpos-PLoc: an ensemble classifier for predicting subcellular localization of Gram-positive bacterial proteins Advantages of combined transmembrane topology and signal peptide prediction-the Phobius web server Prediction of lipoprotein signal peptides in Gram-negative bacteria Prediction of twin-arginine signal peptides Validating subcellular localization prediction tools with mycobacterial proteins Toward bacterial protein sub-cellular location prediction: single-class discrimminant models for all gram-and gram+ compartments Multi-class subcellular location prediction for bacterial proteins Alpha helical trans-membrane proteins: enhanced prediction using a Bayesian approach Beta barrel trans-membrane proteins: enhanced prediction using a Bayesian approach A predictor of membrane class: discriminating alpha-helical and beta-barrel membrane proteins from non-membranous proteins TATPred: a Bayesian method for the identification of twin arginine translocation pathway signal sequences LIPPRED: a web server for accurate prediction of lipoprotein signal sequences and cleavage sites Combining algorithms to predict bacterial protein sub-cellular location: parallel versus concurrent implementations Predicting the subcellular localization of viral proteins within a mammalian host cell Virus-PLoc: a fusion classifier for predicting the subcellular localization of viral proteins within host and virus-infected cells Structure and sequence relationships in the lipocalins and related proteins Structural Relationship of Streptavidin to the Calycin Protein Superfamily Analysis of known bacterial protein vaccine antigens reveals biased physical properties and amino acid composition Adaptation of protein surfaces to subcellular location Hierarchical classification of G-protein-coupled receptors with data-driven selection of attributes and classifiers GPCRTree: online hierarchical classification of GPCR function Optimizing amino acid groupings for GPCR classification On the hierarchical classification of G protein-coupled receptors Proteomic applications of automated GPCR classification VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines Identifying candidate subunit vaccines using an alignment-independent method based on principal amino acid properties DNA and peptide sequences and chemical processes multivariately modeled by principal component analysis and partial least-squares projections to latent structures Principal property-values for 6 nonnatural amino-acids and their application to a structure activity relationship for oxytocin peptide analogs Peptide binding to the HLA-DRB1 supertype: a proteochemometrics analysis Proteochemometrics mapping of the interaction space for retroviral proteases and their substrates Proteochemometrics analysis of substrate interactions with dengue virus NS3 proteases Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures Rough set-based proteochemometrics modeling of G-protein-coupled receptor-ligand interactions Improved approach for proteochemometrics modeling: application to organic compound-amine G protein-coupled receptor interactions Melanocortin receptors: ligands and proteochemometrics modeling Proteochemometrics modeling of the interaction of amine G-protein coupled receptors with a diverse set of ligands Peptide quantitative structureactivity-relationships, a multivariate approach Multivariate parametrization of 55 coded and non-coded amino-acids New chemical descriptors relevant for the design of biologically active peptides. Vaccines based on APCs and peptides are new but unproven strategies; most modern vaccine development relies instead on effective searches for vaccine antigens. keywords: analysis; antigens; approach; binding; candidate; cell; data; database; discovery; epitope; genome; genomic; host; immunogenicity; islands; methods; mhc; peptide; prediction; protein; sequence; system; vaccines; vaccinology cache: cord-016594-lj0us1dq.txt plain text: cord-016594-lj0us1dq.txt item: #94 of 541 id: cord-016652-x8t3lf1x author: Matthews, David title: Viruses and the Nucleolus date: 2011-05-23 words: 6640 flesch: 12 summary: Although many RNA virus proteins have been shown to localise to the nucleolus, most attention has focused on viral capsid proteins. These advances have provided fundamental insights as to how and why the nucleolus is targeted by many different viruses both to usurp normal functioning and to recruit nucleolar proteins to facilitate virus replication. keywords: cell; et al; herpes; human; infection; localization; nuclear; nucleocapsid; nucleolar; nucleolus; nucleus; protein; replication; rna; virus; viruses cache: cord-016652-x8t3lf1x.txt plain text: cord-016652-x8t3lf1x.txt item: #95 of 541 id: cord-017326-1caeui30 author: Seay, Montrell title: Digesting Oneself and Digesting Microbes: Autophagy as a Host Response to Viral Infection date: 2005 words: 11417 flesch: 26 summary: An interesting question is whether viral protein aggregates trigger autophagy by mechanisms that are similar to those involved in autophagy induction initiated by cellular protein aggregates. Thus, the eIF2 kinase-dependent autophagy signaling pathway not only regulates the degradation of long-lived cellular proteins but also regulates the degradation of viral proteins. keywords: autophagy; beclin; cell; death; function; genes; host; hsv-1; infection; kinase; pathway; pkr; protein; replication; role; signaling; virus; viruses cache: cord-017326-1caeui30.txt plain text: cord-017326-1caeui30.txt item: #96 of 541 id: cord-017400-jxbhdch8 author: Koroleva, Olga title: Proteomic Analysis of the Plant Nucleolus date: 2007 words: 8643 flesch: 33 summary: The following websites host current databases of identified nucleolar proteins: http://lamondlab.com/NOPdb/; http://bioinf.scri.sari.ac.uk/cgi-bin/atnopdb/home; http://www.expasy.org/ch2d/. Post-translational modifications (PTMs) are very common in nucleolar proteins, and several hundred specific modifications, many of which are likely to be functionally important in nucleoli, are known. We also discuss more specific tagging methods that have been used to analyse individual protein complexes, as well as methods for analysing post-translational modifications of nucleolar proteins. keywords: analysis; arabidopsis; cell; data; et al; identification; mass; modifications; nuclear; nucleolar; nucleoli; nucleolus; peptides; proteins; proteome; purification cache: cord-017400-jxbhdch8.txt plain text: cord-017400-jxbhdch8.txt item: #97 of 541 id: cord-017775-qohf9pxp author: Loa, Chien Chang title: Recombinant Turkey Coronavirus Nucleocapsid Protein Expressed in Escherichia coli date: 2015-09-10 words: 1682 flesch: 52 summary: This chapter describes expression and purifi cation of TCoV N protein with a prokaryotic system for preparation of a large quantity of highly purifi ed viral protein, which can be used as coating antigen for antibody-capture ELISA for serologic diagnosis of TCoV infection [ 11 , 12 ] . N protein were carried out for preparation of large quantities of highly purifi ed viral proteins. keywords: expression; nucleocapsid; protein; reagent; tcov; turkey cache: cord-017775-qohf9pxp.txt plain text: cord-017775-qohf9pxp.txt item: #98 of 541 id: cord-017817-ztp7w9yh author: Land, Walter Gottlieb title: Cell-Autonomous (Cell-Intrinsic) Stress Responses date: 2018-03-28 words: 17769 flesch: 34 summary: A typical example is represented by oxidative stress and ER stress responses, which appear to act mutually in any form of cellular damage. ATF activating transcription factor, CHOP cytidine-cytidine-adenosine-adenosine thymidine-enhancer-binding homologous protein, eIF2α eukaryotic translational initiation factor 2α, ER endoplasmic reticulum, IRE1α inositol-requiring transmembrane kinase/endoribonuclease 1α, PERK protein kinase-like eukaryotic initiation factor 2α kinase, UPR unfolded protein response, XBP1 X-box binding protein 1. XBP1s, X-box binding protein 1 whereby the s stands for the spliced form of XBP1. keywords: autophagy; cell; complex; damage; damps; degradation; dna; example; heat; immune; innate; keap1; mechanisms; membrane; nrf2; oxidative; pathway; process; protein; regulation; response; role; ros; signalling; stress; stress response; transcription; upr cache: cord-017817-ztp7w9yh.txt plain text: cord-017817-ztp7w9yh.txt item: #99 of 541 id: cord-017866-h5ttoo0z author: Bowman, Grant R. title: Biogenesis of Dense-Core Secretory Granules date: 2010-05-27 words: 13387 flesch: 33 summary: In cells producing mucous-containing DCGs, the cis and medial Golgi appear as flat cisternae, and secretory proteins are evenly distributed in their lumina. Th eir roles in secretion from neuroendocrine cells and as markers for neuroendocrine neoplasia Chro mogranin B (secretogranin I) promotes sorting to the regulated secretory pathway of processing intermediates derived from a peptide hormone precursor Gorr SUo Aggregation chaperones enhance aggregation and storage of secretory proteins in endocrine cells In vitro aggregation of the regulated secretory protein chromogranin A Reconstitution in vitro of the pH-dependent aggregation of pancreatic zymogens en route to the secretory granule: Implication of GP-2 Exocrine granule specific packaging signals are present in the polypeptide moiery of the pancreatic granule membrane protein GP2 and in amylase: Implications for protein targeting to secretory granules Identification of a chromogranin A domain that mediates binding to secretogranin III and targeting to secretory granules in pituitary cells and pancreatic beta-cells Identification of a novel sorting determinant for the regulated pathway in the secretory protein chromogranin A Sorting of three secretory proteins to distinct secretory granules in acidophilic cells of cow anterior pituitary Multiple neuropept ides derived from a common precursor are differentially packaged and transported Structure et ultrastructure de Lacrymaria olor (O.F.M. 1786) Cocrystallization of proinsulin and insulin Vayssie Let aI. A large multigenic family codes for the polypeptides of the crystalline trichocyst matrix in Paramecium Protein secretion in Tetrahymena thermophila. keywords: aggregation; budding; cargo; cells; dcg; dcgs; formation; golgi; granules; isgs; lumenal; mechanisms; membrane; membrane proteins; pathway; proteins; secretion; secretory; secretory granules; secretory pathway; sorting; targeting; tgn; vesicles cache: cord-017866-h5ttoo0z.txt plain text: cord-017866-h5ttoo0z.txt item: #100 of 541 id: cord-017887-pj6pal35 author: OuYang, Bo title: Structural and Functional Properties of Viral Membrane Proteins date: 2018-06-29 words: 11538 flesch: 43 summary: The viral potassium channel Kcv: structural and functional features RNA transfer from poliovirus 135S particles across membranes is mediated by long umbilical connectors Capsid protein VP4 of human rhinovirus induces membrane permeability by the formation of a size-selective multimeric pore Nuclear transport of influenza virus ribonucleoproteins: the viral matrix protein (M1) promotes export and inhibits import Unpacking the incoming influenza virus Influence of amantadine resistance mutations on the pH regulatory function of the M2 protein of influenza A viruses Viroporins: structure and biological functions Chlorovirus-mediated membrane depolarization of Chlorella alters secondary active transport of solutes Hepatitis C virus p7 and NS2 proteins are essential for production of infectious virus Hepatitis C virus p7 protein is crucial for assembly and release of infectious virions Viroporins from RNA viruses induce caspase-dependent apoptosis The influenza virus M2 protein cytoplasmic tail interacts with the M1 protein and influences virus assembly at the site of virus budding Cytoplasmic domain of influenza B virus BM2 protein plays critical roles in production of infectious virus Solution structure and functional analysis of the influenza B proton channel Identification of specific regions in hepatitis C virus core, NS2 and NS5A that genetically interact with p7 and co-ordinate infectious virus production Subcellular localization and function of an epitope-tagged p7 viroporin in hepatitis C virus-producing cells Mechanism of membrane fusion by viral envelope proteins Structures and mechanisms of viral membrane fusion proteins: multiple variations on a common theme Structure of influenza haemagglutinin at the pH of membrane fusion HIV-1 envelope glycoprotein biosynthesis, trafficking, and incorporation Core structure of gp41 from the HIV envelope glycoprotein Mechanism of membrane fusion by viral envelope proteins Intermonomer interactions in hemagglutinin subunits HA1 and HA2 affecting hemagglutinin stability and influenza virus infectivity Class II virus membrane fusion proteins Class II fusion proteins Structure of the dengue virus envelope protein after membrane fusion Crystal structure of dengue virus type 1 envelope protein in the postfusion conformation and its implications for membrane fusion Characterization of a membraneassociated trimeric low-pH-induced form of the class II viral fusion protein E from tick-borne encephalitis virus and its crystallization Class III viral membrane fusion proteins Characterization of EBV gB indicates properties of both class I and class II viral fusion proteins Class III viral membrane fusion proteins Structural basis of influenza virus fusion inhibition by the antiviral drug Arbidol Arbidol as a broad-spectrum antiviral: an update Improved pharmacological and structural properties of HIV fusion inhibitor AP3 over Enfuvirtide: highlighting advantages of artificial peptide strategy Enfuvirtide: the first therapy to inhibit the entry of HIV-1 into host CD4 lymphocytes B-cell-lineage immunogen design in vaccine development with HIV-1 as a case study B cell responses to HIV-1 infection and vaccination: pathways to preventing infection Structural basis for the function and inhibition of an influenza virus proton channel Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus Crystal structure of the glycophorin We will focus our discussion on two classes of transmembrane (TM) proteins encoded by viruses, viroporins (or viral channels) and membrane fusion proteins, as these proteins have been sought after as antiviral targets and they often exhibit peculiar structural features not seen in other membrane proteins. keywords: am2; binding; c virus; channel; domain; drug; env; fig; fusion; fusion proteins; influenza; influenza virus; membrane; membrane fusion; membrane proteins; nmr; protein; proton; structure; tmd; virus cache: cord-017887-pj6pal35.txt plain text: cord-017887-pj6pal35.txt item: #101 of 541 id: cord-017968-17d37a2z author: Lewinski, Martin title: Systems Approaches to Map In Vivo RNA–Protein Interactions in Arabidopsis thaliana date: 2018-08-30 words: 6573 flesch: 38 summary: Arabidopsis chloroplast RNA binding proteins CP31A and CP29A associate with large transcript pools and confer cold stress tolerance by influencing multiple chloroplast RNA processing steps The RNA-binding protein repertoire of embryonic stem cells Genome-wide identification and phylogenetic analysis of plant RNA binding proteins comprising both RNA recognition motifs and contiguous glycine residues Genome-wide identification, biochemical characterization, and expression analyses of the YTH domain-containing RNA-binding protein family in Arabidopsis and Rice The cardiomyocyte RNA-binding proteome: links to intermediary metabolism and heart disease HITS-CLIP yields genome-wide insights into brain alternative RNA processing A glycine-rich RNA-binding protein affects gibberellin biosynthesis in Arabidopsis ) atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes RBP45 and RBP47, two oligouridylatespecific hnRNP-like proteins interacting with poly(A)+ RNA in nuclei of plant cells A mutation in the Arabidopsis HYL1 gene encoding a dsRNA binding protein affects responses to abscisic acid, auxin, and cytokinin Gene expression regulatory networks in Trypanosoma brucei: insights into the role of the mRNA-binding proteome The RNA-binding protein FPA regulates flg22-triggered defense responses and transcription factor activity by alternative polyadenylation FCA, a gene controlling flowering time in Arabidopsis, encodes a protein containing RNA-binding domains The RNA-binding protein repertoire of Arabidopsis thaliana Conserved mRNA-binding proteomes in eukaryotic organisms GraphProt: modeling binding preferences of RNAbinding proteins Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7 Global analysis of yeast mRNPs SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export Comprehensive identification of mRNA-binding proteins of Leishmania donovani by interactome capture Pseudomonas HopU1 affects interaction of plant immune receptor mRNAs to the RNA-binding protein GRP7 Three types of nuclear genes encoding chloroplast RNAbinding proteins (cp29, cp31 and cp33) are present in Arabidopsis thaliana: presence of cp31 in chloroplasts and its homologue in nuclei/cytoplasms Cold shock domain proteins affect seed germination and growth of Arabidopsis thaliana under abiotic stress conditions Role for LSM genes in the regulation of circadian rhythms A member of the Whirly family is a multifunctional RNA-and DNA-binding protein that is essential for chloroplast biogenesis A putative RNA-binding protein positively regulates salicylic acid-mediated immunity in Arabidopsis In planta determination of the mRNA-binding proteome of Arabidopsis etiolated seedlings Regulation of miRNA abundance by RNA binding protein TOUGH in Arabidopsis Arabidopsis RNA-binding protein UBA2a relocalizes into nuclear speckles in response to abscisic acid PEPPER, a novel K-homology domain gene, regulates vegetative and gynoecium development in Arabidopsis Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L Slave to the rhythm Polypyrimidine tract binding protein homologs from Arabidopsis are key regulators of alternative splicing with implications in fundamental developmental processes The RNA-recognition motif in chloroplasts A circadian clock-regulated toggle switch explains AtGRP7 and AtGRP8 oscillations in Arabidopsis thaliana keywords: arabidopsis; atgrp7; binding; chloroplast; cross; et al; mrna; proteins; rbps; rna; splicing; sr45; thaliana; transcripts; vivo cache: cord-017968-17d37a2z.txt plain text: cord-017968-17d37a2z.txt item: #102 of 541 id: cord-017999-saxwqc2j author: Travers, Andrew A. title: Gene Regulation by HMGA and HMGB Chromosomal Proteins and Related Architectural DNA-Binding Proteins date: 2005 words: 6341 flesch: 36 summary: This organisation is normally effected by abundant DNA binding proteins, termed architectural DNA-binding proteins, that either induce DNA bending or facilitate the formation of multicomponent DNA-protein complexes. This combination of bound proteins can then recruit the remodelling complex hSWI/SNF. keywords: bend; binding; chromatin; complex; dna; factors; histone; hmg; hmga; hmgb; proteins; sites; structure; transcription cache: cord-017999-saxwqc2j.txt plain text: cord-017999-saxwqc2j.txt item: #103 of 541 id: cord-018018-2yyv8vuy author: Rybicki, Ed title: History and Promise of Plant-Made Vaccines for Animals date: 2018-07-04 words: 9139 flesch: 16 summary: The early historical account of molecular farming for veterinary vaccines given above gives an idea of the array of technologies available and used up to the mid-2000s: transgenic and transplastomic expression of subunit proteins; recombinant plant viruses either used to express whole vaccine candidate genes, or to display chosen peptides fused to their capsid proteins; fusion of vaccine protein genes to carrier proteins to improve immunogenicity, including by inherent adjuvant properties; candidate parenteral and oral vaccines to both viruses and bacteria; therapeutics for animals made in plants; use of plant cell cultures to make antigens. The case for plant-made veterinary immunotherapeutics Protein body induction: a new tool to produce and recover recombinant proteins in plants Optimizing the yield of recombinant pharmaceutical proteins in plants New viral vector for superproduction of epitopes of vaccine proteins in plants Expression of an animal virus antigenic site on the surface of a plant virus particle Expression of Human papillomavirus type 16 major capsid protein in transgenic Nicotiana tabacum cv Optimization of BY-2 cell suspension culture medium for the production of a human antibody using a combination of fractional factorial designs and the response surface method Orally fed seeds producing designer IgAs protect weaned piglets against enterotoxigenic Escherichia coli infection Oral immunogenicity of human papillomavirus-like particles expressed in potato Expression of Bacillus anthracis protective antigen in transgenic chloroplasts of tobacco, a non-food/feed crop Induction of a protective antibody response to foot and mouth disease virus in mice following oral or parenteral immunization with alfalfa transgenic plants expressing the viral structural protein VP1 Protection of mice against challenge with foot and mouth disease virus (FMDV) by immunization with foliar extracts from plants infected with recombinant tobacco mosaic virus expressing the FMDV structural protein VP1 Protective lactogenic immunity conferred by an edible peptide vaccine to bovine rotavirus produced in transgenic plants One-Health: a safe, efficient, dual-use vaccine for humans and animals against middle east respiratory syndrome coronavirus and rabies virus Induction of protective immunity in swine by recombinant bamboo mosaic virus expressing foot-and-mouth disease virus epitopes Expression of the fusion glycoprotein of Newcastle disease virus in transgenic rice and its immunogenicity in mice A plant-based multicomponent vaccine protects mice from enteric diseases Expression in plants and immunogenicity of plant virus-based experimental rabies vaccine Development of a candidate vaccine for Newcastle disease virus by epitope display in the Cucumber mosaic virus capsid protein keywords: animal; benthamiana; candidate; cell; challenge; development; disease; et al; expression; group; human; mice; plant; production; protein; recombinant; tobacco; transgenic; use; vaccines; virus cache: cord-018018-2yyv8vuy.txt plain text: cord-018018-2yyv8vuy.txt item: #104 of 541 id: cord-018265-twp33bb6 author: Becker, Pablo D. title: Community-acquired pneumonia: paving the way towards new vaccination concepts date: 2007 words: 14131 flesch: 32 summary: Furthermore, DNA coding for vaccine antigens appears to induce excellent immunological memory, which can be reawakened by later immunization or exposure to the pathogen. An epidermal DNA-based influenza vaccine, which contained the HA gene from A/Panama/2007/99 delivered by particle-mediated epidermal delivery was also tested in humans by PowderJect keywords: antibodies; antigens; cell; children; delivery; development; disease; dna; efficacy; immunity; immunization; infection; influenza; mucosal; pneumococcal; pneumoniae; protection; protein; recombinant; responses; rsv; sars; studies; vaccination; vaccine; virus cache: cord-018265-twp33bb6.txt plain text: cord-018265-twp33bb6.txt item: #105 of 541 id: cord-018276-elb93kp6 author: Li, Shitao title: Proteomics Defines Protein Interaction Network of Signaling Pathways date: 2012-12-27 words: 8295 flesch: 46 summary: Analysis of protein–protein interaction (PPI) has contributed numerous insights to the understanding of the regulation of signal pathways. Protein interaction plays essential role in cell structure and function. keywords: analysis; bait; cation; cell; complex; data; et al; interaction; mass; network; nity; protein; puri cache: cord-018276-elb93kp6.txt plain text: cord-018276-elb93kp6.txt item: #106 of 541 id: cord-018437-yjvwa1ot author: Mitchell, Michael title: Taxonomy date: 2013-08-26 words: 9285 flesch: 42 summary: Structure-function relations The DNA sequence of human herpesvirus-6: structure, coding content, and genome evolution Processing of genome 5′ termini as a strategy of negative-strand RNA viruses to avoid RIG-Idependent interferon induction Respiratory syncytial virus and parainfl uenza virus Infl uenza virus, Chap 42 Global and regional distribution of HIV-1 genetic subtypes and recombinants in Parainfl uenza viruses Gene mapping of the putative structural region of the hepatitis C virus genome by in vitro processing analysis Evolutionary history and phylogeography of human viruses What does virus evolution tell us about virus origins? Nucleotide sequence and genome organization of human parvovirus B19 isolated from the serum of a child during aplastic crisis CXCR4 as a functional coreceptor for human immunodeficiency virus type 1 infection of primary macrophages The genome length of human parainfl uenza virus type 2 follows the rule of six, and recombinant viruses recovered from non-poly-hexameric-length antigenomic cDNAs contain a biased distribution of correcting mutations Respiratory syncytial virus nonstructural proteins decrease levels of multiple members of the cellular interferon pathways Infl uenza virus evolution, host adaptation, and pandemic formation Mechanisms and enzymes involved in SARS coronavirus genome expression keywords: classifi; dna; envelope; family; genes; genome; host; human; proteins; reading; rna; sequence; species; type; uenza; viral; virions; virus; viruses cache: cord-018437-yjvwa1ot.txt plain text: cord-018437-yjvwa1ot.txt item: #107 of 541 id: cord-018479-mvnm98hv author: Rehm, Fabian B. H. title: Applications of Microbial Biopolymers in Display Technology date: 2017-11-16 words: 4632 flesch: 24 summary: The study revealed a biotin binding capacity of 61 ng per μg of bead protein and demonstrated the detection of goat polyclonal biotinylated IgG in FACS using a secondary conjugated antibody. The cytocompatability of polyhydroxyalkanoates coated with a fusion protein of PHA repressor protein (PhaR) and Lys-Gln-Ala-Gly-Asp-Val (KQAGDV) polypeptide Expression of active recombinant human tissue-type plasminogen activator by using in vivo polyhydroxybutyrate granule display In vivo production of scFv-displaying biopolymer beads using a selfassembly-promoting fusion partner Bacterial polyhydroxyalkanoate granules: biogenesis, structure, and potential use as nano-/micro-beads in biotechnological and biomedical applications Recombinant protein production by in vivo polymer inclusion display Properties, production, and applications of camelid singledomain antibody fragments In vivo polyester immobilized sortase for tagless protein purification Bioengineering of bacteria to assemble custom-made polyester affinity resins Biochemical and enzymological properties of the polyhydroxybutyrate synthase from the extremely halophilic archaeon strain 56 Insights into the surface topology of polyhydroxyalkanoate synthase: self-assembly of functionalized inclusions Tolerance of the Ralstonia eutropha class keywords: antigen; applications; beads; binding; cell; display; pha; protein; purification; surface; target cache: cord-018479-mvnm98hv.txt plain text: cord-018479-mvnm98hv.txt item: #108 of 541 id: cord-018493-q24f86e9 author: Ranjan, Prabhat title: Importance of Natural Proteins in Infectious Diseases date: 2015-08-08 words: 3935 flesch: 33 summary: Proteins might also be involved in playing solely protective roles against infections like various cell surface receptor proteins (Toll-like receptors, Nod-like receptors, etc.), which trigger protective immune responses. Likewise, almost all the elements of our immune system, e.g., Immunoglobulins (antibodies), various cell surface proteins (T and B cell receptors, Major histocompatibility complex, CD4, CD8, CD3, etc.), the several adaptor proteins and enzymes, involved in signal transduction pathways, are all of protein origin and crucial for combating against external infections. keywords: cell; chaperones; diseases; domain; glycoproteins; host; prion; proteins; receptors; shock; surface; virus cache: cord-018493-q24f86e9.txt plain text: cord-018493-q24f86e9.txt item: #109 of 541 id: cord-018647-bveks6t1 author: Butnariu, Monica title: Plant Nanobionics: Application of Nanobiosensors in Plant Biology date: 2019-10-01 words: 16819 flesch: 37 summary: A series of new genes for resistance to insect attack, transferable to plants (genes encoding δ-endotoxin production from B. thuringiensis) has been discovered; genes for the synthesis of enzymes or enzyme inhibitors; plant genes encoding the synthesis of specific lectins; genes that cause induction of synthesis of plant compounds such as phytoalexins. Given the practical significance of plant resistance to harmful insects, research has been extended to other plant species, producing eggplant plants resistant to the attack of Coleoptera, broccoli with resistance to certain lepidopteran species, maize with resistance to B. fusca, etc., as well as a number of advances in leguminous plants. keywords: analyte; binding; concentration; detection; electrochemical; electrode; enzyme; et al; genes; groups; host; interaction; membrane; molecules; nbss; optical; oxygen; plants; proteins; reaction; receptors; recognition; redox; resistance; response; signal; species; surface; transducer; use cache: cord-018647-bveks6t1.txt plain text: cord-018647-bveks6t1.txt item: #110 of 541 id: cord-018963-2lia97db author: Xu, Ying title: Protein Structure Prediction by Protein Threading date: 2010-04-29 words: 15314 flesch: 39 summary: The protein threading problem with sequence amino acid interaction preferences is NP-complete Introduction to ProteinArchitecture: The StructuralBiology ofProteins A unified statistical framework for sequence comparison and structure comparison Emergence of preferred structures in a simple model of protein folding Are protein folds atypical? Designability of protein structures: A lattice-model study using the Miyazawa-Jernigan matrix A distance-dependent atomic knowledge-based potential for improved protein structure selection Geometric cooperativity and anti-cooperativity of threebody interactions in native proteins Multimeric threading-based prediction of protein-protein interactions on a genomic scale: Application to the Saccharomyces cerevisiae proteome Protein distance constraints predicted by neural networks and probability density functions Peons: A neuralnetwork-based consensus predictor that improves fold recognition Threading analysis suggests that the obese gene product may be a helical cytokine Comparative genomics ofthe Archaea (Euryarchaeota): Evolution of conserved protein families, the stable core, and the variable shell How many species are there on earth Improvement ofthe GenTHREADER method for genomic fold recognition Protein Structure Prediction by Protein Threading The Genomic Threading Database: A comprehensive resource for structural annotations of the genomes from key organisms Novel knowledge-based mean force potential at atomic level Statistical significance of protein structure prediction by threading Statistical significance of hierarchical multibody potentials based on Delaunay tessellation and their application in sequence-structure alignment SCOP: A structural classification of proteins database for the investigation of sequences and structures Protein superfamilies and domain superfolds CATH-A hierarchic classification of protein domain structures A local alignment method for protein structure motifs Threading with explicit models for evolutionary conservation ofstructure and sequence Combination ofthreading potentials and sequence profiles improves fold recognition Combinatorial Optimization: Algorithms and Complexity New techniques in structural NMR-anisotropic interactions Protein fold recognition through application of residual dipolar coupling data Protein structure prediction using sparse dipolar coupling data The anatomy and taxonomy ofprotein structure Graph minors .2. To keep up with the rate at which protein structures are being solved, there is a clear need for more automated domain-partitioning methods to process the newly solved structures. keywords: algorithm; alignment; amino; decomposition; energy; et al; families; fold; function; graph; number; prediction; problem; protein; protein structure; protein threading; query; sequence; structure; template; threading; tree cache: cord-018963-2lia97db.txt plain text: cord-018963-2lia97db.txt item: #111 of 541 id: cord-018969-0zrnfaad author: Giese, Matthias title: Types of Recombinant Vaccines date: 2015-09-24 words: 14241 flesch: 44 summary: Vaccine proteins made by the host are natural proteins and contain important posttranslational modifi cations such as the correct glycosylation. By covalent linkage of PRP with T cell dependent protein antigens, a conjugated vaccine was created to overcome the T cell independent characteristics of PRP. keywords: antigen; bacteria; bees; cells; control; dna; expression; feeding; fig; gas; host; immune; infection; mucosal; nov; plague; plasmid; protective; protein; response; shigella; specifi; studies; system; tick; vaccination; vaccine; varroa; virus; viruses; vlps cache: cord-018969-0zrnfaad.txt plain text: cord-018969-0zrnfaad.txt item: #112 of 541 id: cord-020097-eh5deunk author: None title: Cumulative Author Index for 2006 (Volumes 115–122) date: 2006-10-27 words: 1485 flesch: -330 summary: An endornavirus from a hypovirulent strain of the violet root rot fungus Importance of the extracellular and cytoplasmic/transmembrane domains of the haemagglutinin protein of rinderpest virus for recovery of viable virus from cDNA copies Envelope gene capture and insect retrovirus evolution: The relationship between errantivirus and baculovirus envelope proteins Multiclonal pattern of Jaagsiekte sheep retrovirus integration sites in ovine pulmonary adenocarcinoma Venezuelan equine encephalitis virus complex-specific monoclonal antibody provides broad protection, in murine models, against airborne challenge with viruses from serogroups I, II and III Patterns of sequence evolution at epitopes for host antibodies and cytotoxic T-lymphocytes in human immunodeficiency virus type Phylogenetic analysis of the gag region encoding the matrix protein of small ruminant lentiviruses: Comparative analysis and molecular epidemiological applications Gene expression array analyses predict increased proto-oncogene expression in MMTV induced mammary tumors Evolutionary genomics of archaeal viruses: Unique viral genomes in the third domain of life HIV-l and the microRNA-guided silencing pathway: An intricate and multifaceted encounter A modified viral satellite DNA-based gene silencing vector is effective in association with heterologous begomoviruses TATAbinding protein and TBP-associated factors during herpes simplex virus type 1 infection: Localization at viral DNA replication sites Immunohistochemical examination of the role of Fas ligand and lymphocytes in the pathogenesis of human liver yellow fever Complete sequence and organization of the human adenovirus serotype 46 genome Molecular characterization and phylogenetic study of Maedi Visna and Caprine Arthritis Encephalitis viral sequences in sheep Lymphocytopathogenic activity in vitro correlates with high virulence in vivo for BVDV type 2 strains: Criteria for a third biotype of BVDV Inactivation of White Spot Syndrome Virus (WSSV) by normal rabbit serum: Implications for the role of the envelope protein VP28 in WSSV infection of shrimp Low prevalence of primary antiretroviral resistance mutations and predominance of HIV-1 clade C at polymerase gene in newly diagnosed individuals from south Brazil Characterization of a highly virulent feline calicivirus and attenuation of this virus Interaction of the hepatitis B virus protein HBx with the human transcription regulatory protein p120E4F in vitro Translation reinitiation and leaky scanning in plant viruses Phylogenetic analysis of recent isolates of classical swine fever virus from Colombia Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein Rabies virus-induced apoptosis involves caspase-dependent and caspase-independent pathways Translational control during virus infection Epstein-Barr virus immunossuppression of innate immunity mediated by phagocytes Binding of shrimp cellular proteins to Taura syndrome viral capsid proteins VP1 Collaborative study to evaluate a new ELISA test to monitor the effectiveness of rabies vaccination in domestic carnivores Efficient inhibition of hepatitis B virus replication by small interfering RNAs targeted to the viral X gene in mice Preparation and characterization of a novel monoclonal antibody specific to severe acute respiratory syndrome-coronavirus nucleocapsid protein The kinetics of proinflammatory cytokines in murine peritoneal macrophages infected with envelope protein-glycosylated or non-glycosylated West Nile virus Members of adenovirus species B utilize CD80 and CD86 as cellular attachment receptors Exogenous nitric oxide inhibits Crimean Congo hemorrhagic fever virus Structural and antigenic analysis of the yellow head virus nucleocapsid protein p20 Efficient expression of the 15-kDa form of infectious pancreatic necrosis virus VP5 by suppression of a UGA codon Phylogenetic relationships of Brazilian bovine respiratory syncytial virus isolates and molecular homology modeling of attachment glycoprotein Genetic manipulation of two fowlpox virus late transcriptional regulatory elements influences their ability to direct expression of foreign genes A new RNA virus found in black tiger shrimp Penaeus monodon from Thailand Conformational maturation of the nucleoprotein synthesized in influenza C virus-infected cells HIV-1-mediated syncytium formation promotes cell-to-cell transfer of Tax protein and Systemic antiviral silencing in plants Sequencing and comparative analysis of a pig bovine viral diarrhea virus genome EsiRNAs inhibit Hepatitis B virus replication in mice model more efficiently than synthesized siRNAs Chronological and geographical variations in the small RNA segment of the teratogenic Akabane virus HCV NS2 protein inhibits cell proliferation and induces cell cycle arrest in the S-phase in mammalian cells through down-regulation of cyclin A expression Pepper mild mottle virus pathogenicity determinants and cross protection effect of attenuated mutants in pepper Hepatitis E virus genotyping based on full-length genome and partial genomic regions Location and phylogenetic analysis of the region immediately upstream of the granulin gene of the Clostera anachoreta granulovirus Molecular characterization of rabies virus isolates in China during Proteolytic cleavage and shedding of the bovine prion protein in two cell culture systems Antigenic structure analysis of glycosylated protein 3 of porcine reproductive and respiratory syndrome virus Generation of virus-like particles consisting of the major capsid protein VP1 of goose hemorrhagic polyomavirus and their application in serological tests Amino acid changes in the recombinant Dengue 3 Envelope domain III determine its antigenicity and immunogenicity in mice keywords: analysis; cell; expression; gene; hepatitis; human; protein; syndrome; virus cache: cord-020097-eh5deunk.txt plain text: cord-020097-eh5deunk.txt item: #113 of 541 id: cord-020101-5rib7pe8 author: None title: Cumulative Author Index for 2008 date: 2008-11-17 words: 2143 flesch: -170 summary: Murine leukemia virus reverse transcriptase: Structural comparison with HIV-1 reverse transcriptase The GPRLQPY motif located at the carboxy-terminal of the spike protein induces antibodies that neutralize Porcine epidemic diarrhea virus Detection of ovine herpesvirus 2 major capsid gene transcripts as an indicator of virus replication in shedding sheep and clinically affected animals Genetic characterization of equine influenza viruses isolated in Italy between A new living cell-based assay system for monitoring genome-length hepatitis C virus RNA replication Unraveling the puzzle of human anellovirus infections by comparison with avian infections with the chicken anemia virus The contribution of feathers in the spread of chicken anemia virus Cloning and subcellular localization of the phosphoprotein and nucleocapsid proteins of Potato yellow dwarf virus, type species of the genus Nucleorhabdovirus The p26 gene of the Autographa californica nucleopolyhedrovirus: Timing of transcription, and cellular localization and dimerization of product Complete genomic sequence of turkey coronavirus Recombinant L and P protein complex of Rinderpest virus catalyses mRNA synthesis in vitro Molecular divergence of Grapevine virus A (GVA) variants associated with Shiraz disease in South Africa Sequence analysis of a reovirus isolated from the winter moth Operophtera brumata (Lepidoptera: Geometridae) and its parasitoid wasp Phobocampe tempestiva (Hymenoptera: Ichneumonidae SARS coronavirus replicase proteins in pathogenesis Virus-induced gene silencing in Medicago truncatula and Lathyrus odorata Evaluating the 3C-like protease activity of SARS-Coronavirus: Recommendations for standardized assays for drug discovery HBx modulates iron regulatory protein 1-mediated iron metabolism via reactive oxygen species Pathogenetic mechanisms of severe acute respiratory syndrome Detection of a novel circovirus in mute swans (Cygnus olor) by using nested broadspectrum PCR Chimaeric HIV-1 subtype C Gag molecules with large in-frame C-terminal polypeptide fusions form virus-like particles Cross-species recombination in the haemagglutinin gene of canine distemper virus Sapovirus-like particles derived from polyprotein Cauliflower mosaic virus gene VI product N-terminus contains regions involved in resistance-breakage, self-association and interactions with movement protein Adenovirus vector induced innate immune responses: Impact upon efficacy and toxicity in gene therapy and vaccine applications Interfering with cellular signaling pathways enhances sensitization to combined sodium butyrate and GCV treatment in EBV-positive tumor cells Evidence for recombination between PCV2a and PCV2b in the field Retroviral reverse transcriptases (other than those of HIV-1 and murine leukemia virus): A comparison of their molecular and biochemical properties Mitochondrial plasmids of sugar beet amplified via rolling circle method detected during curtovirus screening Appearance of intratypic recombination of enterovirus 71 in Taiwan from The circulation of subgenogroups B5 and C5 of enterovirus 71 in Taiwan from In vitro replication of Bamboo mosaic virus satellite Characterization of the interaction of domain III of the envelope protein of dengue virus with putative receptors from CHO cells Intrahost evolution of envelope glycoprotein and OrfA sequences after experimental infection of cats with a molecular clone and a biological isolate of feline immunodeficiency virus The SARS-Coronavirus PLnc domain of nsp3 as a replication/ transcription scaffolding protein Limited compatibility between the RNA polymerase components of influenza virus type A and B Serotype-specificity of recombinant fusion proteins containing domain III of dengue virus Very virulent infectious bursal disease virus isolated from wild birds in Korea: Epidemiological implications Genetic analysis and evaluation of the reassortment of influenza B viruses isolated in Taiwan during the Enhanced immune responses of mice inoculated recombinant adenoviruses expressing GP5 by fusion with GP3 and/or GP4 of PRRS virus Effect of antiviral treatment and host susceptibility on positive selection in hepatitis C virus Novel HIV-1 reverse transcriptase inhibitors Synthesis of recombinant human parainfluenza virus 1 and 3 nucleocapsid proteins in yeast Saccharomyces cerevisiae Evolutionary analyses of European H1N2 swine influenza keywords: analysis; cell; gene; hepatitis c; infection; molecular; murine leukemia; protein; replication; transcriptase; type; virus; virus replication cache: cord-020101-5rib7pe8.txt plain text: cord-020101-5rib7pe8.txt item: #114 of 541 id: cord-020235-stcrozdw author: None title: Abstracts of Papers Presented at the 38th Meeting of the Deutsche Gesellschaft für Hygiene und Mikrobiologie, Virology Section, Göttingen, 5.–8.10.1981 date: 2012-03-15 words: 13511 flesch: 54 summary: 2. the number of virus producing cells is not cor related with the appe arance of slgM or sIgG. 3. virus yields seem to be influenced by the cell cycle: the number of chick emb ryo fibro blasts producing plaques in infectious center assays is increased after synchro nisa tion of the cells before infection. Recent studies on protein kinases from a number of tumor viruses have raised the possibility that the phosphorylation of cell proteins is involved in the processes leading to cell transformation. keywords: acid; activity; analysis; antibodies; antigen; cells; cultures; disease; dna; fragments; genome; glycoproteins; hsv; human; infection; influenza; inst; mice; particles; positive; protein; restriction; results; rna; sera; sites; specific; strains; test; type; univ; virus; viruses cache: cord-020235-stcrozdw.txt plain text: cord-020235-stcrozdw.txt item: #115 of 541 id: cord-020664-m47ejlsn author: Schlüter, Klaus-Dieter title: Intrakrine, parakrine und autokrine Funktionen des PTH/PTHrP-Systems date: 2006 words: 7832 flesch: 42 summary: Eine verminderte Expression von PTHrP, Tierexperiment zeigen, dass durch Gabe von Guanin-Nukleotid-Analoga die Expression von PTHrP spezifisch reprimiert wurde. keywords: aber; aktivierung; als; auch; auf; aus; bei; bone; cancer; cells; dass; dem; der; des; die; diese; durch; eine; et al; expression; fçr; gene; growth; hormone; ist; kann; konnte; konzentrationen; mit; nicht; noch; oder; parakrine; parathyroid; peptide; protein; pth1r; pthrp; receptor; regulation; scheint; sein; sich; signal; sind; tip39; und; von; weiteren; werden; wie; wird; wirkung; zellen; zur; çber cache: cord-020664-m47ejlsn.txt plain text: cord-020664-m47ejlsn.txt item: #116 of 541 id: cord-020757-q4ivezyq author: Saikumar, Pothana title: Apoptosis and Cell Death: Relevance to Lung date: 2010-05-21 words: 7428 flesch: 33 summary: Cell death has become an area of intense interest and investigation in science and medicine because of the recognition that cell death, in general, and apoptosis, in par-ticular, are important features of many biologic processes. As time has progressed, however, apoptotic cell death has been shown to occur in many cell types under a variety of physiologic and pathologic conditions. keywords: activation; apoptosis; caspase-8; caspases; cell; cell death; death; factor; fas; infl; lung; membrane; protein; receptor; role; tnf cache: cord-020757-q4ivezyq.txt plain text: cord-020757-q4ivezyq.txt item: #117 of 541 id: cord-020788-a33vcapl author: Gottardi, Cara J. title: Signals and Mechanisms of Sorting in Epithelial Polarity date: 2008-05-22 words: 13913 flesch: 29 summary: Yeast syntaxins Ssolp and Sso2p belong to a family of related membrane proteins that function in vesicular transport Role ofmicrotubules in polarized delivery of apical membrane proteins to the brush border ofthe intestinal epithelium Distribution of transport proteins over animal cell membranes Podocytosis of small molecules and ions by caveolae The calmodulin antagonist, W-13, alters transcytosis, recyclingand morphology ofthe endocyticpathway in Madine-Darby canine kidney cells Mutational and secondary structural analysis of the basolateral sorting signal of the polymeric immunoglobulin receptor Vesicular stomatitis virus glycoprotein is sorted and concentrated during export from the endoplasmic reticulum Cloning of a rab3 isotype predominately expressed in adipocytes The NPXY internalization signal of the LDL receptor adopts a reverse turn conformation Biogenesis of the rat hepatocyte plasma membrane in vivo: Comparison of the pathways taken by apical and basolateral proteins using subcellular fractionation. The differential distribution of membrane proteins between the plasmalemmal surfaces of polarized epithelial cells enables these cells to both respond to and effect changes upon their environment in a directed fashion. keywords: atpase; binding; cells; delivery; domain; epithelial; et al; golgi; gpi; localization; machinery; mdck; membrane; membrane proteins; pathway; plasma; polarity; proteins; receptor; signal; sorting; surface; targeting; transport; vesicle cache: cord-020788-a33vcapl.txt plain text: cord-020788-a33vcapl.txt item: #118 of 541 id: cord-021393-9loesliv author: Meade, H.M. title: EXPRESSION OF RECOMBINANT PROTEINS IN THE MILK OF TRANSGENIC ANIMALS date: 2007-09-02 words: 8096 flesch: 40 summary: In general, the glycosylation found on human proteins secreted into transgenic animal milk has been generally similar to plasma protein glycosylation. Protein biosynthesis is carried out in epithelial cells, and milk proteins are discharged into the lumen of the alveolus by exocytosis and then into the ducts. keywords: animals; casein; cells; et al; expression; gene; gland; goats; human; mammary; mice; microinjection; milk; production; protein; sheep; transgenic cache: cord-021393-9loesliv.txt plain text: cord-021393-9loesliv.txt item: #119 of 541 id: cord-021500-sy6lnt7b author: Jean Harry, G. title: Myelination, Dysmyelination, and Demyelination date: 2007-05-09 words: 17617 flesch: 27 summary: Kaiser Found The nodes of Ranvier Molecular genetics of X-linked mutants Selective expression of DM-20, an alternatively spliced myelin proteolipid protein gene product The PO glycoprotein of peripheral nerve myelin Cell kinetics and cell death in the optic nerve of the myelin deficient rat Acute effects of triethyltin on the rat myelin sheath Schwann cell precursors and their development Effect of cytochalasin D on secretion by rat pancreatic acini Sources of cholesterol for kidney and nerve during development The neuritogenicity and encephalitogenicity of P2 in the rat, guinea-pig and rabbit Structure and expression of proteolipid protein in the peripheral nervous system Conversion of normal behavior to shiverer by myelin basic protein antisense cDNA in transgenic mice Organization of microtubules in myelinating Schwann cells Novel member of the zinc finger superfamily: a C2-HC finger that recognizes a glia-specific gene Restoration of myelin formation by a single type of myelin basic protein in transgenic shiverer mice Pax3: a paired domain gene as a regulator in PNS myelination Compact myelin exists in the absence of basic protein in the shiverer mutant mouse Beyond self-assembly: from microtubules to morphogenesis Purification and partial characterization of two glycoproteins in bovine peripheral nerve myelin membrane Functions of intermediate filaments Oligodendroglial cell death in jimpy mice: an explanation for the myelin deficit Development of unmyelinated fibers in peripheral nerve: an immunohistochemical and electronmicroscopic study Changes in the state of actin during the exocytotic reaction of permeabilized rat mast cells Localization of the gene encoding myelin basic protein to mouse chromosome 18E3-4 and rat chromosome 1 p11-p12 Decrease in oligodendrocyte carbonic anhydrase activity preceding myelin degeneration in cuprizone induced demyelination Triethyllead-induced hypomyelination in the developing rat forebrain Protein composition of forebrain myelin isolated from triethyllead-intoxicated young rats Suppressive effect of triethyllead on entry of proteins into the CNS myelin sheath in vitro Effect of triethyllead on posttranslational processing of myelin proteins An isoform of ankyrin is localized at nodes of Ranvier in myelinated axons of central and peripheral nerves Lead Lead encephalopathy in the developing rat: effect upon myelination Undernutrition in the developing rat: effect upon myelination Deletion of the serine 34 codon from the major peripheral myelin protein P0 gene in Charcot-Marie-Tooth disease type lB Two forms of 1B236/myelin-associated glycoprotein, a cell adhesion molecule for postnatal neural development, are produced by alternative splicing Mechanism of demyelination, in tellurium neuropathy: electron microscopic observations Demyelination and remyelination in lead neuropathy: electron microscopic studies Receptor activity and signal transduction in myelin Enzymes and receptors of myelin The Neural Crest Structure and acylation of proteolipid protein Myelin-associated enzymes Merosin, a protein specific for basement membranes of Schwann cells, striated muscle and trophoblast, is expressed late in nerve and muscle development Unwrapping the genes of myelin Isolation and sequence of a cDNA encoding the major structural protein of peripheral myelin The myelin proteolipid protein gene and its expression Expression of myelin proteolipid and basic protein mRNAs in cultured cells The experimental production of edema in the central nervous system of the rat by triethyltin compounds Interaction and fusion of unilamellar vesicles containing cerebrosides and sulfatides induced by myelin basic protein Modulation by glycosphingolipids of membrane-membrane interaction induced by myelin basic protein and mellitin Immunoelectron microscopic localization of neural cell adhesion molecules (L1, N-CAM, and MAG) and their shared carbohydrate epitope and myelin basic protein in developing sciatic nerve Hexachlorophene intoxication: characterization of myelin and myelin related fractions in the rat during early postnatal development Polyneuropathy and IgM monoclonal gammopathy: studies on the pathogenetic role of anti-myelin-associated glycoprotein antibody Effect of pre-and postnatal essential fatty acid deficiency on brain in development and myelination The primary structure of fatty acid-binding protein from nurse shark liver: structural and evolutionary relationship to the mammalian fatty acid-binding protein family Structure and molecular interactions of myelin basic protein and its antigenic peptides P0 promoter directs expression of reporter and toxin genes to Schwann cells of transgenic mice Structure and chromosomal localization of the gene for the oligodendrocyte-myelin glycoprotein The oligodendrocyte-myelin glycoprotein belongs to a distinct family of proteins and contains the HNK-1 carbohydrate A phosphatidylinositoMinked peanut agglutinin-binding glycoprotein in central nervous system myelin and on oligodendrocytes Structure and function of myelin protein genes Organization of myelin protein genes: myelinassociated glycoprotein Schwann cell development and the regulation of myelination Schwann cell development, differentiation, and myelination Recombination within the myelin basic protein gene created the dysmyelinating shiverer mouse mutation Biochemical and molecular bases of myelinopathy Myelin formation, structure, and biochemistry Schwann cells as targets for neurotoxicants Biochemistry of lipids. Assignment of the myelin basic protein gene to human chromosome 18q22-qter Axon-regulated expression of a Schwann cell transcript that is homologous to a growth arrest-specific gene 2',3'-Cyclic nucleotide 3'-phosphodiesterase, an oligodendrocyte-Schwann cell and myelin-associated enzyme of the nervous system Quantitative analysis of myelin protein gene expression during development in the rat sciatic nerve D, and cAMP response element binding protein by Schwann cells and their precursors in vivo and in vitro Myelin basic protein in brains of rat with low dose lead encephalopathy Identifying the protein products of brain-specific genes with antibodies to chemically synthesized peptides A leucine-to-proline mutation in the putative first transmembrane domain of the 22-kDa peripheral myelin in the trembler-J mouse Trembler mouse carrier a point mutation in a myelin gene Some new observations in triethyl-tin of rats Experimental study on segmental demyelination in tellurum neuropathy Expression of carbonic anhydrase II mRNA and protein in oligodendrocytes during toxic demyelination in the young adult mouse Ultrastructure of axons in disturbed CNS myelination in pt rabbit Experimental paraprotein neuropathy, demyelination by passive transfer of IgM anti-myelin-associated glycoprotein The DM20 protein of myelin: intracellular and surface expression patterns in transfectants Myelin deficity produced by early postnatal exposure to inorganic lead or triethyltin are persistent Primary demyelination induced by exposure to tellurium alters mRNA levels for nerve growth factor receptor, SCIP, 2',3'-cyclic nucleotide 3'-phosphodiesterase, and myelin proteolipid protein in rat sciatic nerve Tellurium-induced alterations in HMG-CoA reductase gene expression and enzyme activity: differential effects in sciatic nerve and liver suggests tissue-specific regulation of cholesterol synthesis Primary demyelination induced by exposure to tellurium alters Schwanncell gene expression: a model for intracellular targeting of NGFreceptor Alterations in gene expression associated with primary demyelination and remyelination in the peripheral nervous system Experimental lead encephalopathy in the suckling rat: concentration of lead in cellular fractions enriched in brain capillaries Effect of inorganic lead exposure on myelination in the rat Telluriuminduced neuropathy: a model for reversible reductions in myelin protein gene expression Posttranslational modification of myelin proteins The localization of laminin and fibronectin on the Schwann cell basal lamina keywords: axons; brain; cells; cholesterol; cns; cns myelin; development; et al; expression; gene; glycoprotein; levels; mbp; membrane; mice; mouse; myelin; myelin protein; myelination; nerve; oligodendrocyte; plp; pns; pns myelin; protein; rat; rats; schwann; schwann cells; synthesis; system cache: cord-021500-sy6lnt7b.txt plain text: cord-021500-sy6lnt7b.txt item: #120 of 541 id: cord-021626-ck2kybtp author: Walker-Smith, John title: Dietary protein intolerance date: 2013-10-21 words: 13884 flesch: 46 summary: Five children with gastrointestinal symptoms due to milk protein intolerance had evidence of complement activation after milk challenge with 5 ml of milk. The symptoms that occur after challenge vary considerably and range from an alarming anaphylactic reaction that comes on rapidly after the child has ingested cows' milk, to the development of diarrhoea, with stools obviously blood-stained 24 or more hours after exposure to milk protein (Table 5 .6). keywords: allergy; challenge; children; cows; diet; disease; enteropathy; food; gluten; intolerance; milk; mucosa; protein; reaction; soy; symptoms; years cache: cord-021626-ck2kybtp.txt plain text: cord-021626-ck2kybtp.txt item: #121 of 541 id: cord-021772-5v4gor2v author: Levine, Gwendolyn J. title: Cerebrospinal Fluid and Central Nervous System Cytology date: 2019-05-31 words: 12659 flesch: 41 summary: 10, 20 Approximately 80% to 95% of CSF protein is albumin, and 5% to 12% of CSF total protein comprises gammaglobulins. 20 Increased bilirubin leakage into the SAS or high concentrations of CSF protein (>100-150 mg/dL) may cause xanthrochromia. keywords: analysis; canine; cases; cats; cells; cns; concentration; csf; diagnosis; disease; dogs; fluid; neutrophilic; pleocytosis; protein; samples; spinal; study cache: cord-021772-5v4gor2v.txt plain text: cord-021772-5v4gor2v.txt item: #122 of 541 id: cord-022200-hqc8r31t author: HYATT, ALEX D. title: Protein A–Gold: Nonspecific Binding and Cross-Contamination date: 2012-12-02 words: 3593 flesch: 49 summary: Strategies in colloidal gold labeling of cytoskeletal elements are discussed at length by Birrell and Griffith (1989) . Thus, by controlling the reduction of tetrachloroauric acid, gold probes of varying diameters can be produced. keywords: antibodies; binding; colloidal; gold; labeling; protein cache: cord-022200-hqc8r31t.txt plain text: cord-022200-hqc8r31t.txt item: #123 of 541 id: cord-022235-6ircruag author: Pugsley, Anthony P. title: Later stages in the eukaryotic secretory pathway date: 2012-12-02 words: 15247 flesch: 50 summary: As we shall see, the physical separation of Golgi enzymes is also indicated by the succession of posttranslational modifications to which secretory proteins are subjected, by in situ immunocytochemistry, and by the separation of Golgi-derived vesicles containing different en zymes. How then do secretory proteins move between these compart ments, and is the secretory pathway a continuous gradient of secretory organelles or are they functionally and structurally independent? keywords: cells; cisternae; clathrin; enzymes; golgi; granules; lysosomal; mannose; membrane; membrane proteins; pathway; proteins; receptors; residues; secretory; secretory pathway; secretory proteins; section; signal; sorting; studies; surface; tgn; vesicles cache: cord-022235-6ircruag.txt plain text: cord-022235-6ircruag.txt item: #124 of 541 id: cord-022262-ck2lhojz author: Gromeier, Matthias title: Genetics, Pathogenesis and Evolution of Picornaviruses date: 2007-09-02 words: 28053 flesch: 39 summary: With this experiment, reverse genetics of RNA viruses was born as the RNA genome was now amenable to manipulations developed for DNA. As is discussed in Chapter 7, this phenomenon has profound biological consequences for RNA viruses. keywords: capsid; cell; cleavage; conserved; disease; et al; evolution; expression; figure; gene; genome; host; human; ires; new; picornaviruses; poliovirus; poliovirus rna; polyprotein; proteins; pr~; receptor; recombination; region; replication; rna; rna viruses; sequence; strand; structure; synthesis; translation; type; viruses; vpg; wimmer et cache: cord-022262-ck2lhojz.txt plain text: cord-022262-ck2lhojz.txt item: #125 of 541 id: cord-022354-aqtceqqo author: HUNTER, ERIC title: Membrane Insertion and Transport of Viral Glycoproteins: A Mutational Analysis date: 2012-12-02 words: 17775 flesch: 32 summary: Perlman and Halvorson (1983) and von Heijne (1983) have examined sequences of a number of membrane proteins and have described amino acid sequence patterns that allow prediction of signal peptidase cleavage sites with greater than 90% accuracy. Many cell surface and membrane proteins of animal viruses are bound to the lipid bilayer by a membrane-spanning hydrophobic peptide close to the carboxy terminus of the polypeptide (reviewed by Warren, 1981; Armstrong et aL, 1981) . keywords: acid; amino; amino acid; anchor; cell; complex; domain; env; et al; gene; glycoproteins; golgi; hydrophobic; influenza; intracellular; leu; leu leu; membrane; mutant; peptide; protein; region; sequence; signal; surface; transport; virus cache: cord-022354-aqtceqqo.txt plain text: cord-022354-aqtceqqo.txt item: #126 of 541 id: cord-022499-7d58f1k3 author: Mall, Sanjay title: Transmembrane α helices date: 2004-01-07 words: 12227 flesch: 45 summary: A spin-label study of lipid-protein interactions A mutant cytochrome b5 with a lengthened membrane anchor escapes from the endoplasmic reticulum and reaches the plasma membrane Hydrophobic mismatch and long-range protein/lipid interactions in bacteriorhodopsin/phosphatidylcholine vesicles Fluorescence quenching and electron spin resonance study of percolation in a two-phase lipid bilayer containing bacteriorhodopsin Transmembrane domain-dependent sorting of proteins to the ER and plasma membrane in yeast Membrane protein structure and stability: Implications of the first crystallographic analyses Control of the transmembrane orientation and interhelical interactions within membranes by hydrophobic helix length Hydrophobicity of the peptide C=O. • -H--N hydrogen bonded group Subcellular organization of glycosylation in mammalian cells Detergent structure in crystals of a bacterial photosynthetic reaction centre Structure of the detergent phase and proteindetergent interactions in crystals of the wild-type (Strain Y) Rhodobacter sphaeroides photochemical reaction center Molecular dynamics of Pfl coat protein in a phospholipid bilayer Conformational changes of phospholipid headgroups induced by a cationic integral membrane peptide as seen by deuterium magnetic resonance Influence of the intrinsic membrane protein bacteriorhodopsin on gel-phase domain topology in two-component phase-separated bilayers Transmembrane helix structure, dynamics, and interactions: Multi-nanosecond molecular dynamics simulations Annular and non-annular binding sites on the (Ca 2+ + Mg2+)-ATPase Interactions of cholesterol hemisuccinate with phospholipids and (Ca2+-Mg2+)-ATPase Functional rafts in cell membranes Mutational analysis of the signal-anchor domain of influenza virus neuraminidase Dependence of lipid membrane phase u'ansition temperature on the mismatch of protein and lipid hydrophobic thickness Lipid enrichment and selectivity of integral membrane proteins in two-component lipid bilayers Characterization of the single Ca 2+ binding site on the Ca2+-ATPase reconstituted with short and long chain phosphatidylcholines Molecular organization and dynamics of 1-palmitoyl-2-oleoylphosphatidylcholine bilayers containing a transmembrane alpha-helical peptide A Golgi retention signal in a membrane-spanning domain of coronavirus E1 protein Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6/~ resolution Molecular interactions between lecithin and sphingomyelin Principles of membrane protein assembly and structure Architecture of helix bundle membrane proteins: An analysis of cytochrome c oxidase from bovine mitochondria Hydrophobic mismatch and the incorporation of peptides into lipid bilayers: A possible mechanism for retention in the Golgi Experimentally determined bydrophobicity scale for proteins at membrane interfaces Molecular dynamics simulations of individual alpha-helices of bacteriorhodopsin in dimyristoylphosphatidylcholine. Whereas ESR spectra of spin-labeled lipids in the presence of membrane proteins typically show two-component spectra, as described above, ESR spectra for lipid bilayers containing the peptide L24 and for a tryptophan-containing peptide of the type AW2(LA)nW2A are single-component (de Planque et aL, 1998; Subczynski et al., 1998) . keywords: bilayer; binding; chains; et al; helices; helix; hydrophobic; hydrophobic thickness; length; lipid; lipid bilayer; membrane proteins; peptide; phase; protein; residues; thickness; transmembrane cache: cord-022499-7d58f1k3.txt plain text: cord-022499-7d58f1k3.txt item: #127 of 541 id: cord-022779-himray6q author: None title: Abstracts of oral presentations date: 2005-06-10 words: 3624 flesch: 39 summary: This procedure -called SICLOPPS for Split Intein Circular Ligation Of Peptides and ProteinS-provides a biosynthetic pathway for peptides that are metabolically stable, and can be produced with spatial and temporal control We will present the results of the work which involves our intensive effort in: • Development of the method for monitoring and analyzing quality of peptide chip synthesis • Improvement in peptide chip synthesis • Development of the methods for quantitative analysis of (a) the specific binding of antibodies/proteins to peptides on chip and (b) kinase enzymatic activities against substrate peptides on chip. keywords: -sheet; acid; activity; chemical; ligation; method; peptides; properties; protein; results; structure cache: cord-022779-himray6q.txt plain text: cord-022779-himray6q.txt item: #128 of 541 id: cord-022888-dnsdg04n author: None title: Poster Sessions date: 2009-08-19 words: 189173 flesch: 41 summary: Our aim is to describe how B cell lymphoma cells respond to TGF-b compared to normal peripheral B cells, to create an overview of the different signaling pathways involved, and to characterize the mechanisms behind the loss of sensitivity to TGF-b. Methods: Proliferation assays were performed on 11 different B-cell lymphoma cell lines and normal peripheral B cells to screen for TGF-b-induced effects. Using a CD3 and CD28 activation model system -TLR4 presence on CD4+ cells is found in mouse T cells, human T cells and Jurkat cell lines. keywords: + cells; ability; absence; activity; addition; analysis; antibodies; antibody; antigen; apoptosis; apoptotic; assay; associated; autoimmune; b cells; b t; binding; blood; bone; c mice; cancer cells; capacity; cd4; cd8 +; cd8 cells; cd8 t; cell activation; cell activity; cell culture; cell cycle; cell death; cell development; cell differentiation; cell epitopes; cell function; cell level; cell lines; cell membrane; cell population; cell proliferation; cell receptor; cell responses; cell subsets; cell surface; cell tolerance; cell types; cells cells; changes; chronic; class; clinical; colitis; complex; conclusion; contrast; control; control cells; cross; ctl; cytokine; cytokine production; cytometry; cytotoxic t; data; day; days; dcs; deficient; delta t; dendritic; disease; dna; early; effector cells; effector t; effects; elisa; expansion; experiments; expression; expression levels; factor; family; findings; flow; following; formation; function; gamma; gd cells; gd t; gene; gene expression; group; high; hiv; hla; host; human; ifn; ifng; igg; il-10; il-2; il-4; il-6; immune; immunity; increase; independent; induction; infected; infection; inflammation; inflammatory; inhibition; inkt; interaction; intracellular; levels; lps; macrophages; major; marrow cells; mast cells; mechanisms; membrane; memory t; methods; mhc; mice; model; molecules; monocytes; mouse; mouse t; mrna; murine; negative; neutrophils; new; nkt cells; non; normal; novel; number; objectives; pathway; patients; pcr; peptide; peripheral; plasma cells; play; positive; potential; presence; presentation; primary; production; promoter; protein; protein expression; receptors; regulation; regulatory; release; results; role; secretion; serum; signaling; skin; sle; specific; spleen; stem cells; stimulation; studies; study; surface expression; system; t cells; t em; t h; t helper; t lymphocytes; target cells; tcr; test; th1 cells; time; tissue; tlr; tnf; tolerance; transcription; treatment; tumor cells; type; university; vaccination; vaccine; vg9vd2 t; virus; vitro; vivo; work cache: cord-022888-dnsdg04n.txt plain text: cord-022888-dnsdg04n.txt item: #129 of 541 id: cord-022940-atbjwpo5 author: None title: Poster Sessions date: 2016-09-07 words: 241687 flesch: 44 summary: Among used cancer cell lines, ERICD was highly expressed and ARID3A had lower expression in U-2OS (osteosarcoma), A-172 (glioblastoma) and A549 (lung cancer). Clear cell renal cell cancer (ccRCC) with metastases has pour prognosis: 5-year survival is about 9%. keywords: a549 cells; acid; activation; activities; activity; activity levels; acute; addition; administration; affinity; agents; aim; albumin; allele; alterations; alternative; amino; analysis; analysis results; animals; ankara; anti; antibodies; antibody; anticancer; antioxidant; apoptosis; applications; approach; assay; association; bacteria; beta; binding; biology; blood; body; bone; brain; breast cancer; cancer cells; cancer group; cancer patients; cancer stem; cancer treatment; cancers; cause; cell cycle; cell death; cell growth; cell lines; cell proliferation; cell survival; cell viability; changes; characterization; chemical; cholesterol; chronic; clinical; coli; colorectal; combination; comparison; complex; complexes; compounds; concentrations; conclusion; conditions; content; control cells; control group; control study; controls; correlation; culture; curcumin; current; cytotoxic; damage; data; day; days; decrease; department; detection; determination; development; diabetes; differences; differentiation; discussion; disease; dna; domain; dose; drug; effects; elevated; elisa; energy; enzyme; enzyme activity; ethanol; experimental; expression analysis; expression levels; expressions; extract; factor; faculty; family; fat; findings; flow; fluorescence; fold; food; formation; free; function; gene expression; genes; genetic; genome; genotype; glucose; glutathione; group; growth; gsh; health; hours; human; immune; increase; inflammation; inflammatory; inhibition; inhibitors; injury; institute; insulin; interaction; intracellular; introduction; invasion; investigation; ischemia; kinase; laboratory; lead; levels; light; like; lipid; liver; low; lung; male; manner; markers; mass; materials; matrix; mcf-7; mda; mda levels; mean; mechanisms; medical; medicine; medium; membrane; metabolism; methods; methylation; mice; microscopy; migration; mirnas; mitochondrial; model; modified; molecular; molecules; mrna; muscle; mutant; mutations; n =; nanoparticles; negative; non; normal; novel; number; obese; obesity; oil; order; oxidative; oxygen; p =; p-02.08.5; parameters; pathway; patients; pcr; peptide; phase; plant; plasma; play; point; polymorphisms; population; potential; presence; present; process; processes; production; products; profile; progression; promoter; properties; prostate; prostate cancer; protective; protein; protein expression; protein levels; purpose; radical; range; rate; rats; reaction; receptor; recombinant; region; regulation; related; relationship; research; resistance; response; results; risk; role; samples; science; scientific; screening; sequence; serum; serum levels; signaling; site; size; sod; species; specific; stability; stage; status; stem cells; strain; stress; structure; studies; study; study group; subjects; surface; survival; synthesis; system; target; technique; temperature; test; tested; therapeutic; therapy; time; tissue; tnf; total; transcription; treatment; treatment group; tumor; tumor cells; turkey; type; university; use; values; vitamin; vitro; water; weight; western; wild; women; work; years cache: cord-022940-atbjwpo5.txt plain text: cord-022940-atbjwpo5.txt item: #130 of 541 id: cord-022955-vy0qgtll author: None title: Proteases date: 2005-06-20 words: 36483 flesch: 40 summary: Specific molecular associations or shared scaffolds between the involved proteases and/or protein inhibitors and defined three-dimensional structures have also been reported. It was used affinity chromatography, electrophoresis, western-blotting, ELISA, determination of proteins activity. keywords: acid; activation; activities; activity; amino; analysis; binding; brain; calcium; cancer; catalytic; cells; cleavage; complex; control; degradation; domain; effect; enzyme; expression; factor; family; form; function; gcpii; gene; growth; human; hydrolysis; inhibition; inhibitors; levels; like; mail; mechanism; membrane; model; molecular; pathway; peptide; presence; present; protease; protease activity; protease inhibitors; protein; proteolysis; regulation; results; role; sequence; serine; serine protease; site; specificity; structure; studies; study; substrate; system; target; terminal; treatment; trypsin; type; ubiquitin; vitro; zymogen cache: cord-022955-vy0qgtll.txt plain text: cord-022955-vy0qgtll.txt item: #131 of 541 id: cord-023026-2r84ndzv author: None title: Posters date: 2013-06-14 words: 138804 flesch: 38 summary: Levels of expression of NG2 mRNA and protein in mouse glial cells are regulated by the neurotransmitter glutamate and overexpression of cleaved fragments modulates protein expression in murine glial cells. Interestingly, when we analyzed the in vitro expression pattern of rCD300f in brain cells by Q-PCR and immunohistochemistry, in addition to the expected expression in microglial cells, we detected expression of CD300f in oligodendrocytes and neurons. keywords: activation; activity; acute; addition; adult; analysis; animals; anti; astrocytes; astroglial; axons; blood; brain; brain cells; brain injury; cells; cerebral; changes; chronic; cns; conditions; contrast; control; cord; cortex; cortical; cultures; cytokines; damage; data; days; death; decrease; derived; development; differentiation; disease; eae; effect; evidence; experiments; expression; expression levels; extracellular; factors; findings; formation; function; gene; gene expression; gfap; glial; glucose; glutamate; hippocampal; human; imaging; immune; increase; inflammation; inflammatory; inhibition; injection; injury; ischemic; ko mice; lactate; lesions; levels; loss; lps; macrophages; markers; mechanisms; membrane; metabolic; methods; mice; microglia; microglia activation; microglia cells; migration; model; molecules; morphology; mouse; mrna; myelin; nerve; neural; neurons; new; ng2 cells; non; number; oligodendrocytes; opcs; order; pathway; patients; pcr; phenotype; play; post; potential; precursor cells; presence; present; primary; processes; production; progenitor cells; progression; proliferation; properties; protein; protein expression; rats; receptors; reduced; regulation; release; remyelination; response; results; role; schwann cells; signaling; slices; spinal; stem cells; stress; studies; study; surface; survival; synaptic; system; test; therapeutic; time; tissue; transgenic; treatment; type; uptake; vitro; vivo; weeks cache: cord-023026-2r84ndzv.txt plain text: cord-023026-2r84ndzv.txt item: #132 of 541 id: cord-023143-fcno330z author: None title: Molecular aspects of viral immunity date: 2004-02-19 words: 43520 flesch: 44 summary: The immunohistological analysis suggests that CD8+ T cell dependent disappearence of marginal zone macrophages of follicular dendritic cells and of virus infected cells in general correlates with immunosuppression. Our studies indicate that MHC class I resmcted CD8+ cytotoxic T lymphocytes (CTLs) are activated in response to viral antigens leading to destruction of virus infected cells and loss of transgene expression. keywords: activity; amino; analysis; animals; antibodies; antibody; antigen; b cells; binding; cd4; cd8; cell responses; challenge; class; clones; cns; ctl; ctl response; cytokines; cytotoxic t; days; different; disease; dna; epitopes; expression; gene; hiv; hla; host; human; ifn; immune; immunity; infected; infection; influenza; lcmv; levels; lymphocytes; memory; mhc; mice; model; molecules; mouse; murine; peptides; primary; production; protein; recognition; recombinant; replication; response; results; role; sequence; specific; spleen; strains; studies; t cells; type; vaccine; vaccinia; viral; virus; virus infection; viruses; vivo cache: cord-023143-fcno330z.txt plain text: cord-023143-fcno330z.txt item: #133 of 541 id: cord-023208-w99gc5nx author: None title: Poster Presentation Abstracts date: 2006-09-01 words: 71178 flesch: 41 summary: Peptide structures can be approached by spectroscopy and NMR techniques but data from these approaches too frequently diverge. To increase the stability and the therapeutic efficacy of peptide sequences from myelin oligodendrocyte protein (MOG) that act as multiple sclerosis (MS) antigens, we grafted them onto a framework of a particularly stable class of peptides, the cyclotides. keywords: acid; activation; activity; affinity; aggregation; aim; alpha; amino; amino acid; analogues; analysis; approach; arg; assay; beta; binding; blood; bond; cancer; cell; chain; chemical; chemistry; complex; complexes; compounds; concentration; conformational; conjugates; cyclic; data; derivatives; design; development; disulfide; dna; domain; effect; enzyme; epitope; fmoc; fragment; gly; group; growth; hplc; human; inhibitors; integrin; interaction; ligands; mechanism; membrane; method; mice; model; molecular; molecules; native; new; nmr; non; novel; opioid; order; patients; peptide; peptide analogues; peptide chain; peptide synthesis; phase; phase peptide; phe; position; potential; prepared; presence; products; proline; properties; protein; reaction; receptor; residues; results; role; sequence; site; solution; specific; spectroscopy; stability; strategy; structure; studies; study; surface; synthetic; system; target; terminal; therapeutic; treatment; tumor; turn; type; tyr; use; vivo; water; work cache: cord-023208-w99gc5nx.txt plain text: cord-023208-w99gc5nx.txt item: #134 of 541 id: cord-023209-un2ysc2v author: None title: Poster Presentations date: 2008-10-07 words: 112272 flesch: 42 summary: A specifi c bioassay was developed for screening peptides activity in high salinity conditions in order to evaluate the inhibition of biofi lm growth, based on growing biofi lmforming bacteria in a 96-wells microtiter plate. The insight into the molecular mechanism of peptides activity is obtained in vitro using SAXS method and artifi cial systems mimicking a bacterial cytoplasmic membrane. keywords: acid peptide; acid residues; acids; activation; activities; activity; affi; agents; aggregation; aim; ala; amide; amino; amino acid; amyloid; analogs; analogues; analysis; antimicrobial; application; approach; assay; backbone; binding; biological; blood; bond; brain; c peptide; cancer; cation; cell; chemical; chemistry; cient; city; coil; complex; compounds; concentration; conditions; confi; conformational; conjugates; coupling; cyclic; data; delivery; derivatives; design; development; diseases; dna; domain; drug; ed peptides; effect; effi; experiments; family; fmoc; formation; fragments; free; function; gly; group; helix; hplc; human; identifi; infl; inhibition; inhibitors; interaction; interest; leu; ligation; lipid; mass; mechanism; membrane; method; microwave; model; model peptides; modifi; modifi ed; molecules; native; natural; new; nity; nmr; non; novel; number; order; peptide; peptide analogues; peptide bond; peptide chain; peptide chemistry; peptide fragments; peptide library; peptide ligands; peptide sequence; peptide structure; peptide synthesis; phase peptide; phase synthesis; phe; position; positive; potential; presence; present; process; processes; properties; protein; purifi; range; reaction; receptor; recognition; region; report; residues; results; role; rst; selective; sequence; signifi; site; solution; specifi c; spectroscopy; stability; stable; strategy; structure; studies; study; surface; synthetic; system; target; terminal; terminus; therapy; time; treatment; trp; tumor; type; university; uorescence; uptake; use; vitro; vivo; water; work cache: cord-023209-un2ysc2v.txt plain text: cord-023209-un2ysc2v.txt item: #135 of 541 id: cord-023225-5quigar4 author: None title: Posters date: 2012-08-21 words: 70555 flesch: 41 summary: Aim of this study is the introduction, in the type 1' β turn peptide structure, of the sugar moiety specific for anti-gangliosides antibody recognition by synthesizing specific building blocks. Peptide synthesis was used to verify the accuracy of the determined sequence and to prepare sufficient peptide amount for biological activity studies. keywords: acid; activity; addition; affinity; agents; aggregation; aib; aim; amino; amino acid; amyloid; analogs; analogues; analysis; approach; bacteria; binding; biological; blood; bond; cancer; cell; chain; chemical; chemistry; class; complex; compounds; conditions; conformation; cyclic; cys; data; derivatives; design; development; disease; disulfide; dna; drug; effect; fmoc; formation; function; gly; group; helical; helix; human; hydrophobic; increase; inhibitor; interactions; leu; linear; mechanism; membrane; method; model; moiety; molecules; new; nmr; non; novel; order; peptide; peptide analogues; peptide sequence; peptide synthesis; phase; phase peptide; phe; position; potential; presence; present; process; properties; protein; reaction; receptor; residues; resin; results; role; selective; selectivity; sequence; series; site; solution; specific; specificity; stability; strategy; structure; studies; study; synthetic; system; target; terminal; terminus; treatment; type; university; use; vivo; water; work cache: cord-023225-5quigar4.txt plain text: cord-023225-5quigar4.txt item: #136 of 541 id: cord-023647-dlqs8ay9 author: None title: Sequences and topology date: 2003-03-21 words: 4522 flesch: 38 summary: A 32-kDa Llpo~ortin from Human Mononuclear Cells Appears to be Identical with the Placental Inhibitor of Blood Coagulation Distinct Fercedoxins from Rhodobacter-Capsulstus -Complete Amino Acid Sequences and Molecular Evolution N~ptide Sequence Analysis and Molecular Cloning Reveal Two Calcium Pump Isoforms in the Human Erythrocyte Membgane Cloning and Characterization of a Novel Member of the Cytochrome-P450 Subfamily IVA in Rat Prostate A Directiy Repeated Sequence in the ~-Globin Promoter Resulates Transcription in Murine Efythroleukemla Cells Isolation and Chamcterizatinn of the Alkane-Inducibie NADPH-Cytochrome-P-450 Olf, idoreductsse Gene from Candida-Tropicalls -Identification of Invarlant Residues Wlthin Slmilmr Amino Acid Sequences of Direr'sent Flavoproteins Protein Klnase-C Inhibitor Proteins -Purification from Sheep Brain and Sequence Similarity to Lipocortins and 14-3-3 MCI~ AVEmL~ B& Sequence Homology Between Purple Acid Phosphatases and Phusphoprotein Pho*phatsses --are Phesphoprotcin Phosphatatms Metalloproteins Collt~|nln~ Oil~-bridged Dinuclcar Metal Centers Negative Regulation of the Human ~-Globin Ca~ne by Transcriptional Interference: Role of an Mu Repetitive ~lement Amino Acid Sequence of Chicken Catisequestrin Deduced from C DNA -Comp~rison of Caisequestrin and Aspartactin Caisequestrin, an Intesccilular Calciumbinding Protein of Skeletal Muscle Sarcoplssmic Reticulm, Is HomoloKous to ~, a Putstive latminin-binding Protein of the Exteac¢llular Matr~ BOvSm~ ]Prote~ C Inhihl.gog with Structugll and Fun~ HotDoIO~OU~ ]~-.gtl~ to Hum~zn The 188 ltilm0omal RNA ~-quence of the S~t Anemone Anemom~s ssdcmta and Its Evolutionary INtuition Amomqg Other Eukaryotes Inferred b'om S~l,.m.~ Comlmrttmas of a Heat Shock G~ae in Two Nematorl~ The l~'/O Multtgene Family of Ok~hag of CDNA ~ for the ~ Omin of Human Complement Component ca~bi~una Protein, seqaenoe Homolo~ with thc a C~t~:~a~h Proc Natl Acad S¢t USA1990 Highly Conserved Core Domain and Unique N Terminus with Presumptive Regulatory Moti~ in a Hmman TATA Factor (l'lql~) keywords: acid; amino; amino acid; analysis; cell; conserved; dna; domain; evolution; factor; family; gene; homology; human; member; new; novel; protein; rna; sequence; similarity; structure; virus; yeast cache: cord-023647-dlqs8ay9.txt plain text: cord-023647-dlqs8ay9.txt item: #137 of 541 id: cord-023726-2fduzqyb author: STRAUSS, JAMES H. title: The Structure of Viruses date: 2012-07-27 words: 10619 flesch: 54 summary: The two families of enveloped DNA viruses that we consider here, the poxviruses and the herpesviruses, contain large genomes and complicated virus structures. The structure of most enveloped viruses is not as rigorously constrained as that of icosahedral virus particles. keywords: assembly; budding; cell; enveloped; fig; form; glycoproteins; membrane; nucleocapsid; protein; rna; structure; symmetry; virion; viruses cache: cord-023726-2fduzqyb.txt plain text: cord-023726-2fduzqyb.txt item: #138 of 541 id: cord-023740-g84fa45m author: Oldstone, Michael B.A. title: Mimicry by Virus of Host Molecules: Implications for Autoimmune Disease date: 2014-06-27 words: 2501 flesch: 36 summary: In this instance, antibodies induced against proteins of the infecting virus, but cross-reactive with host proteins such as cytoskeletal or other self-proteins released into fluids during normal cell turnover or enhanced turnover and lysis occurring during virus infection, form complexes with antigen in the circulation. mones, lymphocyte subsets, or cells of the nervous system, etc., can develop as a consequence of virus infection, with all the inherent potential for participating in disease. keywords: cross; disease; host; mimicry; proteins; virus cache: cord-023740-g84fa45m.txt plain text: cord-023740-g84fa45m.txt item: #139 of 541 id: cord-023770-ymxapsv6 author: None title: Closteroviridae date: 2011-11-23 words: 3664 flesch: 48 summary: The natural and experimental host ranges of individual virus species are usually restricted, except for a few members of the genus Crinivirus. No serological relationships reported among different virus species of the genus. keywords: family; genome; genus; kda; members; protein; size; species; virus cache: cord-023770-ymxapsv6.txt plain text: cord-023770-ymxapsv6.txt item: #140 of 541 id: cord-023865-6rafp3x3 author: Surjit, Milan title: The Nucleocapsid Protein of the SARS Coronavirus: Structure, Function and Therapeutic Potential date: 2009-07-22 words: 9217 flesch: 36 summary: Another study done by Wang et al. (2005) has attempted to use plasmid DNA expressing S, M, and N proteins as an efficient vaccine candidate. A bound to the amino-terminal domain of HIV-1 capsid Effects of a SARS-associated coronavirus vaccine in monkeys The nucleocapsid protein of SARS-CoV induces transcription of hfgl2 prothrombinase gene dependent on C/EBP alpha Activation of AP-1 signal transduction pathway by SARS coronavirus nucleocapsid protein Analysis of multimerization of the SARS coronavirus nucleocapsid protein Characterization of monoclonal antibody against SARS coronavirus nucleocapsid antigen and development of an antigen capture ELISA Assembly of severe acute respiratory syndrome coronavirus RNA packaging signal into virus-like particles is nucleocapsid dependent Chronological evolution of IgM, IgA, IgG and neutralisation antibodies after infection with SARS-associated coronavirus Structure of the N-terminal RNA-binding domain of the SARS CoV nucleocapsid protein Generation and characterization of DNA vaccines targeting the nucleocapsid protein of severe acute respiratory syndrome coronavirus Severe acute respiratory syndrome coronavirus open reading frame (ORF) 3b, ORF 6, and nucleocapsid proteins function as interferon antagonists Mass spectrometric characterization of proteins from the SARS Virus: a preliminary report Characterization of F-actin bundling activity of Tetrahymena elongation factor 1 alpha investigated with rabbit skeletal muscle actin Extremely low exposure of a community to severe acute respiratory syndrome coronavirus: false seropositivity due to use of bacterially derived antigens Sumoylation of the nucleocapsid protein of severe acute respiratory syndrome coronavirus Detection of the nucleocapsid protein of severe acute respiratory syndrome coronavirus in serum: comparison with results of other viral markers SARS patients-derived human recombinant antibodies to S and M proteins efficiently neutralize SARS-coronavirus infectivity Activation of NF-kappaB by the full-length nucleocapsid protein of the SARS coronavirus The C-terminal portion of the nucleocapsid protein demonstrates SARS-CoV antigenicity High-yield expression of recombinant SARS coronavirus nucleocapsid protein in methylotrophic yeast Pichia pastoris Immunofluorescence assay for detection of the nucleocapsid antigen of the severe acute respiratory syndrome (SARS)-associated coronavirus in cells derived from throat wash samples of patients with SARS Immunological characterizations of the nucleocapsid protein based SARS vaccine candidates Nucleocapsid protein of SARS coronavirus tightly binds to human cyclophilin A In vitro biochemical and thermodynamic characterization of nucleocapsid protein of SARS The nucleocapsid protein of SARS coronavirus has a high binding affinity to the human cellular heterogeneous nuclear ribonucleoprotein A1 Carboxyl terminus of severe acute respiratory syndrome coronavirus nucleocapsid protein: self-association analysis and nucleic acid binding characterization Lung pathology of fatal severe acute respiratory syndrome Nucleophosmin/B23 is a target of CDK2/cyclin E in centrosome duplication Protective humoral responses to severe acute respiratory syndrome-associated coronavirus: implications for the design of an effective protein-based vaccine Expression of SARS-coronavirus nucleocapsid protein in Escherichia coli and Lactococcus lactis for serodiagnosis and mucosal vaccination Use of the COOH portion of the nucleocapsid protein in an antigen-capturing enzymelinked immunosorbent assay for specific and sensitive detection of severe acute respiratory syndrome coronavirus Smad3 is key to TGF-beta-mediated epithelial-to-mesenchymal transition, fibrosis, tumor suppression and metastasis Characterization of a novel coronavirus associated with severe acute respiratory syndrome Intracellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein: absence of nucleolar accumulation during infection and after expression as a recombinant protein in vero cells Recombinant nucleocapsid protein-based IgG enzyme-linked immunosorbent assay for the serological diagnosis of SARS Characterization and application of monoclonal antibodies against N protein of SARScoronavirus Antigenic characterization of severe acute respiratory syndrome-coronavirus nucleocapsid protein expressed in insect cells: The effect of phosphorlation on immunoreactivity and specificity Inhibition of beta interferon induction by severe acute respiratory syndrome coronavirus suggests a two-step model for activation of interferon regulatory factor 3 Antigenic cross-reactivity between the nucleocapsid protein of severe acute respiratory syndrome (SARS) coronavirus and polyclonal antisera of antigenic group I animal coronaviruses: implication for SARS diagnosis The nucleocapsid protein of the SARS coronavirus is capable of self-association through a C-terminal 209 amino acid interaction domain The SARS coronavirus nucleocapsid protein induces actin reorganization and apoptosis in COS-1 cells in the absence of growth factors The severe acute respiratory syndrome coronavirus nucleocapsid protein is phosphorylated and localizes in the cytoplasm by 14-3-3-mediated translocation The nucleocapsid protein of severe acute respiratory syndrome-coronavirus inhibits the activity of cyclin-cyclin-dependent kinase complex and blocks S phase progression in mammalian cells Nuclear/nucleolar localization properties of C-terminal nucleocapsid protein of SARS coronavirus Specific phosphorylation of nucleophosmin on Thr(199) by cyclin-dependent kinase 2-cyclin E and its role in centrosome duplication Direct sequencing of SARScoronavirus S and keywords: activity; binding; cells; coronavirus; cov; et al; infection; interaction; nucleocapsid; protein; rna; sars; specific; syndrome cache: cord-023865-6rafp3x3.txt plain text: cord-023865-6rafp3x3.txt item: #141 of 541 id: cord-024193-khdvj6t5 author: Zhang, Hong title: Peptide Arrays date: 2012-01-17 words: 11364 flesch: 35 summary: Peptide arrays for screening cancer specific peptides Deciphering the antibodyome-peptide arrays for serum antibody biomarker diagnostics Functional peptide microarrays for specific and sensitive antibody diagnostics Proteomic techniques and activity-based probes for the system-wide study of proteolysis A novel glass slide-based peptide array support with high functionality resisting non-specific protein adsorption Light-directed maskless synthesis of peptide arrays using photolabile amino acid monomers Since then, the substrate specificities for a number of protein kinases have been elucidated and refined sequentially using peptide arrays (Schutkowski et al. 2005) . keywords: activity; amino; antibodies; arrays; cancer; cell; density; drug; et al; kinase; microarrays; peptide; peptide arrays; phosphorylation; profiling; protein; sequences; spot; studies; substrate; synthesis cache: cord-024193-khdvj6t5.txt plain text: cord-024193-khdvj6t5.txt item: #142 of 541 id: cord-024989-0o6agnrc author: Li, Qihao title: Prediction and analysis of key protein structures of 2019-nCoV date: 2020-05-12 words: 3294 flesch: 52 summary: Materials & methods: We obtained the structure and sequence of proteins from related databases and studied them through multiple sequence alignment, homology modeling, sequence analysis, virtual screening, reverse mutation, protein structure overlap and surface property analysis. We entered the amino acid sequence and selected the protein structure of the amino acid sequence with the highest homology to the input sequence as a template, which has been experimentally determined for protein structure. keywords: ace2; amino; bat; ncov; protein; sars; sequence; structure cache: cord-024989-0o6agnrc.txt plain text: cord-024989-0o6agnrc.txt item: #143 of 541 id: cord-026012-r0w0jbpg author: TENNANT, BUD C. title: Gastrointestinal Function date: 2014-06-27 words: 19886 flesch: 48 summary: .Malabsorption syndromes similar to those recog nized in dogs are being recognized with increased frequency in farm animals (Blood et al., 1979) . Familial factors also influence hypogammaglobulinemia (Tennant et al., 1969a) . keywords: absorption; acid; activity; amino; amounts; bile; calves; cells; concentration; digestion; dogs; enzyme; et al; fat; fatty; form; gastric; glucose; intestine; malabsorption; membrane; mucosa; plasma; present; protein; rate; result; rumen; secretion; sodium; transport; vitamin; water cache: cord-026012-r0w0jbpg.txt plain text: cord-026012-r0w0jbpg.txt item: #144 of 541 id: cord-029747-8f463wz0 author: Viedma-Poyatos, Álvaro title: Type III intermediate filaments as targets and effectors of electrophiles and oxidants date: 2020-07-17 words: 12709 flesch: 29 summary: Evidence that the alignment of coiled-coil molecules in vimentin is different from that in keratin intermediate filaments Chemical cross-linking between lysine groups in vimentin oligomers is dependent on local peptide conformations Site-directed spin labeling and electron paramagnetic resonance determination of vimentin head domain structure Structural dynamics of the vimentin coiled-coil contact regions involved in filament assembly as revealed by hydrogen-deuterium exchange Characterization of disulfide crosslink formation of human vimentin at the dimer, tetramer, and intermediate filament levels Atomic structure of the vimentin central alpha-helical domain and its implications for intermediate filament assembly Expression of Vimentin in hair follicle growth cycle of inner Mongolian Cashmere goats Specific in vivo phosphorylation sites determine the assembly dynamics of vimentin intermediate filaments Defect of mitotic vimentin phosphorylation causes microophthalmia and cataract via aneuploidy and senescence in lens epithelial cells Nestin promotes the phosphorylation-dependent disassembly of vimentin intermediate filaments during mitosis Post-translational modifications of intermediate filament proteins: mechanisms and functions Site-specific glycosylation regulates the form and function of the intermediate filament cytoskeleton Human immunodeficiency virus type 1 protease cleaves the intermediate filament proteins vimentin, desmin, and glial fibrillary acidic protein Vimentin acetylation is involved in SIRT5-mediated hepatocellular carcinoma migration Citrullinated Autoantigens, From diagnostic markers to pathogenetic mechanisms Mutation and citrullination modifies vimentin to a novel autoantigen for rheumatoid arthritis Citrullinated vimentin presented on MHC-II in tumor cells is a target for CD4+ T cell-mediated antitumor immunity Abnormal accumulation of citrullinated proteins catalyzed by peptidylarginine deiminase in hippocampal extracts from patients with Alzheimer's disease Citrullination of glial intermediate filaments is an early response in retinal injury Providing cellular signpostspost-translational modifications of intermediate filaments Detection, identification, and quantification of oxidative protein modifications Proteome oxidative modifications and impairment of specific metabolic pathways during cellular senescence and aging Quantitative proteomic characterization of redox-dependent post-translational modifications on protein cysteines Activity-based sensing for site-specific proteomic analysis of cysteine oxidation Protein oxidation and peroxidation Lipoxidation targets: from basic mechanisms to pathophysiology Oxidized protein aggregates: formation and biological effects, Free Radic Lipoxidation adducts with peptides and proteins: deleterious modifications or signalling mechanisms? Adducts with protein residues occur mainly through Schiff base formation with amino groups or , rod and tail domains is shown for the four members of the type III class of IF (upper panel) . keywords: assembly; c328; cells; cysteine; desmin; disease; disulfide; effects; filament; formation; human; ifs; iii; lipoxidation; modifications; oxidative; peripherin; phosphorylation; protein; redox; residues; stress; target; type; vimentin cache: cord-029747-8f463wz0.txt plain text: cord-029747-8f463wz0.txt item: #145 of 541 id: cord-029957-q7v5gli8 author: Prabhu, D. title: In silico Functional Annotation and Characterization of Hypothetical Proteins from Serratia marcescens FGI94 date: 2020-07-31 words: 5802 flesch: 33 summary: Phylogenomics and comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family Basic local alignment search tool Complete genome of Serratia sp. strain FGI 94, a strain associated with leaf-cutter ant fungus gardens Cloning and characterization of spoVR, a gene from Bacillus subtilis involved in spore cortex formation Non-classical protein secretion in bacteria In silico functional annotation of a hypothetical protein from Staphylococcus aureus PSLpred: prediction of subcellular localization of bacterial proteins The molecular mechanism of bacterial lipoprotein modification-how, when and why Wzi is an outer membrane lectin that underpins group 1 capsule assembly in Escherichia coli Prot: web-based support vector machine software for functional classification of a protein from its primary sequence Antibiotic resistant threats report Tetratricopeptide repeat motifs in the world of bacterial pathogens: role in virulence mechanisms The multifunctional LigB adhesin binds homeostatic proteins with potential roles in cutaneous infection by pathogenic Leptospira interrogans The RecA protein as a recombinational repair system Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance Gene expression profile of the plant pathogen Xylella fastidiosa during biofilm formation in vitro Functionally unrelated signaling proteins contain a fold similar to Mg 2+ dependent endoculeases Genetic and biochemical characterization of a gene operon for trans-aconitic acid, a novel nematicide from Bacillus thuringiensis Identification of ZapD as a cell division factor that promotes the assembly of FtsZ in Escherichia coli Unravelling potential virulence factor candidates in Xanthomonas citri subsp. Photodyn SignalP 4.0: discriminating signal peptides from transmembrane regions Iron, copper, zinc, and manganese transport and regulation in pathogenic Enterobacteria: correlations, between strains, site of infection and the relative importance of the different metals transport systems for virulence, Front ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree Tripartite ATP-independent periplasmic (TRAP) transporters and tripartite tricarboxylate transporters (TTT): from uptake to pathogenicity VICMpred: an SVM-based method for the prediction of functional proteins of gramnegative bacteria using amino acid patterns and composition Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20 Functional evolution of BRCT domains from binding DNA to protein Exploring the relationship between lipoprotein mislocalization and activation of the Rcs signal transduction system in Escherichia coli Functional annotation and classification of the hypothetical proteins of Neisseria meningitidis H44/76 Beta-barrel scaffold of fluorescent proteins: folding, stability and role in chromophore formation Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools Manganese homeostasis in group A Streptococcus is critical for resistance to oxidative stress and virulence Principles governing amino acid composition of integral membrane proteins: application to topology prediction DNAtension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway DNA binding: a novel function of Pseudomonas aeruginosa type IV pili The first report of drug resistant bacteria isolated from the brown-banded cockroach, Supella longipalpa The university conserved prokaryotic GTPases, Microbiol A novel metal transporter mediating manganese export (MntX) regulates the Mn toFe intracellular ration and Neisseria meningitidis virulence Toxin-antitoxin systems: their role in persistence, biofilm formation and pathogenicity Charting the landscape of tandem BRCT domain-mediated protein interactions Predicting subcellular localization of proteins for gram-negative bacteria by support vector machines based on n-peptide compositions PSORTb 3.0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes Secretion of bacterial lipoproteins: through the cytoplasmic membrane, the periplasm and beyond Supplementary materials are available for this article at https://doi.org/10.1134/S1062359020300019 and are accessible for authorized users. keywords: acid; amino; bacteria; cell; dna; domain; drug; et al; function; hps; marcescens; membrane; proteins; resistance; role cache: cord-029957-q7v5gli8.txt plain text: cord-029957-q7v5gli8.txt item: #146 of 541 id: cord-031907-ilhr3iu5 author: None title: ISEV2020 Abstract Book date: 2020-07-15 words: 201435 flesch: 40 summary: Normal pancreas cells (hTERT-HPNE and HPDE-H6c7) were co-cultured with cancer cell EVs for 24-48 hours. Before EV isolation cells were kept for 24 h either under normoxia or hypoxia (1% oxygen). keywords: ability; activation; activity; ad evs; addition; aim; analysis; analysis methods; anti; approach; assay; associated; bacterial evs; biological; biomarkers; blood; blood cells; blood evs; blot; bone; brain; breast; breast cancer; cancer cells; cancer evs; cancer introduction; cancer patients; cd63; cd81; cd9; cell communication; cell culture; cell evs; cell exosomes; cell function; cell lines; cell proliferation; cell surface; cell types; cells; cells introduction; changes; characterization; chromatography; composition; concentration; conclusion; conditions; content; control; control evs; cultured; current; cytometry; data; delivery; density; detection; development; diagnosis; differential; disease; distribution; dna; drug; effect; electron; endothelial; enrichment; epithelial; ev analysis; ev cargo; ev evs; ev isolation; ev markers; ev numbers; ev preparations; ev production; ev protein; ev release; ev research; ev rna; ev samples; ev subpopulations; ev surface; ev treatment; ev uptake; evs; exclusion; exosomal; exosomes; experiments; expression; expression analysis; extracellular; factors; findings; flow; fluorescent; fluorescent evs; fold; formation; fractions; free; function; funding; gene; group; growth; host cells; human; human evs; imaging; immune; increase; inflammation; inflammatory; introduction; isolated; isolation methods; key; large; levels; lipid; lung; macrophages; mass; mechanisms; media; medium; membrane; membrane vesicles; mesenchymal; metastasis; methods; mice; microscopy; migration; milk evs; mirna; model; molecular; molecules; mouse; msc evs; mscs; nanoparticle; national; neuronal; neurons; new; non; normal; novel; nta; number; particles; pathway; patients; plasma evs; plasma samples; platelet; platform; play; positive; positive evs; post; potential; presence; present; primary; process; production; profile; profiling; progression; proliferation; properties; prostate; prostate cancer; protein; protein cargo; protein expression; protein markers; proteomic; purification; purity; range; recipient cells; research; resistance; response; results; rna; rnas; role; samples; sec; secretion; sequencing; serum; sevs; signalling; single; size; small evs; specific; specific evs; spectrometry; stem cells; stromal cells; studies; study; summary; surface; system; target cells; targets; tau; techniques; tested; therapeutic; therapy; time; tissue; total; total evs; tracking; transfer; transmission; treatment; tumour cells; ultracentrifugation; university; uptake; urinary evs; urine; usa; usa introduction; use; vesicles; vesicles introduction; vitro; vivo; work cache: cord-031907-ilhr3iu5.txt plain text: cord-031907-ilhr3iu5.txt item: #147 of 541 id: cord-031937-qhlatg84 author: Verma, Anukriti title: Elucidating potential molecular signatures through host-microbe interactions for reactive arthritis and inflammatory bowel disease using combinatorial approach date: 2020-09-15 words: 6766 flesch: 19 summary: KYNU was further mapped with host proteins (direct and indirect) resulting in 1994 interactions. It is suggested that in host-microbe interactions, bacterial proteins entering host cells interact with host proteins and inject their effector components, but has not been proven in ReA and IBD. keywords: analysis; arthritis; associated; disease; expression; genes; hla; host; human; ibd; metabolic; microbe; microorganisms; network; protein; rea; target cache: cord-031937-qhlatg84.txt plain text: cord-031937-qhlatg84.txt item: #148 of 541 id: cord-031957-df4luh5v author: dos Santos-Silva, Carlos André title: Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era date: 2020-09-02 words: 16639 flesch: 34 summary: Thus, there is a need for computational framework methods to predict protein structures based on the knowledge of the sequence. In addition, in recent years, there has been impressive progress in the development of algorithms for protein folding that may aid in the prediction of protein structures from amino acid sequence information. keywords: acid; activity; amps; analysis; antifungal; approaches; binding; bonds; cysteine; database; defensins; disulfide; docking; family; figure; function; gene; identification; information; lipid; methods; modeling; models; motif; novel; pathogen; peptides; plant; potential; prediction; present; protein; residues; sequence; structure cache: cord-031957-df4luh5v.txt plain text: cord-031957-df4luh5v.txt item: #149 of 541 id: cord-033010-o5kiadfm author: Durojaye, Olanrewaju Ayodeji title: Potential therapeutic target identification in the novel 2019 coronavirus: insight from homology modeling and blind docking study date: 2020-10-02 words: 8149 flesch: 48 summary: Qualitative Model Energy Analysis (QMEAN) is a composite scoring function that describes protein structures on the basis of major geometrical aspects. A novel coronavirus and SARS Crystal structures of the main peptidase from the SARS coronavirus inhibited by a substrate-like aza-peptide epoxide Dissection study on the SARS 3C-like protease reveals the critical role of the extra domain in dimerization of the enzyme: defining the extra domain as a new target for design of highly-specific protease inhibitors 3C-like proteinase from SARS coronavirus catalyzes substrate hydrolysis by a general base mechanism Only one protomer is active in the dimer of SARS 3C-like proteinase Biosynthesis, purification, and substrate specificity of severe acute respiratory syndrome coronavirus 3C-like proteinase A trial of lopinavir-ritonavir in adults hospitalized with severe covid-19 EMBOSS: the European molecular biology open software suite SRS, an indexing and retrieval tool for flat file data libraries Issues in bioinformatics benchmarking: the case study of multiple sequence alignment HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 Toward the estimation of the absolute quality of individual protein structure models MolProbity: more and better reference data for improved all-atom structure validation Chapter 2: Protein Composition and Structure Modeling protein quaternary structure of homo-and hetero-oligomers beyond binary interactions by homology UCSF chimera-a visualization system for exploratory research and analysis Fasman GD (1974) Prediction of protein conformation Protein Identification and Analysis Tools on the ExPASy Server The rapid generation of mutation data matrices from protein sequences MEGA7: keywords: 2019; acid; amino; amino acid; binding; coronavirus; docking; model; ncov; protein; proteinase; sars; score; sequence; structure; target protein; template cache: cord-033010-o5kiadfm.txt plain text: cord-033010-o5kiadfm.txt item: #150 of 541 id: cord-033333-880jx1bt author: Salman, Saad title: In silico analysis of protein/peptide-based inhalers against SARS-CoV-2 date: 2020-10-08 words: 3448 flesch: 49 summary: [19] , we report the in silico antigenicity of SPLUNC1 protein while bearing in mind the potential side effects of mAbs [13] . (ACE-2) (PDB ID:1R4L), human palate, lung and nasal epithelium clone protein (4N4X) and human neutralizing S230 light chain antibody (6NB6) and COVID spike protein (PDB ID:6VSB) was obtained from Protein Data Bank keywords: drug; inhalers; lung; peptide; protein; sars; spike; splunc1 cache: cord-033333-880jx1bt.txt plain text: cord-033333-880jx1bt.txt item: #151 of 541 id: cord-034191-qqb2knmo author: Alayi, Tchilabalo D. title: Tandem Mass Tag-Based Serum Proteome Profiling for Biomarker Discovery in Young Duchenne Muscular Dystrophy Boys date: 2020-10-06 words: 8978 flesch: 41 summary: Finally, the last group of serum protein biomarkers that were found significantly decreased in young DMD patients relative to age-matched controls are also novel to this study, which include proteins involved in cell signaling such as leukosialin (SPN), macrophage receptor MARCO (MARCO), vitronectin (VTN), galectin-3-binding protein (LGALS3BP), and ProSAAS (PCSK1N). In the past few years, affinity-based serum proteome profiling methods such as SomaScan aptamer-based technology and antibody bead array have contributed to the discovery of a large number of serum protein biomarkers in DMD. 8, 14, 16 keywords: analysis; biomarkers; controls; data; depletion; dmd; dmd patients; figure; mass; muscle; muscular; patients; proteins; samples; serum; study; tmt; total; young cache: cord-034191-qqb2knmo.txt plain text: cord-034191-qqb2knmo.txt item: #152 of 541 id: cord-034406-i1hbx3pz author: Matthews, Abigail A. title: Developing inhaled protein therapeutics for lung diseases date: 2020-10-30 words: 8744 flesch: 37 summary: As only one medicine Respimat uses SMI, its suitability for protein drug delivery is not clear. It is probable that HYDRA nebulisers may be developed for pulmonary protein drug delivery. keywords: aerosol; aggregation; delivery; diseases; drug; excipients; formulation; inhalation; insulin; lung; nebulisers; particles; protein; stability; studies; therapeutics; use cache: cord-034406-i1hbx3pz.txt plain text: cord-034406-i1hbx3pz.txt item: #153 of 541 id: cord-034823-ogwjzfgf author: Guo, Hao-Bo title: A Suggestion of Converting Protein Intrinsic Disorder to Structural Entropy Using Shannon’s Information Theory date: 2019-06-14 words: 7023 flesch: 50 summary: A major update of the database of disordered proteins The Protein Data Bank Design and synthesis of a minimal bacterial genome International Rice Genome Sequencing Project. The underlying mechanisms of this Gaussian distribution have not been discussed in the literature; however, the distribution density can also be understood as the potential of mean force, or free energy, using the relationship: where R is the gas constant, T is the temperature, and ρ i is the density of proteins at the i-th histogram of protein capacities. keywords: capacity; disorder; distributions; entropy; figure; information; protein; proteomes cache: cord-034823-ogwjzfgf.txt plain text: cord-034823-ogwjzfgf.txt item: #154 of 541 id: cord-048344-ps3mnpzq author: Zhu, Xiaowei title: ProCAT: a data analysis approach for protein microarrays date: 2006-11-16 words: 5732 flesch: 45 summary: Existing DNA microarray analytical methods do not translate to protein microarrays due to differences between the technologies. One particular powerful technology is protein microarrays, which contain a high density of proteins and allow a systematic probing of biochemical activities [2, 3] . keywords: artifacts; background; microarrays; procat; protein; signal; slide; spots; window cache: cord-048344-ps3mnpzq.txt plain text: cord-048344-ps3mnpzq.txt item: #155 of 541 id: cord-048360-n9sih438 author: Villard, Viviane title: Rapid Identification of Malaria Vaccine Candidates Based on α-Helical Coiled Coil Protein Motif date: 2007-07-25 words: 4797 flesch: 41 summary: Found at: doi:10.1371/journal.pone.0000645.s005 (0.05 MB DOC) Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing Reverse vaccinology and genomics Plasmodium falciparum liver stage antigen-1 is well conserved and contains potent B and T cell determinants Protection against Plasmodium falciparum malaria in chimpanzees by immunization with the conserved pre-erythrocytic liver-stage antigen 3 Phase I malaria vaccine trial with a long synthetic peptide derived from the merozoite surface protein 3 antigen Plasmodium falciparum merozoite surface protein 6 displays multiple targets for naturally occurring antibodies that mediate monocyte-dependent parasite killing Template-based coiled-coil antigens elicit neutralizing antibodies to the SARS-coronavirus Phase 1 randomized double-blind safety and immunogenicity trial of Plasmodium falciparum malaria merozoite surface protein FMP1 vaccine De novo design of alpha-helical proteins: basic research to medical applications Genome sequence of the human malaria parasite Plasmodium falciparum A flexible motif search technique based on generalized profiles Transcriptomics and proteomics: tools for the identification of novel drug targets and vaccine candidates for tuberculosis A proteomic view of the Plasmodium falciparum life cycle The Transcriptome of the Intraerythrocytic Developmental Cycle of Plasmodium falciparum Crossreactive antigens between life cycle stages of plasmodium falciparum Antibodies that protect humans against Plasmodium falciparum blood stages do not on their own inhibit parasite growth and invasion in vitro, but act in cooperation with monocytes Mapping of conformational B cell epitopes within alpha-helical coiled coil proteins A de novo designed template for generating conformation-specific antibodies that recognize alpha-helices in proteins Targeting malaria virulence and remodeling proteins to the host erythrocyte A host-targeting signal in virulence proteins reveals a secretome in malarial infection Proteomic analysis identifies novel proteins of the Maurer's clefts, a secretory compartment delivering Plasmodium falciparum proteins to the surface of its host cell Multi-character population study of the vir subtelomeric multigene superfamily of Plasmodium vivax, a major human malaria parasite A Maurer's cleft-associated protein is essential for expression of the major malaria virulence antigen on the surface of infected red blood cells A novel antibody-dependent cellular cytotoxicity mechanism involved in defense against malaria requires costimulation of monocytes FcgammaRII and FcgammaRIII Predicting coiled coils from protein sequences Improved prediction of signal peptides: SignalP 3.0 TMbase-A database of membrane spanning proteins segments Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes Prediction of potential GPImodification sites in proprotein sequences pTARGET Figure S1 CD spectra of the peptides 45 (S1A) and 12 (S1B) Found at: doi:10.1371/journal.pone.0000645.s001 (12.32 MB TIF) Figure S2 ELISA inhibition assay using anti-human peptide specific antibodies. keywords: antibodies; assays; blood; coil; falciparum; human; malaria; parasite; peptides; proteins; sera; specific; table; vaccine cache: cord-048360-n9sih438.txt plain text: cord-048360-n9sih438.txt item: #156 of 541 id: cord-048471-7jszm1nd author: Salim, Omar title: Functional Analysis of the 5′ Genomic Sequence of a Bovine Norovirus date: 2008-05-14 words: 5667 flesch: 44 summary: To date, it has not been possible to explain the difference in the predicted and observed sizes for the JV N-term, and the addition of the 14 amino acid V5 epitope within JV N-term does not account for this apparent large shift in molecular weight. It cannot be ruled out, however, that the wild type JV N-term aberrantly co-migrates with the 39 kDa JV 2C protein in SDS-PAGE. keywords: cells; initiation; ires; kda; protein; rna; term; translation; virus cache: cord-048471-7jszm1nd.txt plain text: cord-048471-7jszm1nd.txt item: #157 of 541 id: cord-103255-4k13re9y author: Daniell, Henry title: Medical molecular farming: production of antibodies, biopharmaceuticals and edible vaccines in plants date: 2001-05-01 words: 4362 flesch: 38 summary: As with antibodies, transient expression systems (in which candidate vaccine sequences are incorporated into plant viral surface proteins) have also been investigated extensively and high levels of expression have been achieved. There has been no evidence of allergic reaction or of a human antimouse antibody (HAMA) response in 60 patients receiving topical oral application of a secretory IgA specific to S. mutans 8 . Proteins of microbial and viral pathogens were some of the earliest examples chosen to show the feasibility of transgenic plant expression systems 14-17 . keywords: antibodies; antibody; chloroplast; expression; plants; production; proteins; tobacco; transgenic; vaccines cache: cord-103255-4k13re9y.txt plain text: cord-103255-4k13re9y.txt item: #158 of 541 id: cord-103320-2rpr7aph author: Bhandari, Bikash K. title: Solubility-Weighted Index: fast and accurate prediction of protein solubility date: 2020-03-26 words: 4893 flesch: 38 summary: To improve protein solubility prediction, we optimised the most recently published set of normalised B-factors using the PSI:Biology dataset (Smith et al. 2003 ) Protein solubility, at least in part, depends upon extrinsic factors such as ionic strength, temperature and pH, as well as intrinsic factors-the physicochemical properties of the protein sequence and structure, including molecular weight, amino acid composition, hydrophobicity, aromaticity, isoelectric point, structural propensities and the polarity of surface residues (Wilkinson and Harrison 1991; keywords: acid; amino; et al; fig; flexibility; prediction; protein; residues; sequence; solubility; swi cache: cord-103320-2rpr7aph.txt plain text: cord-103320-2rpr7aph.txt item: #159 of 541 id: cord-103430-x6zzuu7v author: Contu, Lara title: Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay date: 2020-10-12 words: 8307 flesch: 46 summary: Among the many identified cellular interactors of SFV proteins, the enrichment of factors involved in translation and nonsense-mediated mRNA decay (NMD) was striking, reflecting the virus’ hijacking of the translation machinery and indicating viral countermeasures for escaping NMD by inhibiting NMD at later time points during the infectious cycle. b, Flowchart outlining the experimental approach to transiently express N-7 terminally FLAG-tagged (yellow rectangle) SFV proteins in mammalian cells in order to construct a SFV-host protein-protein 8 interactome. keywords: capsid; cells; figure; host; infection; interactors; nsp2; nsp3; proteins; rna; sfv; translation; viral; virus cache: cord-103430-x6zzuu7v.txt plain text: cord-103430-x6zzuu7v.txt item: #160 of 541 id: cord-103509-hynnba03 author: Wong, Ten-Tsao title: A self-assembled protein nanoparticle serving as a one-shot vaccine carrier date: 2020-09-18 words: 3235 flesch: 44 summary: As shown in figure 1A , when GFP protein with a molecular weight of 27kDa is able to pass through membranes with MWCO of 100kDa, 300kDa and 1000kDa freely, AH3-GFP fusion protein purified from bacterial lysate was prevented from passing through the membrane with an MWCO of 1000kDa. GFP protein has a thermal stable structure that constituted by 11 β-strands and 3 α-helices and some of the loops between strands have been explored as insertion sites for heterologous protein for various purposes (18, 19, 30) . keywords: ah3; complex; fig; fusion; gfp; peptide; protein; vaccine cache: cord-103509-hynnba03.txt plain text: cord-103509-hynnba03.txt item: #161 of 541 id: cord-103528-3tib5o1m author: Ahmed, Asad title: DEELIG: A Deep Learning-based approach to predict protein-ligand binding affinity date: 2020-09-28 words: 3804 flesch: 46 summary: #in56 (number of atoms in 5 or 6 membered rings) • #noncon (ring atoms cannot form conjugated aromatic bonds) • #nonHatm (heavy atoms-nonhydrogen atoms) • RuleOfThree • RuleOfFive (lipinski violations) • QPlogKhsa (binding to human serum albumin) • PercentHuman-OralAbsorption Recent improvements to binding moad: a resource for protein ligand binding affinities and structures Gapped blast and psi-blast: a new generation of protein database search programs Analysis and comparison of 2d fingerprints: insights into database screening performance using eight fingerprint methods The mm/pbsa and mm/gbsa methods to estimate ligandbinding affinities Expert opinion on drug discovery Simboost: a read-across approach for predicting drug-target binding affinities using gradient boosting machines Receptive fields, binocular interaction and functional architecture in the cat's visual cortex Batch normalization: Accelerating deep network training by reducing internal covariate shift Structure of M pro from SARS-CoV-2 and discovery of its inhibitors A series of pdb related databases for everyday needs sc-pdb: a 3d-database of ligandable binding sites-10 years on Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features On the binding affinity of macromolecular interactions: daring to ask why proteins interact Detection of multiscale pockets on protein surfaces using mathematical morphology Adam: A method for stochastic optimization Imagenet classification with deep convolutional neural networks Binding moad (mother of all databases Gradient-based learning applied to document recognition Deepatom: A framework for protein-ligand binding affinity prediction Deep learning in bioinformatics Bindingmoad, a high-quality protein-ligand database Deepdta: deep drug-target binding affinity prediction Pytorch: Tensors and dynamic neural networks in python with strong gpu acceleration. Binding affinity helps in understanding the degree of protein-ligand interactions and has wide protein applications. keywords: affinity; atoms; binding; features; learning; ligand; network; pocket; protein cache: cord-103528-3tib5o1m.txt plain text: cord-103528-3tib5o1m.txt item: #162 of 541 id: cord-103709-86hv27vh author: Zhang, Dong Yan title: Prefusion spike protein stabilization through computational mutagenesis date: 2020-06-19 words: 3245 flesch: 45 summary: Due to the critical role in viral-host interaction and the exposure of spike protein, it has been a focus of most vaccines’ developments. Thus, since the prefusion spike protein exists in a thermodynamically metastable state 1 , a stabilized mutant conformation is critical for the development of vaccines and drugs. keywords: conservation; pipeline; protein; residues; rmsf; sasa; spike; structure cache: cord-103709-86hv27vh.txt plain text: cord-103709-86hv27vh.txt item: #163 of 541 id: cord-104279-choywmwd author: None title: Membrane protein sorting in the yeast secretory pathway: evidence that the vacuole may be the default compartment date: 1992-10-01 words: 9975 flesch: 41 summary: According to the vacuolar default model for yeast membrane protein sorting, not only must ER and Golgi membrane proteins have sorting signals specifying their retention in the appropriate compartment, but plasma membrane proteins are predicted to have sorting information that prevents their localization to the vacuole. Mutations in clathrin may affect both the retention of Golgi membrane proteins and the functional integrity of the sorting pathway (Seeger and Payne, 1992b) . keywords: cells; domain; dpap; dpap b; et al; fig; fragment; golgi; membrane; plasmid; proteins; retention; signal; vacuolar; vacuole; yeast cache: cord-104279-choywmwd.txt plain text: cord-104279-choywmwd.txt item: #164 of 541 id: cord-104282-90t1m430 author: None title: Microsomal aldehyde dehydrogenase is localized to the endoplasmic reticulum via its carboxyl-terminal 35 amino acids date: 1994-09-02 words: 7103 flesch: 44 summary: The elucidation of the mechanisms by which ER localization of msALDH occurs should provide valuable clues for an understanding of the posttranslational targeting and insertion of a class of membrane proteins with a carboxyl-terminal anchor. In addition to the three proteins described above, several other ER membrane proteins are known that also have carboxyl-terminal anchors, such as heine oxygenase (40) and ribosome-binding protein p34 (28), but ER-targeting sequences of these proteins have not yet been identified. keywords: acids; amino; cat; cells; cytochrome; domain; fig; hydrophobic; membrane; msaldh; proteins; sequence; targeting cache: cord-104282-90t1m430.txt plain text: cord-104282-90t1m430.txt item: #165 of 541 id: cord-136540-2h2braww author: Buehler, Markus J. title: Liquified protein vibrations, classification and cross-paradigm de novo image generation using deep neural networks date: 2020-04-16 words: 3685 flesch: 46 summary: Using the DeepDream algorithm, instances of key features of the deep neural network can be made visible in a range of images, allowing us to explore the inner workings of protein surface wave patter neural networks, as well as the creation of new images by finding and highlighting features of protein molecular spectra in a range of photographic input. It is remarkable that the method works for a variety of protein structures with distinct frequency spectra from complex to simple including the pure sine wave cases at different frequencies. keywords: images; method; model; network; patterns; protein; structures; surface cache: cord-136540-2h2braww.txt plain text: cord-136540-2h2braww.txt item: #166 of 541 id: cord-147565-mtdhdkc1 author: Harmalkar, Ameya title: Advances to tackle backbone flexibility in protein docking date: 2020-10-15 words: 3487 flesch: 34 summary: MD use for protein docking has been limited because non-native local minima trap proteins, and dissociation is too slow [28] . To accelerate dissociation of protein partners at sub-optimal binding regions, Ostermeir et al. developed a Hamiltonian replica exchange MD protocol (H-REMD) for protein docking [31] *. keywords: backbone; binding; capri; docking; dynamics; model; prediction; protein; structures; targets cache: cord-147565-mtdhdkc1.txt plain text: cord-147565-mtdhdkc1.txt item: #167 of 541 id: cord-150183-zzzyewjb author: Phillips, J. C. title: Synchronized Attachment and the Darwinian Evolution of Coronaviruses CoV-1 and CoV-2 date: 2020-08-27 words: 2486 flesch: 51 summary: However, to implement this idea in practice with protein sequences, one needs to compress the existing vast array of three-dimensional structural data into a one-dimensional form. Now that we are in the genomic age, with a very large sequence data base available for many proteins and many species, the discovery of these 20 fractals [5, 13] opens a new biophysics field of accurate thermodynamic analysis of small but medically important evolutionary differences. keywords: attachment; extrema; proteins; scale; spike cache: cord-150183-zzzyewjb.txt plain text: cord-150183-zzzyewjb.txt item: #168 of 541 id: cord-171099-d0qr84xg author: Buehler, Markus J. title: Nanomechanical sonification of the 2019-nCoV coronavirus spike protein through a materiomusical approach date: 2020-03-30 words: 4514 flesch: 41 summary: Natur, acatec Ultrathin Free-Standing Bombyx mori Silk Nanofibril Membranes Deformation and failure of protein materials in physiologically extreme conditions and disease Silk-Its Mysteries, How It Is Made, and How It Is Used Materials by design: Merging proteins and music Materiomics: An -omics approach to biomaterials research Nature's hierarchical materials Predictive modelling-based design and experiments for synthesis and spinning of bioinspired silk fibres A series of PDB related databases for everyday needs Structure and stability of the lamin A tail domain and HGPS mutant Evaluating Hierarchical Structure in Music Annotations Sounds interesting: can sonification help us design new proteins? Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation A Self-Consistent Sonification Method to Translate Amino Acid Sequences into Musical Compositions and Application in Protein Design Using Artificial Intelligence Sonification based de novo protein design using artificial intelligence, structure prediction and analysis using molecular modeling E-MSD: an integrated data resource for bioinformatics Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features The anisotropic network model web server at 2015 (ANM 2.0) Presenting musical encoding in two versions - one in the amino-acid scale and one based on equal temperament tuning - the method allows for expressing protein structures in audible space, offering novel avenues to represent, analyze and design architectural features across length- and time-scales. keywords: amino; figure; music; protein; sound; spike; structure; vibrational; virus cache: cord-171099-d0qr84xg.txt plain text: cord-171099-d0qr84xg.txt item: #169 of 541 id: cord-190540-zf5ksac2 author: Rakshit, Kausik title: An effective approach to reduce the penetration potential of Sars-Cov-2 and other viruses by spike protein: Through surface particle electrostatic charge negotiation date: 2020-06-18 words: 2075 flesch: 22 summary: Reviewing the works of different authors, regarding charges, surface charge densities ({sigma}), charge mobility ({mu}) and electrostatic potentials of different aerosols under varied experimental conditions, a similar intensive study has also been carried out to investigate the electron donating and accepting (hole donating) properties of the spike proteins (S-proteins) of different RNA and DNA viruses, including SARS-COV-2. An intensive study have been carried out to find out the generation of electrostatic charges due to the surface emission of electrons (SEE), when a conducting material like silk, nylon or wool makes a friction with the Gr IV elements like Germanium or Silicon, it creates an opposite layer of charges in the outer conducting surface and the inner semiconducting surface separated by a dielectric materials. keywords: charges; coronavirus; electrostatic; protein; sars; spike; surface cache: cord-190540-zf5ksac2.txt plain text: cord-190540-zf5ksac2.txt item: #170 of 541 id: cord-193133-puqcbf8t author: Piplani, Sakshi title: In silico comparison of spike protein-ACE2 binding affinities across species; significance for the possible origin of the SARS-CoV-2 virus date: 2020-05-13 words: 3816 flesch: 43 summary: 29 The X-ray crystal structures of human ACE2 (recode 3SCI) and human SARS spike protein (refcode 5XLR) were retrieved from Protein Data Bank. The SARS-CoV spike protein was also docked with human ACE2 protein to obtain the docking pose for binding energy calculations. keywords: ace2; binding; coronavirus; cov-2; covid-19; human; protein; sars; species; spike cache: cord-193133-puqcbf8t.txt plain text: cord-193133-puqcbf8t.txt item: #171 of 541 id: cord-193489-u6ewlh16 author: Wang, Rui title: Decoding SARS-CoV-2 transmission, evolution and ramification on COVID-19 diagnosis, vaccine, and medicine date: 2020-04-29 words: 6071 flesch: 56 summary: The SARS-CoV-2 spike glycoprotein, or S protein, comprised of two subunits, S1 and S2, of very different properties [13] , see Fig. 5 . bioRxiv SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus The crystal structure of papain-like protease of sars cov-2 Structure of the rna-dependent rna polymerase from covid-19 virus Structural model of the sars coronavirus e channel in lmpg micelles Crystal structure of rna binding domain of nucleocapsid phosphoprotein from sars coronavirus 2. keywords: cluster; cov-2; covid-19; genome; mutations; number; protease; protein; sars; table cache: cord-193489-u6ewlh16.txt plain text: cord-193489-u6ewlh16.txt item: #172 of 541 id: cord-196265-mvnkkcow author: M'esz'aros, B'alint title: Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications date: 2020-04-21 words: 12685 flesch: 35 summary: The central resource for SLiMs is the Eukaryotic Linear Motif database (ELM; http://elm.eu.org/), also serving as an exploratory server for over 280 manually curated SLiM classes with experimental evidence, each defined by a POSIX regular expression (Kumar et al., 2020) . The ACE2 sequence (UniProt:ACE2_HUMAN) was entered in the ELM server (Kumar et al., 2020) and returned several relevant candidate SLiMs in the short cytosolic C-terminal tail. keywords: ace2; actin; attachment; autophagy; binding; cell; coronavirus; cov-2; domain; elm; entry; et al; host; infection; inhibitors; integrin; interaction; kinase; membrane; motif; phosphorylation; protein; receptor; replication; rgd; sars; sequence; sh2; site; spike; tyrosine cache: cord-196265-mvnkkcow.txt plain text: cord-196265-mvnkkcow.txt item: #173 of 541 id: cord-199630-2lmwnfda author: Ray, Sumanta title: Predicting potential drug targets and repurposable drugs for COVID-19 via a deep generative model for graphs date: 2020-07-05 words: 6402 flesch: 45 summary: After the model is trained the drug-CoV-host links are predicted using the following equation: where A i j represents the possible links between all combination of SARS-CoV-2 nodes and drug nodes. To develop suitable therapeutic strategies and design antiviral drugs, a comprehensive understanding of the interactions between viral and human proteins is essential 2 . keywords: cov-2; drugs; graph; host; human; interaction; links; matrix; model; network; nodes; proteins; sars; virus cache: cord-199630-2lmwnfda.txt plain text: cord-199630-2lmwnfda.txt item: #174 of 541 id: cord-222664-4qyrtzhu author: Coban, Mathew title: Attacking COVID-19 Progression using Multi-Drug Therapy for Synergetic Target Engagement date: 2020-07-06 words: 11330 flesch: 36 summary: It was identified in Wuhan city, in the Hubei province of China in December 2019 (Chen et al., 2020; Huang et al., 2020; Zhu et al., 2020) . The spike glycoprotein is a key surface protein that interacts with cell surface receptor, angiotensinconverting enzyme 2 (Ace2) mediating entrance of the virus into host cells (Zhu et al., 2018) . keywords: ace2; binding; caulfield; caulfield et; compounds; cov-2; covid-19; data; docking; drug; dynamics; et al; fig; inhibitors; interaction; ligand; model; patients; protein; residues; results; sars; screening; set; simulations; site; structure; target; tmprss2; virus cache: cord-222664-4qyrtzhu.txt plain text: cord-222664-4qyrtzhu.txt item: #175 of 541 id: cord-243806-26n22jbx author: Vandelli, Andrea title: Structural analysis of SARS-CoV-2 and prediction of the human interactome date: 2020-03-30 words: 5262 flesch: 39 summary: A significant overlap exists with the list of protein interactions reported by Gordon et al. 58 , and among the candidate partners we identified AKAP8L, involved as a DEAD/H-box RNA helicase binding protein involved in HIV infection 59 . in StatPearls Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor Furin cleavage of the SARS coronavirus spike glycoprotein enhances cell-cell fusion but does not affect virion entry Isolation and Characterization of 2019-nCoV-like Coronavirus from Malayan Pangolins Structures of MERS-CoV spike glycoprotein in complex with sialoside attachment receptors Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV Identification of sialic acid-binding function for the Middle East respiratory syndrome coronavirus spike glycoprotein The Structure and Functions of Coronavirus Genomic 3' and 5' Ends A high-throughput approach to profile RNA structure A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs RNA structure drives interaction with proteins An Integrative Study of Protein-RNA Condensates Identifies Scaffolding RNAs and Reveals Players in Fragile X-Associated Tremor/Ataxia Syndrome Phase separation drives X-chromosome inactivation: a hypothesis Identification of a Coronavirus Transcription Enhancer catRAPID omics: a web server for large-scale prediction of protein-RNA interactions Quantitative predictions of protein interactions with long noncoding RNAs Predicting protein associations with long noncoding RNAs RNAct: Protein-RNA interaction predictions for model organisms with supporting experimental data Cloaked similarity between HIV-1 and SARS-CoV suggests an anti-SARS strategy Inhibition of furin-mediated cleavage activation of HIV-1 glycoprotein gp160 Differential downregulation of ACE2 by the spike proteins of severe acute respiratory syndrome coronavirus and human coronavirus NL63 Conserved structural RNA domains in regions coding for cleavage site motifs in hemagglutinin genes of influenza viruses Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China ViennaRNA Package 2.0 The EMBL-EBI search and sequence analysis tools APIs in 2019 RNA-Seq methods for transcriptome analysis The proximal origin of SARS-CoV-2 A pneumonia outbreak associated with a new coronavirus of probable bat origin T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension Distinct Roles for Sialoside and Protein Receptors in Coronavirus Infection Silico evidence for two receptors based strategy of SARS-CoV-2 Host cell proteins interacting with the 3' end of TGEV coronavirus genome influence virus replication Structural determinants and mechanism of HIV-1 genome packaging An Overview of Their Replication and Pathogenesis Protein aggregation, structural disorder and RNA-binding ability: a new approach for physico-chemical and gene ontology classification of multiple datasets UniProt: a worldwide hub of protein knowledge SARS-CoV-2 launches a unique transcriptional signature from in vitro, ex vivo, and in vivo systems omiXcore: a web server for prediction of protein interactions with large RNA Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2 RNA-RNA and RNAprotein interactions in coronavirus replication and transcription Insights into RNA biology from an atlas of mammalian mRNA-binding proteins HIV Gag polyprotein: processing and early viral particle assembly The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function Viral interactions with the Notch pathway What retroviruses teach us about the involvement of c-Myc in leukemias and lymphomas The architecture of SARS-CoV-2 transcriptome. bioRxiv keywords: binding; coronavirus; cov-2; fig; host; human; interactions; protein; region; rna; sars; spike; structure cache: cord-243806-26n22jbx.txt plain text: cord-243806-26n22jbx.txt item: #176 of 541 id: cord-252147-bvtchcbt author: Domingo-Espín, Joan title: Engineered Biological Entities for Drug Delivery and Gene Therapy: Protein Nanoparticles date: 2011-11-15 words: 17227 flesch: 30 summary: The main biological production systems for protein drugs are described below. Finally, some successful examples of protein nanoparticles on the market will be described in addition to protein products currently in clinical trials and under preclinical research in order to envision which type of protein nanoparticles will be available soon on the market. keywords: binding; cancer; cell; complex; delivery; design; dna; drug; drug delivery; expression; gene; gene delivery; human; interactions; molecules; nanoparticles; nuclear; particles; peptides; production; properties; protein; receptor; self; specific; system; targeting; therapy; transfer; tumor; use; vector; virus; vivo; vlps cache: cord-252147-bvtchcbt.txt plain text: cord-252147-bvtchcbt.txt item: #177 of 541 id: cord-252304-lwiulri7 author: Fragnoud, Romain title: Differential proteomic analysis of virus-enriched fractions obtained from plasma pools of patients with dengue fever or severe dengue date: 2015-11-14 words: 8329 flesch: 42 summary: As the dynamic range for plasma proteins is large (over 10 orders of magnitude) and the most abundant proteins (0.1 % of the total number) constitute up to 95 % of the plasmatic protein mass, identification of biomarkers present at low concentrations is a major challenge in proteomic studies dealing with plasma. ELISAs were used to validate differential expression of a selection of identified host proteins in individual plasma samples of patients with dengue fever compared to patients with severe dengue. keywords: acute; analysis; cell; complement; dengue; disease; fever; host; patients; pf4; plasma; proteins; samples; virus cache: cord-252304-lwiulri7.txt plain text: cord-252304-lwiulri7.txt item: #178 of 541 id: cord-252536-gfx4cq03 author: Bieniossek, Christoph title: MultiBac: expanding the research toolbox for multiprotein complexes date: 2011-12-07 words: 7133 flesch: 36 summary: Protein complexes composed of many subunits carry out most essential processes in cells and, therefore, have become the focus of intense research. Notwithstanding, our molecular understanding of the very large number of protein complexes in the cell remains limited to a handful of examples for which detailed nearatomic structures are known. keywords: baculovirus; cells; complexes; dna; eukaryotic; expression; gene; genome; head; insect; loxp; multibac; multigene; production; protein; structure; system cache: cord-252536-gfx4cq03.txt plain text: cord-252536-gfx4cq03.txt item: #179 of 541 id: cord-252576-1ec545o2 author: Wu, Xiangli title: An antifungal defensin from Phaseolus vulgaris cv. ‘Cloud Bean’ date: 2011-01-15 words: 3568 flesch: 47 summary: Antifungal proteins have arrested the attention of investigators because of the tremendous economic implications. Antifungal proteins have also been purified from animals including insects (Iijima et al. 1993) . keywords: activity; antifungal; bean; cloud; defensin; fraction; peptide; proteins cache: cord-252576-1ec545o2.txt plain text: cord-252576-1ec545o2.txt item: #180 of 541 id: cord-253466-7gpije5d author: Netherton, Christopher title: A Guide to Viral Inclusions, Membrane Rearrangements, Factories, and Viroplasm Produced During Virus Replication date: 2007-08-31 words: 26447 flesch: 32 summary: Ultrastructural studies and sequential development of virus isolated from normal and tumor tissue Acidic C terminus of vaccinia virus DNAbinding protein interacts with ribonucleotide reductase Formation of DNA replication structures in herpes virus-infected cells requires a viral DNA binding protein Comparison of the intranuclear distributions of herpes simplex virus proteins involved in various viral functions Origin-independent plasmid replication occurs in vaccinia virus cytoplasmic factories and requires all five known poxvirus replication factors MHC I-dependent antigen presentation is inhibited by poliovirus protein 3A Autophagy in innate and adaptive immunity Poliovirus 3A protein limits interleukin-6 (IL-6), IL-8, and beta interferon secretion during viral infection Inhibition of cellular protein secretion by poliovirus proteins 2B and 3A Inhibition of endoplasmic reticulum-to-Golgi traffic by poliovirus protein 3A: These initially appear close to the nuclear envelope, possibly at sites where the genome first enters the nucleus following capsid disassembly at nuclear pores (Everett and Murray, 2005) , and are then seen throughout the nucleus (Everett et al., 2004) . keywords: asfv; assembly; bodies; capsid; cells; complex; contain; cytoplasmic; dna; dna replication; early; electron; et al; expression; factories; factory; fever; formation; gene; genome; golgi; herpes; host; inclusions; infection; localization; membrane; nuclear; nucleus; poliovirus; polymerase; protein; replicase; replication; replication complex; rna; role; sites; structures; swine; type; vaccinia; vaccinia virus; vesicles; viral; virus; virus factories; virus replication; viruses cache: cord-253466-7gpije5d.txt plain text: cord-253466-7gpije5d.txt item: #181 of 541 id: cord-253844-y6xdcf20 author: Yesudhas, Dhanusha title: COVID-19 outbreak: history, mechanism, transmission, structural studies and therapeutics date: 2020-09-04 words: 7192 flesch: 43 summary: The lung macrophage in SARS-CoV-2 infection: a friend or a foe? SARS-coronavirus replication in human peripheral monocytes/macrophages Structural variations in human ACE2 may influence its binding with SARS-CoV-2 spike protein Intrinsically unstructured proteins and their functions Role of disordered regions in transferring tyrosine to its cognate tRNA The coronavirus nucleocapsid is a multifunctional protein Structure of the N-terminal RNA-binding domain of the SARS CoV nucleocapsid protein The SARS coronavirus nucleocapsid protein-forms and functions Receptor recognition mechanisms of coronaviruses: a decade of structural studies Pre-fusion structure of a human coronavirus spike protein The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade The role of furin cleavage site in SARS-CoV-2 spike protein-mediated membrane fusion in the presence or absence of trypsin A review on the cleavage priming of the spike protein on coronavirus by angiotensin-converting enzyme-2 and furin Structural and functional basis of SARS-CoV-2 entry by using human ACE2 Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2 Protein intrinsic disorder and influenza virulence: the 1918 H1N1 and H5N1 viruses Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 Protease against COVID-19 Therapeutic targets and computational approaches on drug development for COVID-19 Baricitinib as potential treatment for 2019-nCoV acute respiratory disease Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Feasibility and biological rationale of repurposing sunitinib and erlotinib for dengue treatment Plasma inflammatory cytokines and chemokines in severe acute respiratory syndrome Treatment of Middle East Respiratory Syndrome with a combination of lopinavir-ritonavir and interferon-β1b (MIRACLE trial): study protocol for a randomized controlled trial Simultaneous treatment of human bronchial epithelial cells with serine and cysteine protease inhibitors prevents severe acute respiratory syndrome coronavirus entry Identification of the first synthetic inhibitors of the type II transmembrane serine protease TMPRSS2 suitable for inhibition of influenza virus activation Coronavirus replication complex formation utilizes components of cellular autophagy Chloroquine is a potent inhibitor of SARS coronavirus infection and spread Use of hydroxychloroquine and chloroquine during the COVID-19 SARS coronavirus: a new challenge for prevention and therapy Clinical features of patients infected with 2019 novel coronavirus in Wuhan A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia Structure, function, and evolution of coronavirus spike proteins Coronaviruses post-SARS: update on replication and pathogenesis Receptor recognition and cross-species infections of SARS coronavirus Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission SARS-CoV infection in a restaurant from palm civet Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus Proteolytic activation of the SARS-coronavirus spike protein: cutting enzymes at the cutting edge of antiviral research The species severe acute respiratory syndrome related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 A pneumonia outbreak associated with a new coronavirus of probable bat origin Tissue distribution of ACE2 protein, the functional receptor for SARS coronavirus. keywords: ace2; binding; cell; coronavirus; cov-2; disordered; entry; host; human; infection; inhibitor; novel; protein; receptor; residues; sars; spike; structure; transmission cache: cord-253844-y6xdcf20.txt plain text: cord-253844-y6xdcf20.txt item: #182 of 541 id: cord-253987-83h861lp author: Tada, Takuya title: A soluble ACE2 microbody protein fused to a single immunoglobulin Fc domain is a potent inhibitor of SARS-CoV-2 infection in cell culture date: 2020-09-17 words: 6860 flesch: 40 summary: Soluble ACE2 proteins (10 µg) were mixed with 20 µl nickel beads for 1 hour at 4°C. The antiviral activity of ACE2 proteins against live virus was similar to pseudotyped virus, except that in the live virus assay, the wild-type and H345A microbodies were of similar potency. keywords: ace2; ace2 microbody; activity; cells; cov-2; et al; figure; infection; microbody; protein; sars; soluble; spike; virus cache: cord-253987-83h861lp.txt plain text: cord-253987-83h861lp.txt item: #183 of 541 id: cord-254100-u6x5zd4i author: Taliansky, M.E. title: Involvement of the Plant Nucleolus in Virus and Viroid Infections: Parallels with Animal Pathosystems date: 2010-10-15 words: 13999 flesch: 28 summary: Therefore, the main emphasis of this review will be on what is known about the different aspects of interactions between plant virus proteins and the nucleolus, of which the functional significance in control of virus movement and interference with host antiviral defense has started to appear only recently. The most common technique for studying the nucleolar targeting of plant virus proteins is based on the confocal microscopy localization of the proteins which have been tagged with a fluorescent fusion protein (such as green fluorescent protein, GFP). keywords: cbs; cell; et al; fibrillarin; functions; host; infection; interaction; localization; movement; nia; nucleolar; nucleolus; nucleus; orf3; plant; protein; replication; rna; role; silencing; translation; viral; virus; viruses; vpg cache: cord-254100-u6x5zd4i.txt plain text: cord-254100-u6x5zd4i.txt item: #184 of 541 id: cord-254107-02bik024 author: Hillisch, Alexander title: Utility of homology models in the drug discovery process date: 2004-08-31 words: 7383 flesch: 38 summary: An Introduction The response of protein structures to amino-acid sequence changes Fold Recognition Methods Progress in protein structure prediction Assessment of homology-based predictions in CASP5 SCOP: a structural classification of proteins database for the investigation of sequences and structures Databases for protein-ligand complexes LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures PDBsum: summaries and analyses of PDB structures MODBASE, a database of annotated comparative protein structure models, and associated resources Comparative protein modelling by satisfaction of spatial restraints The SWISS-MODEL Repository of annotated threedimensional protein structure homology models Supporting your pipeline with structural knowledge There are numerous examples where protein homology models have supported the discovery and the optimization of lead compounds with respect to potency and selectivity. keywords: binding; compounds; design; discovery; drug; homology; homology models; human; modeling; models; protein; receptor; sequence; structure; target cache: cord-254107-02bik024.txt plain text: cord-254107-02bik024.txt item: #185 of 541 id: cord-254909-8zgvovu4 author: Srivastava, Rajneesh title: Serum profiling of leptospirosis patients to investigate proteomic alterations() date: 2012-12-05 words: 5783 flesch: 25 summary: Proteins showing differential expression in leptospirosis patients were subjected to further functional clustering by using database for annotation, visualization and integrated discovery (DAVID) and protein analysis through evolutionary relationships (PANTHER). This comparative proteomic profiling was performed to identify differentially expressed serum proteins in leptospiral infection. keywords: analysis; complement; dige; disease; expression; infection; leptospiral; leptospirosis; patients; precursor; proteins; serum; spots cache: cord-254909-8zgvovu4.txt plain text: cord-254909-8zgvovu4.txt item: #186 of 541 id: cord-254957-jqp1gto6 author: Klann, Kevin title: Growth factor receptor signaling inhibition prevents SARS-CoV-2 replication date: 2020-08-11 words: 7016 flesch: 41 summary: Proteins exhibiting decreased protein levels were significantly enriched in cell cycle proteins. We identified viral protein phosphorylation and defined phosphorylation-driven host cell signaling changes upon infection. keywords: cell; changes; cov-2; drugs; et al; figure; gfr; host; infection; pathways; phosphorylation; protein; replication; sars; signaling; study cache: cord-254957-jqp1gto6.txt plain text: cord-254957-jqp1gto6.txt item: #187 of 541 id: cord-255371-o9oxchq6 author: Nguyen, Thanh Thi title: Genomic Mutations and Changes in Protein Secondary Structure and Solvent Accessibility of SARS-CoV-2 (COVID-19 Virus) date: 2020-07-10 words: 5655 flesch: 52 summary: For the mutation detection purpose, we apply a dynamic programming algorithm to protein AA sequences to get global pairwise alignments between a reference sequence and a query sequence. There have been various protein secondary structure prediction programs in the literature and many of those were developed based on artificial intelligence models using protein AA sequences such as JPred4 [29] , Spider2 keywords: accessibility; cov-2; gene; mutations; number; protein; sars; sequences; solvent; structure; virus cache: cord-255371-o9oxchq6.txt plain text: cord-255371-o9oxchq6.txt item: #188 of 541 id: cord-256047-mabrmzd9 author: Jacomin, Anne-Claire title: Deubiquitinating Enzymes Related to Autophagy: New Therapeutic Opportunities? date: 2018-08-19 words: 9927 flesch: 28 summary: Protein ubiquitination is a complex process requiring the successive activity of three types of enzymes: an E1 ubiquitin-activating enzyme, an E2 ubiquitin-conjugating enzyme, and an E3 ubiquitin-ligase enzyme. Protein ubiquitination is a complex process requiring the successive activity of three types of enzymes: an E1 ubiquitin-activating enzyme, an E2 ubiquitin-conjugating enzyme, and an E3 ubiquitin-ligase enzyme. keywords: activity; autophagy; beclin1; cells; chains; degradation; dubs; enzyme; membrane; mitophagy; process; protein; regulation; role; ubiquitin; ubiquitination; usp14; usp30 cache: cord-256047-mabrmzd9.txt plain text: cord-256047-mabrmzd9.txt item: #189 of 541 id: cord-256156-mywhe6w9 author: Clausen, Thomas Mandel title: SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2 date: 2020-09-14 words: 8996 flesch: 49 summary: To explore if HS, ACE2 and spike interact at the cell surface, we investigated the impact of ACE2 expression on S protein cell binding. Bound protein was washed with buffer and eluted with 0.2 M imidazole in washing buffer. keywords: ace2; binding; cells; cov-2; et al; fig; heparin; human; infection; protein; r n; rbd; sars; site; spike; sulfate; surface; virus cache: cord-256156-mywhe6w9.txt plain text: cord-256156-mywhe6w9.txt item: #190 of 541 id: cord-256316-1odgm6hm author: Godet, Murielle title: TGEV corona virus ORF4 encodes a membrane protein that is incorporated into virions date: 1992-06-30 words: 5452 flesch: 41 summary: Three days before fusion, the mice were boosted both intraperitoneally and subcutaneously with ORF4 protein purified from 4 X 10' infected cells by 15% SDS-PAGE. ORF4 product is a membrane-associated protein Indirect immunofluorescence assays were performed to determine the subcellular location of ORF4 protein. keywords: a/.; cells; coronavirus; fig; mabs; membrane; orf4; polypeptide; protein; sequence; tgev; virus cache: cord-256316-1odgm6hm.txt plain text: cord-256316-1odgm6hm.txt item: #191 of 541 id: cord-256325-q70rky3r author: Stewart, Cameron R. title: A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease date: 2017-07-04 words: 8331 flesch: 28 summary: Collectively, these data suggest that let-7 miRNAs inhibit HeV by suppressing host proteins required for virus infection. Central to this work was the development of a recombinant HeV expressing the renilla luciferase construct, which allowed for high throughput and rapid measurement of virus infection (Marsh et al. 2013 ). keywords: cell; disease; et al; fibrillarin; genes; henipavirus; hev; host; human; ifn; infection; niv; nuclear; proteins; rna; translation; virus; viruses cache: cord-256325-q70rky3r.txt plain text: cord-256325-q70rky3r.txt item: #192 of 541 id: cord-256340-w4z5avld author: Bailer, SM title: Connecting viral with cellular interactomes date: 2009-07-24 words: 3651 flesch: 33 summary: Moreover, it presented the first virus-host interactome of a member of the herpesvirus family Self-assembling protein microarrays Highthroughput mapping of a dynamic signaling network in mammalian cells Capturing protein interactions in the secretory pathway of living cells Design and application of a cytokine-receptor-based interaction trap Functional organization of the yeast proteome by systematic analysis of protein complexes Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Global landscape of protein complexes in the yeast Saccharomyces cerevisiae A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells Large-scale mapping of human protein-protein interactions by mass spectrometry Viral proteomics: global evaluation of viruses and their interaction with the host Comprehensive characterization of extracellular herpes simplex virus type 1 virions From ORFeomes to protein interaction maps in viruses VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks The landscape of human proteins interacting with viruses and other pathogens This paper integrates protein interaction networks of several pathogens and identifies certain cellular processes that participate in interactions with different pathogen groups. Thus, the yeast cell offers an environment sufficiently natural for the analysis of protein interactions of other species [20 ] . keywords: analysis; host; human; interactions; protein; system; virus; y2h; yeast cache: cord-256340-w4z5avld.txt plain text: cord-256340-w4z5avld.txt item: #193 of 541 id: cord-257392-u6jy6w1m author: Zhao, Yanfeng title: Proteomic analysis of primary duck hepatocytes infected with duck hepatitis B virus date: 2010-06-07 words: 6069 flesch: 33 summary: In vitro experimental infection of primary human hepatocytes with hepatitis B virus Infection of a human hepatoma cell line by hepatitis B virus Initiation of hepatitis B virus genome replication and production of infectious virus following delivery in HepG2 cells by novel recombinant baculovirus vector Persistence of the hepatitis B virus covalently closed circular DNA in HepaRG human hepatocyte-like cells Age-related differences in amplification of covalently closed circular DNA at early times after duck hepatitis B virus infection of ducks Treatment of chronic viral hepatitis in woodchucks by prolonged intrahepatic expression of interleukin-12 Proteome analysis of cultivar-specific deregulations of Oryza sativa indica and O. sativa japonica cellular suspensions undergoing rice yellow mottle virus infection Identification of Epstein-Barr virus (EBV) nuclear antigen 2 (EBNA2) target proteins by proteome analysis: activation of EBNA2 in conditionally immortalized B cells reflects early events after infection of primary B cells by EBV Proteomic analysis of tobacco mosaic virus-infected tomato (Lycopersicon esculentum M.) fruits and detection of viral coat protein Identification of cellular proteins modified in response to African swine fever virus infection by proteomics Proteomic analysis of cellular protein alterations using a hepatitis B virus-producing cellular model Proteomic analysis of HepaRG cells: a novel cell line that supports hepatitis B virus infection Proteomic analysis of hepatitis B surface antigen positive transgenic mouse liver and decrease of cyclophilin A Duck hepatitis B virus: an invaluable model system for HBV infection Infection and uptake of duck hepatitis B virus by duck hepatocytes maintained in the presence of dimethyl sulfoxide Temporal proteome and lipidome profiles reveal hepatitis C virus-associated reprogramming of hepatocellular metabolism and bioenergetics Gene expression in primate liver during viral hemorrhagic fever Cellular proteins in influenza virus particles Quantitative proteomic analysis of lentiviral vectors using 2-DE Identification of glyceraldehyde-3-phosphate dehydrogenase as a cellular protein that binds to the hepatitis B virus posttranscriptional regulatory element Phosphorylation of the hepatitis B virus core protein by glyceraldehyde-3-phosphate dehydrogenase protein kinase activity Protein kinase and NOstimulated ADP-ribosyltransferase activities associated with glyceraldehyde-3-phosphate dehydrogenase isolated from human liver Almeras L: Identification of cellular proteome modifications in response to West Nile virus infection Proteomics analysis of host cells infected with infectious bursal disease virus Quantitative analysis of severe acute respiratory syndrome (SARS)-associated coronavirus-infected cells using proteomic approaches: implications for cellular responses to virus infection Itinerary of hepatitis b viruses: delineation of restriction points critical for infectious entry Actin in transcription and transcription regulation Actin-based motility of vaccinia virus Local actin polymerization and dynamin recruitment in SV40-induced internalization of caveolae Cellular motility driven by assembly and disassembly of actin filaments Adenovirus endocytosis requires actin cytoskeleton reorganization mediated by Rho family GTPases Establishment of a functional human immunodeficiency virus type 1 (HIV-1) reverse transcription complex involves the cytoskeleton SFV infection in CHO cells: cell-type specific restrictions to productive virus entry at the cell surface Escape of herpesviruses from the nucleus US3 of herpes simplex virus type 1 encodes a promiscuous protein kinase that phosphorylates and alters localization of lamin A/C in infected cells Effects of lamin A/C, lamin B1, and viral US3 kinase activity on viral infectivity, virion egress, and the targeting of herpes simplex virus U(L)34-encoded protein to the inner nuclear membrane Epstein-Barr virus BGLF4 kinase induces disassembly of the nuclear lamina to facilitate virion production Glutamine metabolism is essential for human cytomegalovirus infection Molecular chaperones in the cytosol: from nascent chain to folded protein Hsp70 chaperones: cellular functions and molecular mechanism Proteomics analysis of the tombusvirus replicase: Hsp70 molecular chaperone is associated with the replicase and enhances viral RNA replication The cellular chaperone heat shock protein 90 facilitates Flock House virus RNA replication in Drosophila cells Heat shock protein 90 and heat shock protein 70 are components of dengue virus receptor complex in human cells Efficient Hsp90-independent in vitro activation by Hsc70 and Hsp40 of duck hepatitis B virus reverse transcriptase, an assumed Hsp90 client protein Hepatitis B virus replication causes oxidative stress in HepAD38 liver cells Betulinic acid-mediated inhibitory effect on hepatitis B virus by suppression of manganese superoxide dismutase expression Epstein-Barr virus induces an oxidative stress during the early stages of infection in B lymphocytes, epithelial, and lymphoblastoid cell lines Annexin 2: a novel human immunodeficiency virus type 1 Gag binding protein involved in replication in monocyte-derived macrophages Secretory leukocyte protease inhibitor binds to annexin II, a cofactor for macrophage HIV-1 infection Annexin II enhances cytomegalovirus binding and fusion to phospholipid membranes Annexin II incorporated into influenza virus particles supports virus replication by converting plasminogen into plasmin Association of hepatitis B virus polymerase with promyelocytic leukemia nuclear bodies mediated by the S100 family protein p11 Proteome responses to stable hepatitis B virus transfection and following interferon alpha treatment in human liver cell line HepG2 Suitable reference genes for real-time PCR in human HBV-related hepatocellular carcinoma with different clinical prognoses Selection of reference genes for real-time PCR in human hepatocellular carcinoma tissues Validation of putative reference genes for gene expression studies in human hepatocellular carcinoma using real-time quantitative RT-PCR Determination of suitable housekeeping genes for normalisation of quantitative real time PCR analysis of cells infected with human immunodeficiency virus and herpes viruses Reference gene selection for quantitative real-time PCR analysis in virus infected cells: SARS corona virus, Yellow fever virus, Human Herpesvirus-6, Camelpox virus and Cytomegalovirus infections A protein-based set of reference markers for liver tissues and hepatocellular carcinoma Efficient duck hepatitis B virus production by an avian liver tumor cell line Rapid resolution of duck hepatitis B virus infections occurs after massive hepatocellular involvement YZ were responsible for PDHs culture, virus infection and sample preparation. keywords: actin; analysis; annexin; cells; dhbv; duck; expression; hepatitis; human; infection; pdhs; protein; spots; virus cache: cord-257392-u6jy6w1m.txt plain text: cord-257392-u6jy6w1m.txt item: #194 of 541 id: cord-257465-9yrf7ofy author: Finlay, William J. J. title: Phage Display: A Powerful Technology for the Generation of High-Specificity Affinity Reagents from Alternative Immune Sources date: 2016-05-23 words: 6073 flesch: 30 summary: Today however, the progress in chicken antibody phage display has circumvented these problems and made recombinant chicken antibody reagents readily accessible, as we describe below. fi lamentous phage displaying antibody variable domains Multi-subunit proteins on the surface of fi lamentous phage: methodologies for displaying antibody (Fab) heavy and light chains Selecting and screening recombinant antibody libraries Human antibodies from V-gene libraries displayed on phage Semisynthetic combinatorial antibody libraries: a chemical solution to the diversity problem Human antibodies with sub-nanomolar affi nities isolated from a large non-immunized phage display library Fully synthetic human combinatorial antibody libraries (HuCAL) based on modular consensus frameworks and CDRs randomized with trinucleotides Generation of high-affi nity human antibodies by combining donor-derived and synthetic complementarity-determiningregion diversity High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries Picomolar affi nity antibodies from a fully synthetic naive library selected and evolved by ribosome display Affi nity maturation of a humanized rat antibody for anti-RAGE therapy: comprehensive mutagenesis reveals a high level of mutational plasticity both inside and outside the complementarity-determining regions In vitro selection and affi nity maturation of antibodies from a naive combinatorial immunoglobulin library Augmented binary substitution: single-pass CDR germ-lining and stabilization of therapeutic antibodies Protein engineering of antibody binding sites: recovery of specifi c activity in an anti-digoxin single-chain Fv analogue produced in Escherichia coli Human monoclonal Fab fragments derived from a combinatorial library bind to respiratory syncytial virus F glycoprotein and neutralize infectivity Domain interactions in the Fab fragment: a comparative evaluation of the singlechain Fv and Fab format engineered with variable domains of different stability An improved single-chain Fab platform for effi cient display and recombinant expression Reliable cloning of functional antibody variable domains from hybridomas and spleen cell repertoires employing a reengineered phage display system High affi nity ScFvs from a single rabbit immunized with multiple haptens Methods for the generation of chicken monoclonal antibody fragments by phage display keywords: affi; antibodies; antibody; chicken; display; generation; libraries; monoclonal; nity; phage; protein; scfv; specifi cache: cord-257465-9yrf7ofy.txt plain text: cord-257465-9yrf7ofy.txt item: #195 of 541 id: cord-257584-v38tjof3 author: Fahmi, Muhamad title: Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV date: 2020-03-03 words: 2992 flesch: 43 summary: We then determined the presence and absence of homolog proteins of one representative set of annotated 2019-nCoV proteins against other genome sequences in a database using tblastn with a threshold of > 50 and > 25 bits score for protein sequences > The phylogenetic profiling cluster of homolog proteins of one annotated 2019-nCoV protein against other genome sequences revealed two clades of ten 2019-nCoV proteins. keywords: bat; coronavirus; ncov; proteins; sars; tree cache: cord-257584-v38tjof3.txt plain text: cord-257584-v38tjof3.txt item: #196 of 541 id: cord-257802-vgizgq2y author: Uttamchandani, Mahesh title: Applications of microarrays in pathogen detection and biodefence date: 2008-11-12 words: 6576 flesch: 32 summary: [48] also developed protein microarrays for simultaneous diagnostics using parasitic and viral antigens. [49] monitored the antibody profiles of SARS patients using protein microarrays containing 82 purified coronavirus proteins. keywords: agents; antibodies; antibody; antigens; biodefence; detection; diagnostics; dna; microarrays; pathogen; pestis; probes; protein; sars; specific; virus cache: cord-257802-vgizgq2y.txt plain text: cord-257802-vgizgq2y.txt item: #197 of 541 id: cord-258363-gmgbus9i author: Kolla, Venkatadri title: Synthesis of a bacteriophage MB78 late protein by novel ribosomal frameshifting() date: 2000-08-22 words: 4584 flesch: 57 summary: key: cord-258363-gmgbus9i authors: Kolla, Venkatadri; Chakravorty, Maharani; Pandey, Bindu; Srinivasula, Srinivasa M; Mukherjee, Annapurna; Litwack, Gerald title: Synthesis of a bacteriophage MB78 late protein by novel ribosomal frameshifting() date: 2000-08-22 journal: Gene DOI: 10.1016/s0378-1119(00)00264-x sha: doc_id: 258363 cord_uid: gmgbus9i MB78 is a virulent phage of Salmonella typhimurium that possesses a number of interesting features, making it a suitable organism to study the regulation of gene expression. between the 3∞ end of 16S rRNA and the mRNA during elongation of protein synthesis in Escherichia coli Biochemical characterization of the bacterio The authors are thankful to the Department of Biotechnology, Government of India, the University Grants Commission and the National Institutes of Health (NIH ) (to V.K ) for financial assistance and Dr. Ravikumar Rallapalli for discussion. keywords: expression; fragment; frameshifting; kda; mb78; proteins; ribosomal; sequence cache: cord-258363-gmgbus9i.txt plain text: cord-258363-gmgbus9i.txt item: #198 of 541 id: cord-258468-52gej3co author: Marcekova, Zuzana title: Heterologous expression of full-length capsid protein of porcine circovirus 2 in Escherichia coli and its potential use for detection of antibodies date: 2009-08-05 words: 7015 flesch: 41 summary: The open reading frame encoding Cap protein was amplified using PCR from genomic DNA of PCV 2 (L14181 isolate) and the 707 bp long DNA fragment was cloned into pET28b expression vector (Fig. 1B) . In order to eliminate the cluster of rare codons from the 5 end of the cap gene, the expression vector encoding a truncated variant of Cap protein ( Cap-His), which was lacking the first 16 amino acid residues, was constructed (Fig. 1B) . keywords: cap; cap protein; capsid; cells; circovirus; coli; et al; expression; fig; gene; pcv; porcine; protein cache: cord-258468-52gej3co.txt plain text: cord-258468-52gej3co.txt item: #199 of 541 id: cord-258489-pyfc7jde author: Lico, Chiara title: Viral vectors for production of recombinant proteins in plants date: 2008-03-10 words: 11098 flesch: 29 summary: The heat tolerant property of the lichenase (658C) allows easy target proteins purification by heat treatment which precipitates up to 50% of contaminating plant proteins. The third strategy relies on replicating plant viruses. keywords: antibody; antigen; cell; development; et al; expression; gene; host; mosaic; peptide; plant; production; proteins; purification; systems; target; tissue; tmv; tobacco; transgenic; vaccine; vector; virus; viruses cache: cord-258489-pyfc7jde.txt plain text: cord-258489-pyfc7jde.txt item: #200 of 541 id: cord-258624-041cf99j author: Ahmad, Sajjad title: Design of a Novel Multi Epitope-Based Vaccine for Pandemic Coronavirus Disease (COVID-19) by Vaccinomics and Probable Prevention Strategy against Avenging Zoonotics date: 2020-05-23 words: 8231 flesch: 43 summary: The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health — The latest 2019 novel coronavirus outbreak in Wuhan, China Novel Coronavirus (2019-nCoV) Situation Summary | CDC A novel coronavirus outbreak of global health concern ScienceDaily: Your source for the latest research news Database resources of the national center for biotechnology information Exoproteome and secretome derived broad spectrum novel drug and vaccine candidates in Vibrio cholerae targeted by Piper betel derived compounds Combating tigecycline resistant Acinetobacter baumannii: A leap forward towards multi-epitope based vaccine discovery Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes The HMMTOP transmembrane topology prediction server SPAAN: a software program for prediction of adhesins and adhesin-like proteins using neural networks Adhesins as targets for vaccine development The immune epitope database (IEDB): 2018 update Improved method for predicting linear B-cell epitopes BepiPred-2.0: improving sequencebased B-cell epitope prediction using conformational epitopes MHCPred: a server for quantitative prediction of peptide--MHC binding Identification of putative vaccine candidates against Helicobacter pylori exploiting exoproteome and secretome: a reverse vaccinology based approach VirulentPred: a SVM based prediction method for virulent proteins in bacterial pathogens Vaxign: the first web-based vaccine design program for reverse vaccinology and applications for vaccine development AllerTOP-a server for in silico prediction of allergens Multi-epitope vaccines: a promising strategy against tumors and viral infections Peptide vaccine: progress and challenges Development of a multi-epitope peptide vaccine inducing robust T cell responses against brucellosis using immunoinformatics based approaches Exploring dengue genome to construct a multi-epitope based subunit vaccine by utilizing immunoinformatics approach to battle against dengue infection SCRATCH: a protein structure and structural feature prediction server I-TASSER server for protein 3D structure prediction homology modelling of protein structures and complexes others, Galaxy: a platform for interactive large-scale genome analysis GalaxyRefine: protein structure refinement driven by side-chain repacking Disulphide bonds and protein stability Disulfide by Design 2.0: a web-based tool for disulfide engineering in proteins Codon usage: nature's roadmap to expression and folding of proteins JCat: a novel tool to adapt codon usage of a target gene to its potential expression host Novel immunoinformatics approaches to design multi-epitope subunit vaccine for malaria by investigating anopheles salivary protein In-silico design of a multi-epitope vaccine candidate against onchocerciasis and related filarial diseases Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system PATCHDOCK and SymmDock: servers for rigid and symmetric docking FireDock: fast interaction refinement in molecular docking RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps Discovery studio visualizer VMD: visual molecular dynamics A one-pot multicomponent facile synthesis of dihydropyrimidin-2(1: H)-thione derivatives using triphenylgermane as a catalyst and its binding pattern validation Antechamber: an accessory software package for molecular mechanical calculations The FF14SB force field Langevin stabilization of molecular dynamics A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations On the Berendsen thermostat CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data UCSF Chimera-Superimposing and Morphing MMPBSA.py: This was significant to evaluate as homology between virus protein (s) to be used in vaccine designing and the host is likely to cause strong autoimmune reactions in the host [58] . keywords: binding; candidates; cell; construct; coronavirus; covid-19; energy; epitopes; glycoprotein; host; human; mepvc; molecular; protein; receptors; score; structure; system; tlr3; tlr4; vaccine cache: cord-258624-041cf99j.txt plain text: cord-258624-041cf99j.txt item: #201 of 541 id: cord-258784-9bdd9krr author: Wei, Chiming title: New technology and clinical applications of nanomedicine: Highlights of the second annual meeting of the American Academy of Nanomedicine (Part I) date: 2006-12-31 words: 5547 flesch: 30 summary: Poly(PEG-SA) nanoparticles (with transferrin attached to the free end of PEG) were also able to penetrate targeted cancer cells and rapidly transit within the cell to the perinuclear region; these particles were more toxic to cancer cells at relevant doses than the free drug. In India the nanomedicine research includes drug delivery with dendrimer-based nanoarchitecture for the controlled and targeted delivery of anticancer bioactives; mitochondrial drug targeting; gene therapy of genetic disorders like diabetes and cancer using dendrimer-based nano carriers; developing a DNA vaccine against Leichmania donovani; and stem cell research. keywords: aanm; cancer; cells; delivery; development; drug; figure; imaging; meeting; misfolding; nanomedicine; nanoparticles; phd; protein; research; structure; technology; university cache: cord-258784-9bdd9krr.txt plain text: cord-258784-9bdd9krr.txt item: #202 of 541 id: cord-259112-tkj5de7b author: Mandal, Santi M title: Inhaler with electrostatic sterilizer and use of cationic amphiphilic peptides may accelerate recovery from COVID-19 date: 2020-06-17 words: 1631 flesch: 37 summary: A positive charge is required initially to attract negatively charged membranes, and hydrophobic mass aides is required to disturb the membrane just as it makes contact with the hydrophobic site of HR1, HR2 area of viral combination protein and the receptor restricting space of S protein; this may lessen viral passage into the cell. The coronavirus nucleocapsid is a multifunctional protein Structural insights into coronavirus entry Host cell proteases: critical determinants of coronavirus tropism and pathogenesis Coronavirus envelope (E) protein remains at the site of assembly Analysis of SARS-CoV E protein ion channel activity by tuning the protein and lipid charge The coronavirus spike protein is a class I virus fusion protein: structural and functional characterization of the fusion core complex SARS-CoV fusion peptides induce membrane surface ordering and curvature Coronavirus envelope protein: current knowledge Antimicrobial and host-defense peptides as new anti-infective therapeutic strategies Collectins and cationic antimicrobial peptides of the respiratory epithelia Cationic antimicrobial peptides and their multifunctional role in the immune system keywords: air; caps; peptides; protein; virus cache: cord-259112-tkj5de7b.txt plain text: cord-259112-tkj5de7b.txt item: #203 of 541 id: cord-259237-aty0vrat author: Frabutt, Dylan A. title: Arms Race between Enveloped Viruses and the Host ERAD Machinery date: 2016-09-19 words: 9844 flesch: 38 summary: Transmembrane control of HRD1P by HRD3P Association of the SEL1L protein transmembrane domain with HRD1 ubiquitin ligase regulates ERAD-L Usa1 functions as a scaffold of the HRD-ubiquitin ligase The ubiquitin-domain protein HERP forms a complex with components of the endoplasmic reticulum associated degradation pathway Membrane topology of the yeast endoplasmic reticulum-localized ubiquitin ligase Doa10 and comparison with its human ortholog TEB4 (MARCH-IV) Ube2j2 ubiquitinates hydroxylated amino acids on ER-associated degradation substrates HRD1 and UBE2J1 target misfolded MHC class I heavy chains for endoplasmic reticulum-associated degradation Distinct ubiquitin-ligase complexes define convergent pathways for the degradation of ER proteins The yeast ERAD-C ubiquitin ligase Doa10 recognizes an intramembrane degron Htm1p, a mannosidase-like protein, is involved in glycoprotein degradation in yeast IRE1 then activates the transcription factor X-Box Binding Protein 1 (XBP-1), which in turn up-regulates ER chaperones to assist in the folding capacity of the ER as well as ERAD components to boost protein degradation. keywords: associated; cell; complex; control; degradation; endoplasmic; envelope; erad; ermani; expression; folding; glycoproteins; man; membrane; pathway; protein; quality; reticulum; stress; virus; viruses cache: cord-259237-aty0vrat.txt plain text: cord-259237-aty0vrat.txt item: #204 of 541 id: cord-259260-qcfgigga author: Ibrahim, Ibrahim M. title: GRP78: A cell's response to stress date: 2019-06-01 words: 6852 flesch: 47 summary: The interplay between GRP78 expression and Akt activation in human colon cancer cells under celecoxib treatment Pten null prostate tumorigenesis and AKT activation are blocked by targeted knockout of ER chaperone GRP78/BiP in prostate epithelium Impact of prognostic factors on survival rates in patients with ovarian carcinoma, Asian Pac The emerging role of anti-angiogenic therapy in ovarian cancer De-regulation of GRP stress protein expression in human breast cancer cell lines Involvement of GRP78 in the resistance of ovarian carcinoma cells to paclitaxel, Asian Pac Cisplatin in cancer therapy: molecular mechanisms of action Microtubules as a target for anticancer drugs Involvement of endoplasmic reticulum in paclitaxel-induced apoptosis Cancer statistics Targeting GRP78 to enhance melanoma cell death Rethinking ovarian cancer: recommendations for improving outcomes Chronic Exposure of Cisplatin Induces GRP78 Expression in Ovarian Cancer Kringle 5 of human plasminogen induces apoptosis of endothelial and tumor cells through surface-expressed glucose-regulated protein 78 Outcomes following resection of pancreatic cancer Pancreatic cancer Elevated GRP78 expression is associated with poor prognosis in patients with pancreatic cancer GRP78 promotes the invasion of pancreatic cancer cells by FAK and JNK Integrins in cell migration-the actin connection Curcumin suppresses metastasis via Sp-1, FAK inhibition, and Ecadherin upregulation in colorectal cancer Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries Glucose-regulated protein 78 (GRP78) regulates colon cancer metastasis through EMT biomarkers and the NRF-2/HO-1 pathway Overexpression of glucose-regulated protein 78 in colon cancer GRP78 knockdown enhances apoptosis via the down-regulation of oxidative stress and Akt pathway after epirubicin treatment in colon cancer DLD-1 cells Colon cancer cells expressing cell surface GRP78 as a marker for reduced tumorigenicity Cell-surface GRP78 facilitates colorectal cancer cell migration and invasion The survival rates of the GRP78 siRNA treated group is significantly lower than the other two groups which indicate the higher sensitivity of the treated group to paclitaxel treatment after the inhibition of GRP78 protein [97] . keywords: apoptosis; binding; cancer; cell; entry; expression; glucose; grp78; human; increase; infection; protein; receptor; role; stress; surface; virus cache: cord-259260-qcfgigga.txt plain text: cord-259260-qcfgigga.txt item: #205 of 541 id: cord-259412-l8uta7du author: Mattossovich, Rosanna title: O(6)-alkylguanine-DNA Alkyltransferases in Microbes Living on the Edge: From Stability to Applicability date: 2020-04-20 words: 7480 flesch: 37 summary: In modern biotechnology, engineered variants of AGTs are developed to be used as protein tags for the attachment of chemical ligands. Table 1 shows a brief comparison between some examples of protein tags and the SNAP-tag in several application fields. keywords: activity; agents; agts; alkylation; alkyltransferase; dna; enzymes; figure; fluorescent; helix; hmgmt; protein; reaction; repair; ssogt; structure; tag cache: cord-259412-l8uta7du.txt plain text: cord-259412-l8uta7du.txt item: #206 of 541 id: cord-259505-7hiss0j3 author: Kong, Qingming title: Proteomic analysis of purified coronavirus infectious bronchitis virus particles date: 2010-06-09 words: 6930 flesch: 38 summary: + signalling to membrane dynamics Intracellular and extracellular roles of S100 proteins S100-annexin complexes: some insights from structural studies Recruitment of Hsp70 chaperones: a crucial part of viral survival strategies Synthesis and quality control of viral membrane proteins Association of HSP70 with the adenovirus type 5 fiber protein in infected HEp-2 cells Association of heat shock protein 70 with enterovirus capsid precursor P1 in infected human cells Vaccinia virus infection induces a stress response that leads to association of Hsp70 with viral proteins Increased expression of Hsp70 and co-localization with nuclear protein in cells infected with the Hantaan virus Uncoating ATPase is a member of the 70 kilodalton family of stress proteins Hsp90 is required for the activity of a hepatitis B virus reverse transcriptase Two-dimensional blue native/SDS-PAGE analysis reveals heat shock protein chaperone machinery involved in hepatitis B virus production in HepG2.2.15 cells Selective inhibition of virus protein synthesis by prostaglandin A1: a translational block associated with HSP70 synthesis Evolutionary constraints on chaperone-mediated folding provide an antiviral approach refractory to development of drug resistance Molecular chaperone Hsp90 is important for vaccinia virus growth in cells Hsp90 inhibitors suppress HCV replication in replicon cells and humanized liver mice Hepatitis C virus RNA replication is regulated by FKBP8 and Hsp90 The cellular chaperone heat shock protein 90 facilitates Flock House virus RNA replication in Drosophila cells Identification of Hsp90 as a stimulatory host factor involved in influenza virus RNA synthesis Involvement of Hsp90 in assembly and nuclear import of influenza virus RNA polymerase subunits Antiviral activity and RNA polymerase degradation following Hsp90 inhibition in a range of negative strand viruses Herpes simplex virus type 1 DNA polymerase requires the mammalian chaperone hsp90 for proper localization to the nucleus Development and application of Hsp90 inhibitors Enhanced association of mutant triosephosphate isomerase to red cell membranes and to brain microtubules A glycolytic enzyme binding domain on tubulin Glycolytic enzyme-tubulin interactions: role of tubulin carboxy terminals Enolase, a cellular glycolytic enzyme, is required for efficient transcription of Sendai virus genome Specific interaction in vitro and in vivo of glyceraldehyde-3-phosphate dehydrogenase and LA protein with cis-acting RNAs of human parainfluenza virus type 3 Human hepatic glyceraldehyde-3-phosphate dehydrogenase binds to the poly(U) tract of the 3' noncoding region of hepatitis C virus genomic RNA Identification of glyceraldehyde-3-phosphate dehydrogenase as a cellular protein that binds to the hepatitis B virus posttranscriptional regulatory element Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) interaction with 3' ends of Japanese encephalitis virus RNA and colocalization with the viral NS5 protein Functional significance of the interaction of hepatitis A virus RNA with glyceraldehyde 3-phosphate dehydrogenase (GAPDH): opposing effects of GAPDH and polypyrimidine tract binding protein on internal ribosome entry site function Specific phosphorylated forms of glyceraldehyde 3-phosphate dehydrogenase associate with human parainfluenza virus type 3 and inhibit viral transcription in vitro Specific binding of ApoA-I, enhanced cholesterol efflux, and altered plasma membrane morphology in cells expressing ABC1 Apolipoprotein A-I activates Cdc42 signaling through the ABCA1 transporter Apolipoprotein A-I and its amphipathic helix peptide analogues inhibit human immunodeficiency virus-induced syncytium formation Immunoprecipitation, with an antiserum to ovalbumin, of protein NP from influenza A virus and of glycoprotein C from the herpes simplex type I virus Identification and characterization of tenp, a gene transiently expressed before overt cell differentiation during neurogenesis A modified silver staining protocol for visualization of proteins compatible with matrix-assisted laser desorption/ionization and electrospray ionization-mass spectrometry Proteomic analysis of purified coronavirus infectious bronchitis virus particles Proteome Science The authors declare that they have no competing interests. Coronavirus avian infectious bronchitis virus Envelope glycoprotein interactions in coronavirus assembly Characterization of the coronavirus M protein and nucleocapsid interaction in infected cells Coronavirus spike protein inhibits host cell translation by interaction with eIF3f Interaction of the coronavirus infectious bronchitis virus membrane protein with betaactin and its implication in virion assembly and budding Induction of apoptosis in murine coronavirusinfected 17Cl-1 cells Induction of apoptosis in murine coronavirus-infected cultured cells and demonstration of E protein as an apoptosis inducer Host and viral proteins in the virion of Kaposi's sarcoma-associated herpesvirus Virion proteins of Kaposi's sarcomaassociated herpesvirus A mass spectrometry-based proteomic approach to study Marek's Disease Virus gene expression Proteins of purified Epstein-Barr virus Identification of proteins in human cytomegalovirus (HCMV) particles: the HCMV proteome Identification of proteins associated with murine cytomegalovirus virions Vaccinia virus proteome: identification of proteins in vaccinia virus intracellular mature virion particles Krijnse Locker J: Identification of the major membrane and core proteins of vaccinia virus by two-dimensional electrophoresis Protein composition of the vaccinia virus mature virion Specific incorporation of heat shock protein 70 family members into primate lentiviral virions Cellular proteins bound to immunodeficiency viruses: implications for pathogenesis and vaccines Proteomic and biochemical analysis of purified human immunodeficiency virus type 1 produced from infected monocyte-derived macrophages Proteomic analysis of human immunodeficiency virus using liquid chromatography/tandem mass spectrometry effectively distinguishes specific incorporated host proteins Identification of host proteins associated with retroviral vector particles by proteomic analysis of highly purified vector preparations Immunochemical identification of viral and nonviral proteins of the respiratory syncytial virus virion Identification of cellular interaction partners of the influenza virus ribonucleoprotein complex and polymerase complex using proteomic-based approaches Cellular proteins in influenza virus particles Polypeptides of the surface projections and the ribonucleoprotein of avian infectious bronchitis virus Proteomic analysis of SARS associated coronavirus using two-dimensional liquid chromatography mass spectrometry and onedimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by mass spectroemtric analysis Plunder and stowaways: incorporation of cellular proteins by enveloped viruses Viral proteomics Interaction of epithelial ion channels with the actin-based cytoskeleton keywords: actin; analysis; annexin; bronchitis; gel; host; hsp90; ibv; particles; proteins; replication; virions; virus; viruses cache: cord-259505-7hiss0j3.txt plain text: cord-259505-7hiss0j3.txt item: #207 of 541 id: cord-259603-bh198xgl author: Snijder, E.J. title: The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing date: 2016-09-14 words: 24307 flesch: 38 summary: Whereas the poor replication fidelity generally restricts RNA virus genome sizes, it has been postulated that nidovirus genome expansion was enabled by the acquisition of specific replicative functions that counter the error rate of the RNA polymerase (Deng et al., 2014; Eckerle et al., 2010; Snijder et al., 2003) (discussed in more detail later). A recent structural study of the arterivirus nsp10-helicase (Deng et al., 2014) will be discussed in more detail later. keywords: activity; binding; bouvet et; chen et; complex; conserved; coronavirus; cov; covs; domain; et al; exon; fig; genome; helicase; interactions; lehmann et; mrna; mtase; nidovirus; nsp10; nsp8; protein; rdrp; replicase; replication; residues; rna; rna synthesis; role; sars; site; structure; studies; synthesis cache: cord-259603-bh198xgl.txt plain text: cord-259603-bh198xgl.txt item: #208 of 541 id: cord-260057-2m6jdvtc author: Pandey, Preeti title: Insights into the biased activity of dextromethorphan and haloperidol towards SARS-CoV-2 NSP6: in silico binding mechanistic analysis date: 2020-09-23 words: 7847 flesch: 48 summary: NSP6 protein is also involved in blocking ER-induced autophagosome/ autolysosome vesicle formation that plays a protective role in checking viral production inside host cells. FEL of NSP6 protein had multiple minima with small energy barriers in a single broad valley (basin). keywords: binding; complex; covid-19; dextromethorphan; docking; drug; energy; fig; figure; frustration; haloperidol; interactions; nsp6; protein; residues; simulation; structure cache: cord-260057-2m6jdvtc.txt plain text: cord-260057-2m6jdvtc.txt item: #209 of 541 id: cord-260225-bc1hr0fr author: Sirpilla, Olivia title: SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes date: 2020-07-20 words: 8938 flesch: 32 summary: Superfamily 1 Helicase Has RNA and DNA Duplex-Unwinding Activities with 5′-to-3′ Polarity Structure-Function Analysis of Severe Acute Respiratory Syndrome Coronavirus RNA Cap Guanine-N7-Methyltransferase Functional Screen Reveals SARS Coronavirus Nonstructural Protein Nsp14 as a Novel Cap N7 Methyltransferase Characterization of the Guanine-N7 Methyltransferase Activity of Coronavirus Nsp14 on Nucleotide GTP The Cellular RNA Helicase DDX1 Interacts with Coronavirus Nonstructural Protein 14 and Enhances Viral Replication Crystal Structure and Mechanistic Determinants of SARS Coronavirus Nonstructural Protein 15 Define an Endoribonuclease Family Crystal Structure of a Monomeric Form of Severe Acute Respiratory Syndrome Coronavirus Endonuclease Nsp15 Suggests a Role for Hexamerization as an Allosteric Switch Structural and Biochemical Characterization of Endoribonuclease Nsp15 Encoded by Middle East Respiratory Syndrome Coronavirus Binding of the Methyl Donor S-Adenosyl-l-Methionine to Middle East Respiratory Syndrome Coronavirus 2′-O-Methyltransferase nsp16 Promotes Recruitment of the Allosteric Activator nsp10 Coronavirus Nonstructural Protein 16 Is Group 2 Bat Coronaviruses A Two-Pronged Strategy to Suppress Host Protein Synthesis by SARS Coronavirus Nsp1 Protein Severe Acute Respiratory Syndrome Coronavirus Protein Nsp1 Is a Novel Eukaryotic Translation Inhibitor That Represses Multiple Steps of Translation Initiation Severe Acute Respiratory Syndrome Coronavirus Evades Antiviral Signaling: Role of Nsp1 and Rational Design of an Attenuated Strain Unique SARS-CoV Protein Nsp1: Bioinformatics, Biochemistry and Potential Effects on Virulence Coronavirus Nonstructural Protein 1: Common and Distinct Functions in the Regulation of Host and Viral Gene Expression Protein Structure and Sequence Reanalysis of 2019-NCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1 keywords: blast; cells; coronavirus; cov-2; decay; figure; human; immune; information; interaction; mrna; nonsense; nucleocapsid; protein; replication; respiratory; rna; sars; sequences; structure; syndrome cache: cord-260225-bc1hr0fr.txt plain text: cord-260225-bc1hr0fr.txt item: #210 of 541 id: cord-260345-ugd8kkor author: Giles, Ian G. title: A compendium of reviews in biochemistry and molecular biology published in the first half of 1992 date: 1992-12-31 words: 5346 flesch: 43 summary: Biomembrane 24, 99-110. anion channel; contact sites; selective channels; brain mitochondria; lot] channci; conductance; protein; Ca*'; mitoplasts;CatiOllS. L. and Herzfeld J. (1992) NMR studies of retinal proteins. position effect variegation; Drarophila; protein. keywords: acid; amino; analysis; binding; brain; cells; channel; delta; dna; expression; factor; gamma; gene; growth; heat; human; lipid; liver; membrane; messenger; muscle; plasma; protein; rat; receptor; regulation; review; rna; sequence; shock; system cache: cord-260345-ugd8kkor.txt plain text: cord-260345-ugd8kkor.txt item: #211 of 541 id: cord-260440-e63pgcir author: Dinjaski, Nina title: Smart polyhydroxyalkanoate nanobeads by protein based functionalization date: 2015-02-24 words: 9106 flesch: 25 summary: Due to its broad metabolic versatility and genetic plasticity, which allow a variety of renewable carbon sources to be used for PHA production, P. putida is one of the most prominent candidates for protein production. Bio-production of LA and chemical synthesis of PLA, PLGA Completely biosynthesized 4, 96, 131 No possibility of in vivo production and functionalization In vivo functionalization; One-step production of active agent and carrier, no need to produce, purify and conjugate active agent 26, 54, 131 Use of harsh chemicals for production Production from renewable sources 4, 132 Difficulty to scale-up Similar to bioprocesses for PHA production; Certain difficulties to scale-up 132, 133 Production cost comparable with conventional plastics like PET High cost of production; at least twice that of PLA 4, 131 High risk due to flammable and toxic solvents Low risk level 132 Production completed within days Production duration 1-2 weeks 132 Endotoxin contamination less probable due to synthetic origin Endotoxins can be efficiently removed; Use of Gram+ strains allows endotoxin free production 20 Properties Lower number of copolymers that can be produced; Only D-and L-lactic acids (LA) More than 150 monomeric building blocks for polymer design 4, 131 Approved by FDA and European Medicine Agency as drug delivery system Not approved by FDA as drug delivery system 131, 133, 3 Low drug loading No limitations regarding drug loading 32, 131, 133 Protection of drug from degradation Protection of drug from degradation 133, 3, 134 Biodegradable, biocompatible, low cytotoxicity Biodegradable, biocompatible, low cytotoxicity 30, 32, 96, 3 Material properties poor, could be adjusted by regulating D-and L-LA ratios Good thermomechanical properties from brittle, flexible to elastic, fully controllable, easy processability 4, 30, 96, 135 Degradation rate can be controlled Degradation rate can be controlled 130, 3 Drug delivery kinetics can be controlled Drug delivery kinetics can be controlled 32, 130 Easy particle size control Size of in vitro produced particles might be controlled, in vivo production limits control over particle size 30, 32, 34, 134 Application Wind variety of biomedical applications Applicable to a range of diseases 26, 133 Lowering pH at the site of implantation that might lead to sterile sepsis No detected side effect of PHA degradation 130, 131 Best chance for clinical application due to FDA approval. keywords: applications; bacteria; beads; binding; cell; coli; delivery; drug; endotoxin; fusion; gram; granules; nanoparticles; pha; polyhydroxyalkanoate; production; protein; putida; system; type; use; vivo cache: cord-260440-e63pgcir.txt plain text: cord-260440-e63pgcir.txt item: #212 of 541 id: cord-260708-l9w5jhsw author: Lasecka, Lidia title: The molecular biology of nairoviruses, an emerging group of tick-borne arboviruses date: 2013-12-11 words: 10711 flesch: 38 summary: This genus includes a number of human and livestock pathogens, as well as a collection of other viruses about which little is known, not even the host in which they naturally circulate. Region 1, based on sequence similarity with other viruses, appears to be responsible for capsnatching endonuclease activity [52, 136, 189] ; however, this needs to be confirmed experimentally. keywords: binding; cchfv; cells; congo; conserved; crimean; domain; fever; fever virus; hemorrhagic; human; isg15; nairoviruses; protein; replication; rna; sequence; ubiquitin; virus cache: cord-260708-l9w5jhsw.txt plain text: cord-260708-l9w5jhsw.txt item: #213 of 541 id: cord-260869-rym2ik0o author: Lemmermeyer, Tanja title: Characterization of monoclonal antibodies against feline coronavirus accessory protein 7b date: 2016-02-29 words: 6499 flesch: 51 summary: For further characterization including its unambiguous identification in FCoV-infected cells monoclonal antibodies against 7b protein were generated. As the two mAbs were shown previously to recognize FCoV 7b fusion proteins in Western blot experiments (Fig. 2) , we used this method to analyze cell lysates obtained at 24 h p.i. keywords: accessory; antibodies; cells; coronavirus; fcov; feline; fig; mabs; orf; protein; sequence cache: cord-260869-rym2ik0o.txt plain text: cord-260869-rym2ik0o.txt item: #214 of 541 id: cord-260949-w2xuf15h author: Galluzzi, Lorenzo title: Viral Control of Mitochondrial Apoptosis date: 2008-05-30 words: 11009 flesch: 36 summary: E1B 19-kilodalton protein with Bcl-2 in the inhibition of apoptosis in infected cells A cytomegalovirus-encoded mitochondria-localized inhibitor of apoptosis structurally unrelated to Bcl-2 Cytomegalovirus cell death suppressor vMIA blocks Bax-but not Bak-mediated apoptosis by binding and sequestering Bax at mitochondria Cytopathic effects of the cytomegalovirus-encoded apoptosis inhibitory protein vMIA Viral inhibition of inflammation: cowpox virus encodes an inhibitor of the interleukin-1 beta converting enzyme Vaccinia virus encodes a previously uncharacterized mitochondrial-associated inhibitor of apoptosis The vaccinia virus F1L protein interacts with the proapoptotic protein Bak and inhibits Bak activation The myxoma poxvirus protein, M11L, prevents apoptosis by direct interaction with the mitochondrial permeability transition pore Myxoma virus M11L blocks apoptosis through inhibition of conformational activation of Bax at the mitochondria Structure of M11L: A myxoma virus structural homolog of the apoptosis inhibitor, Bcl-2 A structural viral mimic of prosurvival Bcl-2: a pivotal role for sequestering proapoptotic Bax and Bak Functional and structural studies of the vaccinia virus virulence factor N1 reveal a Bcl-2-like anti-apoptotic protein Fowlpox virus encodes a Bcl-2 homologue that protects cells from apoptotic death through interaction with the proapoptotic protein Bak A novel Bcl-2-like inhibitor of apoptosis is encoded by the parapoxvirus ORF virus Epstein-Barr virus encodes a novel homolog of the bcl-2 oncogene that inhibits apoptosis and associates with Bax and Bak Epstein-Barr virus-coded BHRF1 protein, a viral homologue of Bcl-2, protects human B cells from programmed cell death Epstein-Barr virus BALF1 is a BCL-2-like antagonist of the herpesvirus antiapoptotic BCL-2 proteins BHRF1 of Epstein-Barr virus, which is homologous to human proto-oncogene bcl2, is not essential for transformation of B cells or for virus replication in vitro Ultrastructural localization of BHRF1: an Epstein-Barr virus gene product which has homology with bcl-2 Epstein-Barr virus BHRF1 protein protects against cell death induced by DNA-damaging agents and heterologous viral infection A Bcl-2 homolog encoded by Kaposi sarcoma-associated virus, human herpesvirus 8, inhibits apoptosis but does not heterodimerize with Bax or Bak Herpesvirus saimiri encodes a functional homolog of the human bcl-2 oncogene Solution structure of a Bcl-2 homolog from Kaposi sarcoma virus Identification of the in vivo role of a viral bcl-2 Antiapoptotic herpesvirus Bcl-2 homologs escape caspase-mediated conversion to proapoptotic proteins Characterization of an anti-apoptotic glycoprotein encoded by Kaposi's sarcomaassociated herpesvirus which resembles a spliced variant of human survivin African swine fever virus gene A179L, a viral homologue of bcl-2, protects cells from programmed cell death A cytomegalovirus-encoded inhibitor of apoptosis that suppresses caspase-8 activation Complex I binding by a virally encoded RNA regulates mitochondria-induced cell death Epstein-Barr virus (EBV) nuclear antigen leader protein (EBNA-LP) forms complexes with a cellular anti-apoptosis protein Bcl-2 or its EBV counterpart BHRF1 through HS1-associated protein X-1 The hepatitis C virus NS2 protein is an inhibitor of CIDE-B-induced apoptosis E2 of hepatitis C virus inhibits apoptosis Viral FLICE-inhibitory proteins (FLIPs) prevent apoptosis induced by death receptors Modulation of host gene expression by the K15 protein of Kaposi's sarcomaassociated herpesvirus KSHV vFLIP is essential for the survival of infected lymphoma cells The human herpes virus 8-encoded viral FLICE inhibitory protein protects against growth factor withdrawalinduced apoptosis via NF-kappa B activation Mechanism for removal of tumor necrosis factor receptor 1 from the cell surface by the adenovirus RIDalpha/beta complex The adenovirus E3/10.4K-14.5K proteins downmodulate the apoptosis receptor Fas/Apo-1 by inducing its internalization Prevention of apoptosis by a baculovirus gene during infection of insect cells Control of programmed cell death by the baculovirus genes p35 and iap Baculovirus p35 prevents developmentally programmed cell death and rescues a ced-9 mutant in the nematode Caenorhabditis elegans Inhibition of the Caenorhabditis elegans cell-death protease CED-3 by a CED-3 cleavage site in baculovirus p35 protein An apoptosis-inhibiting baculovirus gene with a zinc finger-like motif Cloning and expression of apoptosis inhibitory protein homologs that function to inhibit apoptosis and/or bind tumor necrosis factor receptor-associated factors Drosophila homologs of baculovirus inhibitor of apoptosis proteins function to block cell death IAPs block apoptotic events induced by caspase-8 and cytochrome c by direct inhibition of distinct caspases African swine fever virus IAP-like protein induces the activation of nuclear factor kappa B Nuclear and cytoplasmic survivin: molecular mechanism, prognostic, and therapeutic potential Large pores formed by the oligomerization of proapoptotic Bcl-2 proteins (e.g., Bax, Bak) and/or the voltage-dependent anion channel (VDAC) may promote selectively mitochondrial outer membrane permeabilization (MOMP). keywords: activation; antiapoptotic; apoptosis; bak; bax; bcl; cell; complex; death; domain; family; host; human; infection; interaction; mitochondrial; mmp; proteins; release; virus cache: cord-260949-w2xuf15h.txt plain text: cord-260949-w2xuf15h.txt item: #215 of 541 id: cord-261159-9pkg7mbh author: Regnier, Fred E. title: Chromatography of complex protein mixtures date: 1987-07-17 words: 10954 flesch: 50 summary: able, the equally important task of optimizing their operation for protein separation was undertaken. Although SEC is of limited resolving power in the purification of membrane proteins [ 121, it has sufficient resolution to be used in the selection of detergents for solubilization [ 91, optimization of detergent concentration [ 111, and quick estimation of the purity of a sample purified by other techniques [ 131. keywords: anion; chromatography; column; exchange; fractionation; hydrophobic; iec; igg; membrane; membrane proteins; mobile; phase; proteins; purification; resolution; ribosomal; rpc; sec; separation; use cache: cord-261159-9pkg7mbh.txt plain text: cord-261159-9pkg7mbh.txt item: #216 of 541 id: cord-261375-6fu3dzi9 author: Hoppe, Sebastian title: Microarray-based method for screening of immunogenic proteins from bacteria date: 2012-03-21 words: 6695 flesch: 47 summary: key: cord-261375-6fu3dzi9 authors: Hoppe, Sebastian; Bier, Frank F; von Nickisch-Rosenegk, Markus title: Microarray-based method for screening of immunogenic proteins from bacteria date: 2012-03-21 journal: J Nanobiotechnology DOI: 10.1186/1477-3155-10-12 sha: doc_id: 261375 cord_uid: 6fu3dzi9 BACKGROUND: Detection of immunogenic proteins remains an important task for life sciences as it nourishes the understanding of pathogenicity, illuminates new potential vaccine candidates and broadens the spectrum of biomarkers applicable in diagnostic tools. It enables us to screen for immunogenic proteins in a shorter time, with more samples and statistical reliability. keywords: blot; campylobacter; cells; expression; halotag; immunogenic; jejuni; kda; method; microarray; proteins; screening cache: cord-261375-6fu3dzi9.txt plain text: cord-261375-6fu3dzi9.txt item: #217 of 541 id: cord-261472-qcu73sdu author: Yao, Yong Xiu title: Cleavage and Serum Reactivity of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein date: 2004-07-01 words: 3859 flesch: 43 summary: To investigate SCoV S protein, full-length and individual domains of S protein were expressed on the surface of insect cells and were characterized for cleavability and reactivity with serum samples obtained from patients during the convalescent phase of SARS. No human CoV OC43 serum samples were available for the present study, so the reactivity of CoV OC43 with SARS S protein could not be assessed. keywords: cells; expression; patients; protein; reactivity; samples; sars; serum; use cache: cord-261472-qcu73sdu.txt plain text: cord-261472-qcu73sdu.txt item: #218 of 541 id: cord-261961-u4d0vvmq author: St-Germain, Jonathan R. title: A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research date: 2020-08-28 words: 2741 flesch: 25 summary: A number of virus protein interactions were also detected with components of the UFMylation system (DDRGK1, CDK5RAP3, UFL1 and UFSP2), which was recently shown to play a key role in ER-phagy 10 , highlighting interesting links between specific autophagy pathways and SARS-CoV-2. As a whole, the virus-host interactome is significantly enriched in proteins associated with the endoplasmic reticulum (ER)/nuclear, Golgi and plasma membranes, and ER-Golgi trafficking vesicles ( Even amongst those viral proteins that appear to localize exclusively to the ER-Golgi-PM endomembrane membrane system, specificity in virus-host interactomes was observed, likely reflecting preferences for interactions with different subsets of membrane proteins and/or localization to unique membrane lipid nanodomains. keywords: approaches; data; host; mass; membrane; proteins; proteomics; replication; sars; virus cache: cord-261961-u4d0vvmq.txt plain text: cord-261961-u4d0vvmq.txt item: #219 of 541 id: cord-262043-66qle52a author: Basit, Abdul title: Truncated human angiotensin converting enzyme 2; a potential inhibitor of SARS-CoV-2 spike glycoprotein and potent COVID-19 therapeutic agent date: 2020-05-20 words: 4883 flesch: 43 summary: Another recent study has reported a 23 amino acid based peptide, a homologue of ACE2 binding interface, which successfully bind with S protein with low nanomolar affinity . Based on the HADDOCK score and the docking RMSD value, the docked complexes of ACE2 and tACE2 with RBD were analyzed for binding affinity DG (kcal mol À1 ) and stability using protein binding energy prediction (PRODIGY) server (Xue et al., 2016) . keywords: ace2; affinity; binding; complex; cov-2; docking; protein; rbd; residues; sars cache: cord-262043-66qle52a.txt plain text: cord-262043-66qle52a.txt item: #220 of 541 id: cord-262119-s6hc7fxs author: Ostaszewski, Marek title: COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms date: 2020-10-27 words: 12366 flesch: 31 summary: COVID-19 pathways featured in the previous section cover mechanisms reported so far. By aligning our efforts, we strive to provide COVID-19 specific pathway models, synchronize content with similar resources and encourage discussion and feedback at every stage of the curation process. keywords: activation; acute; analysis; apoptosis; cell; community; coronavirus; cov-2; covid-19; covid-19 disease; data; diagrams; disease; disease map; expression; host; human; infection; interactions; interferon; map; mechanisms; modelling; models; pathway; patients; protein; response; sars; syndrome; systems; type cache: cord-262119-s6hc7fxs.txt plain text: cord-262119-s6hc7fxs.txt item: #221 of 541 id: cord-262268-gm99cadh author: Wang, Jingqiang title: Assessment of Immunoreactive Synthetic Peptides from the Structural Proteins of Severe Acute Respiratory Syndrome Coronavirus date: 2003-12-01 words: 4033 flesch: 44 summary: Conclusions: Five peptides from SARS structural proteins, especially two from the COOH terminus of the N protein, appear to be highly immunogenic and may be useful for serologic assays. The identification of these antigenic peptides contributes to the understanding of the immunogenicity and persistence of SARS coronavirus. keywords: antibodies; coronavirus; elisa; n385; patients; peptides; protein; sars; sera cache: cord-262268-gm99cadh.txt plain text: cord-262268-gm99cadh.txt item: #222 of 541 id: cord-262585-5vjqrnwh author: Hraber, Peter title: Resources to Discover and Use Short Linear Motifs in Viral Proteins date: 2019-08-16 words: 5671 flesch: 36 summary: A fusion intermediate gp41 immunogen elicits neutralizing antibodies to HIV-1 Immunosilencing a highly immunogenic protein trimerization domain Vaccination with soluble headless hemagglutinin protects mice from challenge with divergent influenza viruses Human chemokine MIP1a increases efficiency of targeted DNA fusion vaccines Dengue E protein domain III-based DNA immunisation induces strong antibody responses to all four viral serotypes Options for synthetic DNA order screening, revisited A transatlantic perspective on 20 emerging issues in biological engineering Biodefense in the Age of Synthetic Biology Short linear motifs -ex nihilo evolution of protein regulation Convergent evolution and mimicry of protein linear motifs in host-pathogen interactions The present and the future of motif-mediated protein-protein interactions A million peptide motifs for the molecular biologist Viral proteins can modulate immunity in several ways, which include: shutdown of host macromolecular synthesis, inhibiting antigen production or apoptosis, and interference with such processes as antigen presentation by MHC, natural killer (NK) cell function, antiviral cytokines, or interferon responses. keywords: discovery; domain; elm; function; host; immune; interactions; linear; motifs; protein; sequence; slims; viralzone; virus cache: cord-262585-5vjqrnwh.txt plain text: cord-262585-5vjqrnwh.txt item: #223 of 541 id: cord-262748-v4xue7ha author: Xu, Yongtao title: Identification of Peptide Inhibitors of Enveloped Viruses Using Support Vector Machine date: 2015-12-04 words: 4645 flesch: 34 summary: Although the exact fusion mechanism remains elusive, it was suggested that the three classes of viral fusion proteins share a similar mechanism of membrane fusion. Although the exact fusion mechanism remains elusive and the three classes of viral fusion proteins exhibit distinct structural folds, they may share a similar mechanism of membrane fusion [3] . keywords: acid; activities; amino; fusion; inhibitors; model; peptides; protein; svm; virus cache: cord-262748-v4xue7ha.txt plain text: cord-262748-v4xue7ha.txt item: #224 of 541 id: cord-262904-0b0ljjq1 author: Lon, Jerome Rumdon title: Prediction and evolution of B cell epitopes of surface protein in SARS-CoV-2 date: 2020-10-29 words: 5009 flesch: 48 summary: Coronavirus 2019-nCoV: a brief perspective from the front line The reproductive number of COVID-19 is higher compared to SARS coronavirus Recent advances in B-cell epitope prediction methods Bioinformatics resources and tools for conformational B-cell epitope prediction Comprehensive evolution and molecular characteristics of a large number of SARS-CoV-2 genomes reveal its epidemic trends RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy Characterization of the SARS-CoV-2 S protein: biophysical, biochemical, structural, and antigenic analysis The Proteomics Protocols Handbook Sequence and structure-based prediction of eukaryotic protein phosphorylation sites SWISS-MODEL: homology modelling of protein structures and complexes PROCHECK: a program to check the stereochemical quality of protein structures SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling SEPPA 3.0-enhanced spatial epitope prediction enabling glycoprotein antigens ElliPro: a new structure-based tool for the prediction of antibody epitopes Prediction of chain flexibility in proteins Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide The antigenic index: a novel algorithm for predicting antigenic determinants convenient online submission • thorough peer review by experienced researchers in your field • rapid publication on acceptance • support for research data, including large and complex data types • gold Open Access which fosters wider collaboration and increased citations maximum visibility for your research: over 100M website views per year • At BMC, research is always in progress. According to the prediction, there was an outside-in transmembrane helix in 23 residues from position 1214th to position 1236th at the N-terminal of the S protein, which was almost consistent with the study indicating that the transmembrane domain of S protein was at the position from 1213 to 1237th [24] , an inside-out transmembrane helix in 23 residues from position 12th to position 34th at the N-terminal of the E protein. keywords: cell; cov-2; e protein; epitopes; protein; s protein; sars; structure cache: cord-262904-0b0ljjq1.txt plain text: cord-262904-0b0ljjq1.txt item: #225 of 541 id: cord-263315-g7os15m1 author: Martins-da-Silva, Andrea title: Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response date: 2018-01-18 words: 7015 flesch: 41 summary: When mRNA levels changed at 12 or 24 h post transfection (either by up-or down-regulation), we detected a corresponding change in secreted protein levels 12 or 24 h after the mRNA level changes. Based on the data presented in Figure 3A , we observed that in the majority of the molecules (six out of seven) there was a correlated change of secreted protein levels 12 h to 24 h after changes in mRNA levels. keywords: antiviral; cells; change; dsrna; expression; factor; fold; infection; insect; interferon; levels; ll5; mrna; non; protein; response; secretion; transfection; virus cache: cord-263315-g7os15m1.txt plain text: cord-263315-g7os15m1.txt item: #226 of 541 id: cord-264031-0y7xbgun author: Wierbowski, Shayne D. title: A 3D Structural Interactome to Explore the Impact of Evolutionary Divergence, Population Variation, and Small-molecule Drugs on SARS-CoV-2-Human Protein-Protein Interactions date: 2020-10-13 words: 5081 flesch: 22 summary: Our finding that disease mutations and viral proteins 197 affect human proteins at distinct sites is consistent with a two-hit hypothesis of comorbidities whereby 198 proteins whose function is already affected by genetic background may be further compromised by viral 199 infection. Disruption of native protein-protein interactions is one mechanism of disease 189 pathology, and disease mutations are known to be enriched along protein interfaces 70, 71 . keywords: cov-2; disease; human; interaction; interactome; interface; mutations; population; protein; sars; structural; variants; viral cache: cord-264031-0y7xbgun.txt plain text: cord-264031-0y7xbgun.txt item: #227 of 541 id: cord-264392-he1vekrt author: Lambeth, L. S. title: Complete genome sequence of Nariva virus, a rodent paramyxovirus date: 2008-12-23 words: 4373 flesch: 48 summary: This was then followed by PCR to fill in the 'gaps' using specific primers designed from NarPV Nariva virus genome 201 sequences obtained from the cDNA subtraction or degenerate primers designed using highly conserved consensus sequences of known paramyxoviruses in the subfamily Paramyxovirinae. c Alignment of the V-specific protein sequences NarPV F protein, SGRNK, is dibasic and does not conform to the consensus sequence motif for cleavage by furin, R-X-K/R-R keywords: cdna; genome; members; mospv; narpv; paramyxovirinae; paramyxoviruses; pcr; protein; sequence; subfamily; virus cache: cord-264392-he1vekrt.txt plain text: cord-264392-he1vekrt.txt item: #228 of 541 id: cord-264996-og3sg0qw author: Howell, Gareth J. title: Cell Biology of Membrane Trafficking in Human Disease date: 2006-09-17 words: 20376 flesch: 29 summary: Sorting of proteins from donor to target membranes involves the recognition of cytoplasmic sequences in membrane proteins by clathrin-associated AP complexes. However, their exact role in the internalization of membrane proteins and soluble protein ligands is controversial. keywords: actin; apparatus; binding; caveolae; caveolin-1; cell; clathrin; complex; copii; degradation; disease; endocytosis; endoplasmic; endosome; et al; expression; factor; formation; function; fusion; gene; golgi; intracellular; lysosomal; lysosomes; membrane; mutations; novel; number; pathway; patients; plasma; plasma membrane; protein; receptor; reticulum; role; secretory; snare; sorting; specific; syndrome; target; tgn; transport; traycking; type; vesicles; virus cache: cord-264996-og3sg0qw.txt plain text: cord-264996-og3sg0qw.txt item: #229 of 541 id: cord-265087-g4k6pc82 author: Munteanu, Cristian Robert title: Natural/random protein classification models based on star network topological indices date: 2008-10-21 words: 3892 flesch: 30 summary: Novel 2D maps and coupling numbers for protein sequences. þ 4:8Sh0 þ 254:9H þ 1860:2W À 1931:0S þ 39:4J À 139:2X0 À 73:0X3 þ 146:7X4 À 159:3X5 À 6:6Tr4e þ 7:1X2e, where N is the number of studied protein sequences (Nat+Rnd), R c is the canonical regression coefficient, U is the Wilk's statistics, F is the Fisher's statistics and p is the p-level (probability of error). keywords: acid; amino; et al; graph; model; protein; random; sequences; star; tis cache: cord-265087-g4k6pc82.txt plain text: cord-265087-g4k6pc82.txt item: #230 of 541 id: cord-265642-7mu530yp author: Syomin, B. V. title: Virus-Like Particles as an Instrument of Vaccine Production date: 2019-06-17 words: 7110 flesch: 38 summary: One of the most important properties of VLPs is mimicking virus particles and the consequent ability to induce a strong immune response to the antigen which they demonstrate irrespective of the source of the monomers which multimerize into VLPs, these being either insect viruses, in particular the gypsy virus THE PRODUCT RANGE A number of VLP vaccines are available on pharmaceutical markets in many countries. keywords: antigen; cells; development; disease; example; expression; hepatitis; human; particles; production; protein; response; surface; system; vaccines; virus; vlps cache: cord-265642-7mu530yp.txt plain text: cord-265642-7mu530yp.txt item: #231 of 541 id: cord-265887-g5zhoyo9 author: Mukherjee, Shruti title: Host-membrane interacting interface of the SARS coronavirus envelope protein: Immense functional potential of C-terminal domain date: 2020-08-11 words: 9093 flesch: 30 summary: Analysis of constructed E gene mutants of mouse hepatitis virus confirms a pivotal role for E protein in coronavirus assembly Coronavirus pseudoparticles formed with recombinant M and E proteins induce alpha interferon synthesis by leukocytes Membrane Lipid Composition: Effect on Membrane and Organelle Structure, Function and Compartmentalization and Therapeutic Avenues Protein aggregation in a membrane environment Protein aggregation and membrane lipid modifications under lactic acid stress in wild type and OPI1 deleted Saccharomyces cerevisiae strains Biological phase separation: cell biology meets biophysics Membrane lipids: where they are and how they behave SARS coronavirus E protein in phospholipid bilayers: an x-ray study Membrane topology and insertion of membrane proteins: search for topogenic signals Another triple-spanning envelope protein among intracellularly budding RNA viruses: the torovirus E protein Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding Identifying SARS-CoV-2 Coevolution in defining the functional specificity Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes Improving the accuracy of transmembrane protein topology prediction using evolutionary information Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server Analysis of membrane and surface protein sequences with the hydrophobic moment plot Trends in substitution models of molecular evolution The rapid generation of mutation data matrices from protein sequences MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms Membrane topology of coronavirus E protein Characterization of the coronavirus mouse hepatitis virus strain A59 small membrane protein E Two deletion variants of Middle East respiratory syndrome coronavirus found in a patient with characteristic symptoms Coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus Coronavirus virulence genes with main focus on SARS-CoV envelope gene Genome-wide analysis of protein-protein interactions and involvement of viral proteins in SARS-CoV replication Hexamethylene amiloride blocks E protein ion channels and inhibits coronavirus replication 2020. (44) The absence of a canonical cleaved signal sequence suggests equal likelihood for the protein to be a type II (with its C-terminal targeted to the ER lumen) or type III (with its N-terminal targeted to the ER lumen) membrane protein. keywords: cell; coronavirus; cov; cov e; e protein; envelope protein; function; golgi; host; ion; lipid; membrane; membrane protein; peptide; proteins; sars; sequence; studies; terminal cache: cord-265887-g5zhoyo9.txt plain text: cord-265887-g5zhoyo9.txt item: #232 of 541 id: cord-266147-s8rxzm0t author: Burnouf, Thierry title: Modern Plasma Fractionation date: 2007-03-28 words: 8837 flesch: 35 summary: An updated list of the major therapeutic applications of plasma protein products can be found elsewhere. Modern plasma product production technology remains largely based on the ethanol fractionation process, but much has evolved in the last few years to improve product purity, to enhance the recovery of immunoglobulin G, and to isolate new plasma proteins, such as α1-protease inhibitor, von Willebrand factor, and protein C. Because of the human origin of the starting material and the pooling of 10 000 to 50 000 donations required for industrial processing, the major risk associated to plasma products is the transmission of blood-borne infectious agents. keywords: blood; chromatography; factor; fractionation; fviii; heat; igg; inactivation; plasma; process; production; products; protein; removal; safety; steps; treatment; viruses cache: cord-266147-s8rxzm0t.txt plain text: cord-266147-s8rxzm0t.txt item: #233 of 541 id: cord-266444-rw94yls8 author: Dominguez Andres, Ana title: SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells date: 2020-08-19 words: 5655 flesch: 34 summary: Thus, to maximize the discovery of ORF9c dysregulated proteins, results from both technologies were combined. Together with the observations on cellular immune pathways, this association with 16 the UBP suggested that ORF9c induces changes in UBP components that alter the stability of cellular proteins implicated in cytokine signaling, antigen presentation, innate immunity, and the cell cycle. keywords: analysis; cells; changes; cov-2; data; fig; immune; mg132; orf9c; pathways; proteasome; proteins; sars; signaling; table cache: cord-266444-rw94yls8.txt plain text: cord-266444-rw94yls8.txt item: #234 of 541 id: cord-266481-9afb0yvt author: Naskalska, Antonina title: Membrane Protein of Human Coronavirus NL63 Is Responsible for Interaction with the Adhesion Receptor date: 2019-07-17 words: 5691 flesch: 42 summary: Fields virology A structural view of coronavirus-receptor interactions Structure, function, and evolution of coronavirus spike proteins Mechanisms of coronavirus cell entry mediated by the viral spike protein Point mutations in the S protein connect the sialic acid binding activity with the enteropathogenicity of transmissible gastroenteritis coronavirus Crystal structure of bovine coronavirus spike protein lectin domain Mapping of the receptor-binding domain and amino acids critical for attachment in the spike protein of avian coronavirus infectious bronchitis virus Human coronavirus HKU1 spike protein uses O-acetylated sialic acid as an attachment receptor determinant and employs hemagglutinin-esterase protein as a receptordestroying enzyme Coronavirus spike proteins in viral entry and pathogenesis Identification of a receptor-binding domain of the spike glycoprotein of human coronavirus HCoV-229E Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides Cooperative involvement of the S1 and S2 subunits of the murine coronavirus spike protein in receptor binding and extended host range Core structure of S2 from the human coronavirus NL63 spike glycoprotein Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor Characterization of the spike protein of human coronavirus NL63 in receptor binding and pseudotype virus entry Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy Interaction between the spike protein of human coronavirus NL63 and its cellular receptor ACE2 Differential downregulation of ACE2 by the spike proteins of HCoV-NL63 Adhesion to Cells Journal of Virology severe acute respiratory syndrome coronavirus and human coronavirus NL63 Identification of residues in the receptor-binding domain (RBD) of the spike protein of human coronavirus NL63 that are critical for the RBD-ACE2 receptor interaction Cell surface heparan sulfate and its roles in assisting viral infections Molecular modeling of proteinglycosaminoglycan interactions Mapping of the coronavirus membrane protein domains involved in interaction with the spike protein A conserved domain in the coronavirus membrane protein tail is important for virus assembly A single tyrosine in the severe acute respiratory syndrome coronavirus membrane protein cytoplasmic tail is important for efficient interaction with spike protein Identifying SARS-CoV membrane protein amino acid residues linked to virus-like particle assembly A structural analysis of M protein in coronavirus assembly and morphology Analyses of coronavirus assembly interactions with interspecies membrane and nucleocapsid protein chimeras Organization of two transmissible gastroenteritis coronavirus membrane protein topologies within the virion and core Membrane protein molecules of transmissible gastroenteritis coronavirus also expose the carboxy-terminal region on the external surface of the virion Murine coronavirus with an extended host range uses heparan sulfate as an entry receptor Cleavage of group 1 coronavirus spike proteins: how furin cleavage is traded off against heparan sulfate binding upon cell culture adaptation Heparan sulfate is a selective attachment factor for the avian coronavirus infectious bronchitis virus Beaudette Attachment of mouse hepatitis virus to O-acetylated sialic acid is mediated by hemagglutinin-esterase and not by the spike protein Structure, function and evolution of the hemagglutininesterase proteins of corona-and toroviruses The acetyl-esterase activity of the hemagglutinin-esterase protein of human coronavirus OC43 strongly enhances the production of infectious virus Viral entry mechanisms: cellular and viral mediators of herpes simplex virus entry Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin Evaluation of modified vaccinia virus Ankara based recombinant SARS vaccine in ferrets Ezrin interacts with the SARS coronavirus spike protein and restrains infection at the entry stage SARS CoV subunit vaccine: antibody-mediated neutralisation and enhancement Fiji: an opensource platform for biological-image analysis Entry of human coronavirus NL63 into the cell Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes Supramolecular architecture of the coronavirus particle Using viruslike particles lacking the spike (S) protein, we demonstrate that binding to the cell is not S protein dependent. keywords: binding; cells; coronavirus; entry; hcov; human; interaction; membrane; nl63; poland; protein; receptor; spike; vlps cache: cord-266481-9afb0yvt.txt plain text: cord-266481-9afb0yvt.txt item: #235 of 541 id: cord-266543-ng9zr299 author: Klebe, Gerhard title: Virtual ligand screening: strategies, perspectives and limitations date: 2006-06-20 words: 11104 flesch: 38 summary: Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model Structure-based drug discovery using GPCR homology modeling: successful virtual screening for antagonists of the alpha1A adrenergic receptor Docking ligands onto binding site representations derived from proteins built by homology modelling Ligand-supported homology modelling of protein binding sites using knowledge-based potentials Implications of protein flexibility for drug discovery Molecular docking to ensembles of protein structures Ligand docking to proteins with discrete side-chain flexibility FlexE: efficient molecular docking considering protein structure variations Testing a flexible-receptor docking algorithm in a model binding site Accommodating protein flexibility in computational drug design Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as a test case Probing flexibility and 'induced-fit' phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations Unveiling the full potential of flexible receptor docking using multiple crystallographic structures Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes Expect the unexpected or caveat for drug designers: multiple structure determinations using aldose reductase crystals treated under varying conditions pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design Understanding protein-ligand interactions: the price of protein flexibility ZZ Made EZ: influence of inhibitor configuration on enzyme selectivity Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition Approaches to the description and prediction of binding affinity of small-molecule ligands to macromolecular receptors Reconstructing the binding site of factor Xa in trypsin reveals ligand-induced structural plasticity Predicting binding modes, binding affinities and 'hot spots' for protein-ligand complexes using a knowledge-based scoring function A computational procedure for determining energetically favorable binding sites on biologically important macromolecules SuperStar: a knowledge based approach for identifying interaction sites in proteins Knowledge-based scoring function to predict proteinligand interactions Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions Utilising structural knowledge in drug design strategies: applications using Relibase ZINC-a free database of commercially available compounds for virtual screening The art and practice of structure-based drug design: a molecular modelling perspective Fragment-based drug discovery Fragment-based lead discovery Current trends in lead discovery: are we looking for the appropriate properties? Consideration of such criteria will drive docking solutions especially into regions either frequently trapped by other bound ligands or featured by complementary analytical tools as being particularly relevant for binding. keywords: analysis; binding; compounds; crystal; data; discovery; docking; drug; ligand; molecules; pocket; protein; scoring; screening; site; structure; target; water cache: cord-266543-ng9zr299.txt plain text: cord-266543-ng9zr299.txt item: #236 of 541 id: cord-266617-z8uecyl6 author: Pavesi, Angelo title: Asymmetric evolution in viral overlapping genes is a source of selective protein adaptation date: 2019-04-03 words: 6694 flesch: 41 summary: Overlapping genes can undergo “symmetric evolution” (similar selection pressures on the two proteins) or “asymmetric evolution” (significantly different selection pressures on the two proteins). These findings suggest that overlapping genes, besides to increase the coding ability of viruses, are also a source of selective protein adaptation. keywords: acid; amino; asymmetric; et al; evolution; frame; genes; overlapping; protein; substitutions cache: cord-266617-z8uecyl6.txt plain text: cord-266617-z8uecyl6.txt item: #237 of 541 id: cord-266977-5swwc6kr author: Secker, Thomas.J. title: Journal of Hospital Infection A cold water, ultrasonic activated stream efficiently removes proteins and prion-associated amyloid from surgical stainless steel date: 2020-09-19 words: 4564 flesch: 30 summary: Sterile Service Department decontamination procedures for surgical instruments struggle to demonstrate efficient removal of the hardiest infectious contaminants, such as prion proteins. instruments struggle to demonstrate efficient removal of the hardiest infectious contaminants, 23 such as prion proteins. keywords: amyloid; brain; cleaning; decontamination; prion; protein; removal; stainless; steel; surfaces; uas cache: cord-266977-5swwc6kr.txt plain text: cord-266977-5swwc6kr.txt item: #238 of 541 id: cord-267475-6f4h3cck author: Kozak, Marilyn title: Pushing the limits of the scanning mechanism for initiation of translation date: 2002-10-16 words: 24556 flesch: 32 summary: The upstream AUG codons often create small ORFs (upORFs) which are indeed translated, as shown by detecting the encoded peptide (Hackett et al., 1986; Raney et al., 2000; Wang and Wessler, 2001) or by fusing a reporter gene to the upORF (Abastado et al., 1991; Donzé et al., 1995; Liu et al., 1999; Steel et al., 1996; Tanaka et al., 2001; Xu et al., 2001) . The position effect, indicative of scanning, is seen when a mutation creates an AUG codon upstream from the normal start codon and translation shifts to the upstream site (Bergenhem et al., 1992; Cai et al., 1992; Gross et al., 1998; Harington et al., 1994; Liu et al., 1999; Lock et al., 1991; Mével-Ninio et al., 1996; Muralidhar et al., 1994; Wada et al., 1995) . keywords: alternative; aug; aug codon; aug start; cases; cells; codon; context; control; downstream; et al; expression; factor; fig; frame; gene; human; initiation; internal; isoforms; kozak; leader; leaky; leaky scanning; mechanism; mrna; position; production; promoter; protein; reading; region; regulation; ribosomes; scanning; sequence; site; splicing; start; start codon; structure; transcripts; translation; translation initiation; uporf; upstream; virus cache: cord-267475-6f4h3cck.txt plain text: cord-267475-6f4h3cck.txt item: #239 of 541 id: cord-268239-neb6xxlf author: Illiano, Anna title: Protein Glycosylation Investigated by Mass Spectrometry: An Overview date: 2020-08-28 words: 9557 flesch: 26 summary: Preliminary Insights Matrix-assisted laser desorption/ionisation mass spectrometry of oligosaccharides and glycoconjugates Site Heterogeneity and Structural Diversity Determined by Combined Lectin Affinity Chromatography/IMS/CID/MS Techniques Applications of ion mobility mass spectrometry for high throughput, high resolution glycan analysis Resolving and assigning N-linked glycan structural isomers from ovalbumin by IMS-MS Profiling of Human Serum Glycans Associated with Liver Cancer and Cirrhosis by IMS-MS Structural glycomic analyses at high sensitivity: A decade of progress A systematic approach to protein glycosylation analysis: A path through the maze High-throughput glycomics: Optimization of sample preparation High-throughput Serum N-Glycomics: Method Comparison and Application to Study Rheumatoid Arthritis and Pregnancy-associated Changes A novel, ultrasensitive approach for quantitative carbohydrate composition and linkage analysis using LC-ESI ion trap tandem mass spectrometry Automated, high-throughput serum glycoprofiling platform A Robust and Versatile Automated Glycoanalytical Technology for Serum Antibodies and Acute Phase Proteins: Ovarian Cancer Case Study Improved and semi-automated reductive β-elimination workflow for higher throughput protein O-glycosylation analysis Quantitative profiling of glycans and glycopeptides: An informatics' perspective A Review of Software Applications and Databases for the Interpretation of Glycopeptide Data A review of methods for interpretation of glycopeptide tandem mass spectral data Recent advances in glycoinformatic platforms for glycomics and glycoproteomics Indeed, abnormalities in protein glycosylation are correlated with several disease states such as cancer, inflammatory diseases, and congenial disorders. keywords: analysis; cancer; cell; figure; fragmentation; glycans; glycopeptides; glycoproteins; glycosylation; hcd; human; ions; mass; method; mrm; protein; ptms; quantification; serum; spectrometry; structures; type cache: cord-268239-neb6xxlf.txt plain text: cord-268239-neb6xxlf.txt item: #240 of 541 id: cord-268326-sbz3uk5h author: Bonam, Srinivasa Reddy title: Lysosomes as a therapeutic target date: 2019-09-02 words: 17914 flesch: 25 summary: There is an obvious requirement for safety, to ensure that a drug used as a lysosome modu lator for a particular type of lysosomal disease does not increase vulnerability to another disease. Intracellular distribution patterns of enzymes in rat-liver tissue Lysosomal membrane permeabilization and cell death Signals from the lysosome: a control centre for cellular clearance and energy metabolism This article is an encyclopaedia of lysosomal physiology The lysosome as a regulatory hub Lysosome positioning coordinates mTORC1 activity and autophagy The coming of age of chaperone-mediated autophagy Lysosome biogenesis and lysosomal membrane proteins: trafficking meets function Lysosomal disorders: from storage to cellular damage Enzyme replacement therapy for lysosomal diseases: lessons from 20 years of experience and remaining challenges Chemical modulators of autophagy as biological probes and potential therapeutics Pharmacological regulators of autophagy and their link with modulators of lupus disease Mechanism and medical implications of mammalian autophagy Autophagy: a new concept in autoimmunity regulation and a novel therapeutic option Critical functions of the lysosome in cancer biology The lysosome as a cellular centre for signalling, metabolism and quality control CLN8 is an endoplasmic reticulum cargo receptor that regulates lysosome biogenesis The mannose 6-phosphate receptor and the biogenesis of lysosomes Role of LIMP-2 in the intracellular trafficking of β-glucosidase in different human cellular models Lysosomal acidification mechanisms Vacuolar ATPases: rotary proton pumps in physiology and pathophysiology A TRP channel in the lysosome regulates large particle phagocytosis via focal exocytosis MCOLN1 is a ROS sensor in lysosomes that regulates autophagy Lysosomal storage diseases: from pathophysiology to therapy keywords: accumulation; activity; autoimmune; autophagy; cathepsin; cells; chaperone; cma; degradation; disease; disorders; dysfunction; enzyme; example; expression; function; gaucher; inflammatory; inhibitor; lsds; lupus; lysosomal; lysosomes; membrane; mice; molecules; pathways; patients; peptide; potential; processes; protein; regulation; role; storage; table; target; tfeb; type cache: cord-268326-sbz3uk5h.txt plain text: cord-268326-sbz3uk5h.txt item: #241 of 541 id: cord-268416-8hw80qx8 author: Grunewald, Matthew E. title: The coronavirus nucleocapsid protein is ADP-ribosylated date: 2018-04-01 words: 4804 flesch: 40 summary: Specifically, MHV N protein at amino acid S197 is phosphorylated in infected cells, but this modification is absent on N protein in virions (Wu et al., 2014) . ADP-ribosylation of N protein was also observed in cells exogenously expressing N protein by transduction using Venezuelan equine encephalitis virus replicon particles (VRPs). keywords: adp; adpr; cells; cov; et al; infection; mhv; protein; ribosylation; virus cache: cord-268416-8hw80qx8.txt plain text: cord-268416-8hw80qx8.txt item: #242 of 541 id: cord-269011-230p8rsf author: de Haan, Cornelis A.M. title: Molecular Interactions in the Assembly of Coronaviruses date: 2005-08-31 words: 22995 flesch: 36 summary: MHV M proteins carry a well-conserved SS(X)TTXXP sequence at their extreme amino terminus. As the expression of these enzymes varies in cells, conservation of the SS(X)TTXXP motif in MHV M protein may serve to increase opportunities for the protein to become glycosylated in different cell types. keywords: amino; assembly; binding; budding; cells; coronavirus; domain; envelope; et al; fusion; golgi; haan et; hepatitis; interaction; membrane; membrane protein; mhv; mouse; n protein; nucleocapsid; particles; protein; receptor; rna; s protein; sequence; spike; spike protein; terminal; tgev; virions; viruses cache: cord-269011-230p8rsf.txt plain text: cord-269011-230p8rsf.txt item: #243 of 541 id: cord-269531-7gy4epzo author: Kumar, Pankaj title: Proteomic analysis of purified turkey adenovirus 3 virions date: 2015-07-09 words: 4336 flesch: 33 summary: Using MS based approaches, a number of host proteins have been reported to be incorporated into RNA viruses (human immunodeficiency virus-1 Non availability of turkey host protein specific antisera made it difficult to verify the packaging of host proteins in TAdV-3 virions. keywords: adenovirus; analysis; cscl; host; proteins; replication; table; tadv-3; turkey; virions; virus cache: cord-269531-7gy4epzo.txt plain text: cord-269531-7gy4epzo.txt item: #244 of 541 id: cord-270273-a4iu9qg6 author: Ruiz, Federico M. title: Chicken GRIFIN: Structural characterization in crystals and in solution date: 2017-12-15 words: 8292 flesch: 42 summary: In parallel, protein solutions without lactose were kept in equilibration buffer without deuteration and quenched in the same way, this undeurated control sample used for identification of the peptic peptides. Deamidation within peptide 58e70 (after seven days at 25 C/40 C reaching 9.2%/13.5% [19] ) may also have an impact on the protein's lectin activity, if not protected by bound ligand. keywords: analysis; binding; chicken; crystal; fig; galectin; grifin; human; lactose; lens; ligand; presence; protein; sequence; site; solution; structure cache: cord-270273-a4iu9qg6.txt plain text: cord-270273-a4iu9qg6.txt item: #245 of 541 id: cord-270514-36k9xo7f author: van der Woude, Roosmarijn title: Drivers of recombinant soluble influenza A virus hemagglutinin and neuraminidase expression in mammalian cells date: 2020-08-14 words: 3977 flesch: 40 summary: Here we report our observations gleaned over a decade of recombinant HA and NA protein expression in mammalian cells. HA and NA protein expression and purification was confirmed by western blotting using a StrepMAB-HRP classic antibody. keywords: expression; gcn4; influenza; proteins; recombinant; sfgfp; virus cache: cord-270514-36k9xo7f.txt plain text: cord-270514-36k9xo7f.txt item: #246 of 541 id: cord-270587-k56fze59 author: Scherbinina, Sofya I. title: Three-Dimensional Structures of Carbohydrates and Where to Find Them date: 2020-10-18 words: 12396 flesch: 26 summary: The majority of existing repositories for carbohydrate 3D structures offer open-access data via web interface. The majority of existing repositories for carbohydrate 3D structures offer open-access data via web interface. keywords: analysis; bank; carbohydrate; complexes; data; database; dynamics; energy; field; figure; force; glycan; glycoproteins; interactions; modeling; molecular; nmr; oligosaccharides; pdb; protein; simulations; software; structure; table; tools; visualization; web cache: cord-270587-k56fze59.txt plain text: cord-270587-k56fze59.txt item: #247 of 541 id: cord-270594-62xotol3 author: He, Lei title: Identification and characterization of vp7 gene in Bombyx mori cytoplasmic polyhedrosis virus date: 2017-09-05 words: 4463 flesch: 48 summary: To prepare polyclonal antibody against VP7 proteins of BmCPV, the cDNA with primers listed in Table 1 was amplified with PCR. VP7 recombinant protein was purified from the transfected cells. keywords: antibody; bmcpv; bmn; cells; expression; fig; gene; genome; proteins; segments; silkworm; virus; vp7 cache: cord-270594-62xotol3.txt plain text: cord-270594-62xotol3.txt item: #248 of 541 id: cord-271091-ffn59sgf author: Galao, Rui P title: Saccharomyces cerevisiae: a versatile eukaryotic system in virology date: 2007-10-10 words: 6551 flesch: 35 summary: The strategy to use yeast cells for vaccination could also be used to elicit protective immune responses against human pathogenic yeasts. The amino terminal deletion mutants of hepatitis C virus nonstructural protein NS5A function as transcriptional activators in yeast Hepatitis C virus nonstructural protein 5A contains potential transcriptional activator domains Characterization of the nuclear localization signal and subcellular distribution of hepatitis C virus nonstructural protein NS5A Hepatitis C virus nonstructural region 5A protein is a potent transcriptional activator The hepatitis C virus core protein interacts with NS5A and activates its caspase-mediated proteolytic cleavage Use of an in vitro model and yeast two-hybrid system to investigate the pathogenesis of hepatitis C Cleavage of hepatitis C virus nonstructural protein 5A by a caspase-like protease(s) in mammalian cells Hepatitis C virus core protein: an update on its molecular biology, cellular functions and clinical implications The core protein of hepatitis C virus is imported into the nucleus by transport receptor Kap123p but inhibits Kap121p-dependent nuclear import of yeast AP1-like transcription factor in yeast cells Differential subcellular localization of hepatitis C virus core gene products. keywords: cell; cerevisiae; drug; factors; gene; hcv; hepatitis; host; protein; replication; rna; studies; virus; viruses; yeast cache: cord-271091-ffn59sgf.txt plain text: cord-271091-ffn59sgf.txt item: #249 of 541 id: cord-271470-j58mr9xk author: Zhu, Feifei title: Glycoproteome in silkworm Bombyx mori and alteration by BmCPV infection date: 2020-04-29 words: 3385 flesch: 43 summary: j58mr9xk Abstract The biological functions of protein glycosylation have been increasingly recognized but not yet been very well understood, especially in lower organisms. Significance This study reveals the characteristics of the glycoproteome in the silkworm strain P50, and quantitatively compared to that infected by the virus BmCPV, which underlines the impact of virus infection on the alteration of protein glycosylation in invertebrate species. keywords: bmcpv; bombyx; glycoproteins; glycosylation; infection; mori; protein; silkworm; study; virus cache: cord-271470-j58mr9xk.txt plain text: cord-271470-j58mr9xk.txt item: #250 of 541 id: cord-271642-i71g2tmd author: Mullen, Lisa M. title: Phage display in the study of infectious diseases date: 2006-02-07 words: 4624 flesch: 31 summary: Phage display lends itself perfectly to the investigation of possible binding partners for a particular ligand and this application of phage display was first exploited by Jacobsson and Frykberg There are two types of phage display library: random peptide libraries (RPLs) and natural peptide libraries (NPLs). keywords: display; host; identification; interactions; libraries; library; microbial; peptide; phage; phage display; protein cache: cord-271642-i71g2tmd.txt plain text: cord-271642-i71g2tmd.txt item: #251 of 541 id: cord-271693-7tg21up3 author: Zheng, Fan title: Identifying persistent structures in multiscale ‘omics data date: 2020-10-03 words: 4895 flesch: 43 summary: The goal of the first phase is to detect network communities, i.e. groups of densely connected biological entities. Likewise, protein communities revealed from protein networks can vary widely in sizes depending on the method. keywords: analysis; cell; communities; community; data; fig; hidef; human; networks; protein; supplementary cache: cord-271693-7tg21up3.txt plain text: cord-271693-7tg21up3.txt item: #252 of 541 id: cord-272241-2fwz8z8n author: Kumar, Amit title: Exploring the SARS-CoV-2 structural proteins for multi-epitope vaccine development: an in-silico approach date: 2020-09-09 words: 4612 flesch: 42 summary: WHO | Coronavirus disease World Health Organization Immunization with SARS Coronavirus vaccines leads to pulmonary immunopathology on challenge with the SARS virus Insights into the immunological properties of intrinsically disordered malaria proteins using proteome scale predictions The authors would like to thank IIT Mandi for research facilities. Microbes Infect Molecular basis of COVID-19 relationships in different species: a one health perspective Structural and evolutionary analysis indicate that the SARS-CoV-2 Mpro is a challenging target for small-molecule inhibitor design Probable molecular mechanism of remdesivir for the treatment of COVID-19: need to know more Preliminary identification of potential vaccine targets for the COVID-19 Coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies A DNA vaccine induces SARS coronavirus neutralization and protective immunity in mice This important paper detail about vaccine development Identification of an epitope of SARS-coronavirus nucleocapsid protein Long-lived memory T lymphocyte responses against SARS coronavirus nucleocapsid protein in SARS-recovered patients Lack of peripheral memory B cell responses in recovered patients with severe acute respiratory syndrome: a six-year follow-up study Virus-specific memory CD8 T cells provide substantial protection from lethal severe acute respiratory syndrome coronavirus infection Designing B-and T-cell multi-epitope based subunit vaccine using immunoinformatics approach to control Zika virus infection Strategic development of a next-generation multi-epitope vaccine to prevent nipah virus zoonotic infection In silico/ keywords: cell; complex; construct; coronavirus; cov-2; epitopes; prediction; protein; residues; sars; server; structure; vaccine cache: cord-272241-2fwz8z8n.txt plain text: cord-272241-2fwz8z8n.txt item: #253 of 541 id: cord-272260-88l9bq4i author: Han, L.Y. title: Prediction of functional class of novel viral proteins by a statistical learning method irrespective of sequence similarity date: 2005-01-05 words: 4118 flesch: 36 summary: tRNA region A tutorial on support vector machine for pattern recognition Support vector machines for predicting HIV protease cleavage sites in protein SVM-Prot: web-based support vector machine software for functional classification of a protein from its primary sequence Enzyme family classification by support vector machines Characterization of the intron in the phage T4 thymidylate synthase gene and evidence for its self-excision from the primary transcript Enhanced functional annotation of protein sequences via the use of structural descriptors Multi-class protein fold recognition using support vector machines and neural networks Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis GeneRAGE: a robust algorithm for sequence clustering and domain detection Protein interaction maps for complete genomes based on gene fusion events An efficient algorithm for large-scale detection of protein families The complete nucleotide sequence of bacteriophage HP1 DNA Identification of a novel protein encoded by the BamHI A region of the Epstein-Barr virus Protein function prediction using hidden Markov models and neural networks An N-terminal mutation in the bacteriophage T4 In addition to the prediction of protein functional class (Cai et al., 2003 Han et al., 2004; Karchin et al., 2002) , SVM has also been used for a variety of protein classification problems including fold recognition (Ding and Dubchak, 2001) , analysis of solvent accessibility (Yuan et al., 2002) , prediction of secondary structures (Hua and Sun, 2001) , and protein-protein interactions (Bock and Gough, 2001) . keywords: class; classification; et al; function; novel; proteins; samples; sequence; svmprot cache: cord-272260-88l9bq4i.txt plain text: cord-272260-88l9bq4i.txt item: #254 of 541 id: cord-272268-8vrcwwll author: Kedersha, Nancy title: Chapter 4 Regulation of Translation by Stress Granules and Processing Bodies date: 2009-10-27 words: 8608 flesch: 34 summary: The deacetylase HDAC6 is a novel critical component of stress granules involved in the stress response Disruption of microtubules inhibits cytoplasmic ribonucleoprotein stress granule formation Interaction with 14-3-3 adaptors regulates the sorting of hMex-3B RNA-binding protein to distinct classes of RNA granules hnRNP A1 relocalization to the stress granules reflects a role in the stress response Formation of stress granules inhibits apoptosis by suppressing stress-responsive MAPK pathways Codependent functions of RSK2 and the apoptosis-promoting factor TIA-1 in stress granule assembly and cell survival An essential function of the SRC-3 coactivator in suppression of cytokine mRNA translation and inflammatory response Microtubuledependent association of AKAP350A and CCAR1 with RNA stress granules Sequestration of TRAF2 into stress granules interrupts tumor necrosis factor signaling under stress conditions Tdrd3 is a novel stress granule-associated protein interacting with the Fragile-X syndrome protein FMRP TDRD3, a novel tudor domain-containing protein, localizes to cytoplasmic stress granules Hsp90 regulates the function of argonaute 2 and its recruitment to stress granules and P-bodies Translation initiation factor eIF4G-1 binds to eIF3 through the eIF3e subunit Recycling of eukaryotic posttermination ribosomal complexes Inhibition of cytoplasmic mRNA stress granule formation by a viral proteinase How viruses avoid stress Importance of eIF2alpha phosphorylation and stress granule assembly in alphavirus translation regulation Reovirus induces and benefits from an integrated cellular stress response Interaction of TIA-1/TIAR with West Nile and dengue virus products in infected cells interferes with stress granule formation and processing body assembly Sendai virus trailer RNA binds TIAR, a cellular protein involved in virus-induced apoptosis Mouse hepatitis coronavirus replication induces host translational shutoff and mRNA decay, with concomitant formation of stress granules and processing bodies Interactions between brome mosaic virus RNAs and cytoplasmic processing bodies Antiviral protein APOBEC3G localizes to ribonucleoprotein complexes found in P bodies and stress granules A micrococcal nuclease homologue in RNAi effector complexes Inosine-containing dsRNA binds a stress-granule-like complex and downregulates gene expression in trans LINE-1 ORF1 protein localizes in stress granules with other RNA-binding proteins, including components of RNAi RISC Retrotransposons revisited: the restraint and rehabilitation of parasites Fragile X syndrome: loss of local mRNA regulation alters synaptic development and function Fragile X mental retardation protein shifts between polyribosomes and stress granules after neuronal injury by arsenite stress or in vivo hippocampal electrode insertion Cells lacking the fragile X mental retardation protein (FMRP) have normal RISC activity but exhibit altered stress granule assembly Activation of the integrated stress response during T helper cell differentiation A RING-type ubiquitin ligase family member required to repress follicular helper T cells and autoimmunity MK2-induced tristetraprolin:14-3-3 complexes prevent stress granule association and ARE-mRNA decay Prolonged translation arrest in reperfused hippocampal cornu Ammonis 1 is mediated by stress granules Persistent redistribution of poly-adenylated mRNAs correlates with translation arrest and cell death following global brain ischemia and reperfusion Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies Quantitative analysis of Argonaute protein reveals microRNA-dependent localization to stress granules The anti-HIV-1 editing enzyme APOBEC3G binds HIV-1 RNA and messenger RNAs that shuttle between polysomes and stress granules Human retroviral host restriction factors APOBEC3G and APOBEC3F localize to mRNA processing bodies Ataxin-2 interacts with the DEAD/H-box RNA helicase DDX6 and interferes with P-bodies and stress granules Post-translational arginylation of calreticulin: a new isospecies of calreticulin component of stress granules Distinct structural features of caprin-1 mediate its interaction with G3BP-1 and its induction of phosphorylation of eukaryotic translation initiation factor 2alpha, entry to cytoplasmic stress granules, and selective interaction with a subset of mRNAs Identification of FUSE-binding proteins as interacting partners of TIA proteins The cold-inducible RNAbinding protein migrates from the nucleus to cytoplasmic stress granules by a methylationdependent mechanism and acts as a translational repressor The eIF4G-homolog p97 can activate translation independent of caspase cleavage MBNL1 associates with YB-1 in cytoplasmic stress granules The DEAD-box RNA helicase DDX3 associates with export messenger ribonucleoproteins as well as tip-associated protein and participates in translational control Recruitment of the RNA helicase RHAU to stress granules via a unique RNA-binding domain A functional link between Disrupted-In-Schizophrenia 1 and the eukaryotic translation initiation factor 3 The enhancer of decapping proteins, Edc1p and Edc2p, bind RNA and stimulate the activity of the decapping enzyme Multiple processing body factors and the ARE binding protein TTP activate mRNA decapping A role for the eIF4E-binding protein 4E-T in P-body formation and mRNA decay Regulation of stress granule dynamics by Grb7 and FAK signalling pathway Trapping of messenger RNA by Fragile X Mental Retardation protein into cytoplasmic granules induces translation repression The multifunctional FUS, EWS and TAF15 proto-oncoproteins show cell type-specific expression patterns and involvement in cell spreading and stress response Functional dissection of the human TNRC6 (GW182-related) family of proteins Ge-1 is a central component of the mammalian cytoplasmic mRNA processing body Nuclear RNA export factor 7 is localized in processing bodies and neuronal RNA granules through interactions with shuttling hnRNPs hnRNP K interacts with RNA binding motif protein 42 and functions in the maintenance of cellular ATP level during stress conditions Human hnRNP Q re-localizes to cytoplasmic granules upon PMA, thapsigargin, arsenite and heat-shock treatments Stress granule assembly is mediated by prion-like aggregation of TIA-1 HuR binding to cytoplasmic mRNA is perturbed by heat shock Importin 8 is a gene silencing factor that targets argonaute proteins to distinct mRNAs Intracellular localization of human inositol 1,3,4,5,6-pentakisphosphate 2-kinase Localization of the developmental timing regulator Lin28 to mRNP complexes, P-bodies and stress granules The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci Identification of novel argonaute-associated proteins Neural RNA-binding protein Musashi1 inhibits translation initiation by competing with eIF4G for PABP Inhibition of G(1) to S phase progression by a novel zinc finger protein P58(TFL) at P-bodies Identification of PatL1, a human homolog to yeast P body component Pat1 Selective localization of PCBP2 to cytoplasmic processing bodies Identification of the junctional plaque protein plakophilin 3 in cytoplasmic particles containing RNA-binding proteins and the recruitment of plakophilins 1 and 3 to stress granules Polysome-bound endonuclease PMR1 is targeted to stress granules via stress-specific binding to TIA-1 Dendritic localization of the translational repressor Pumilio 2 and its contribution to dendritic stress granules RNA-associated protein 55 (RAP55) localizes to mRNA processing bodies and stress granules Rpp 20 interacts with SMN and is re-distributed into SMN granules in response to stress The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs Sam68 functions in nuclear export and translation of HIV-1 RNA SGNP: an essential Stress Granule/Nucleolar Protein potentially involved in 5.8s rRNA processing/transport Mammalian Smaug is a translational repressor that forms cytoplasmic foci similar to stress granules Staufen recruitment into stress granules does not affect early mRNA transport in oligodendrocytes Mammalian Staufen 1 is recruited to stress granules and impairs their assembly Survival motor neuron protein facilitates assembly of stress granules Probing the mRNA processing body using protein macroarrays and autoantigenomics ZBP1 regulates mRNA stability during cellular stress A PKR-like eukaryotic initiation factor 2alpha kinase from zebrafish contains Z-DNA binding domains instead of dsRNA binding domains RNA-binding proteins TIA-1 and TIAR link the phosphorylation of eIF-2a to the assembly of mammalian stress granules Cytoplasmic heat shock granules are formed from precursor particles and are associated with a specific set of mRNAs Plant stress granules and mRNA processing bodies are distinct from heat stress granules Mammalian stress granules: highly dynamic sites of mRNA triage during stress induced translational arrest TIA-1 is a translational silencer that selectively regulates the expression of TNF-alpha Visibly stressed: the role of eIF2, TIA-1, and stress granules in protein translation Stressful initiations Evidence that ternary complex (eIF2-GTP-tRNA(i)(Met))-deficient preinitiation complexes are core constituents of mammalian stress granules Mammalian stress granules represent sites of accumulation of stalled translation initiation complexes The RasGAPassociated endoribonuclease G3BP assembles stress granules Rasputin, more promiscuous than ever: a review of G3BP MK2-induced tristetraprolin: 14-3-3 complexes prevent stress granule association and ARE-mRNA decay Inhibition of eukaryotic translation initiation by the marine natural product pateamine A RNAmediated sequestration of the RNA helicase eIF4A by pateamine A inhibits translation initiation Eukaryotic initiation factor 2alpha-independent pathway of stress granule induction by the natural product pateamine A Inhibition of ribosome recruitment induces stress granule formation independently of eukaryotic initiation factor 2alpha phosphorylation An antiviral response directed by PKR phosphorylation of the RNA helicase A Decapping and decay of messenger RNA occur in cytoplasmic processing bodies Cytoplasmic foci are sites of mRNA decay in human cells P bodies: at the crossroads of post-transcriptional pathways P bodies and the control of mRNA translation and degradation The highways and byways of mRNA decay The control of mRNA decapping and P-body formation Perk is essential for translational regulation and cell survival during the unfolded protein response Signal integration via PKR The exonjunction-complex-component metastatic lymph node 51 functions in stress-granule assembly Distinctive properties of the 5'-untranslated region of human hsp70 mRNA Mammalian stress granules and processing bodies Translational control is required for the unfolded protein response and in vivo glucose homeostasis Metazoan stress granule assembly is mediated by P-eIF2 {alpha}-dependent and -independent mechanisms Heme-regulated inhibitor (HRI) kinase-mediated phosphorylation of eukaryotic translation initiation factor 2 (eIF2) inhibits translation, induces stress granule formation, and mediates survival upon arsenite exposure Stress-dependent relocalization of translationally primed mRNPs to cytoplasmic granules that are kinetically and spatially distinct from P-bodies Accumulation of polyadenylated mRNA, Pab1p, eIF4E, and eIF4G with P-bodies in Saccharomyces cerevisiae P bodies promote stress granule assembly in Saccharomyces cerevisiae Robust heat shock induces eIF2{alpha}-phosphorylation-independent assembly of stress granules containing eIF3 and 40S ribosomal subunits in budding yeast, Saccharomyces cerevisiae Stress granules and processing bodies are dynamically linked sites of mRNP remodeling Subnuclear organelles: new insights into form and function The translational regulator CPEB1 provides a link between dcp1 bodies and stress granules Dynamic shuttling of TIA-1 accompanies the recruitment of mRNA to mammalian stress granules A functional RNAi screen links O-GlcNAc modification of ribosomal proteins to stress granule and processing body assembly Dynein motor contributes to stress granule dynamics in primary neurons keywords: assembly; binding; bodies; cells; eif2a; formation; granules; initiation; mrna; pbs; proteins; response; sgs; stress; tia-1; translation; virus cache: cord-272268-8vrcwwll.txt plain text: cord-272268-8vrcwwll.txt item: #255 of 541 id: cord-272467-8heg5iql author: Armstrong, John title: Expression of coronavirus E1 and rotavirus VP10 membrane proteins from synthetic RNA date: 2004-02-19 words: 2756 flesch: 51 summary: E l protein was synthesized in oocytes as a spectrum of forms, the most mobile of which comigrated with the unmodified protein from the reticulocyte lysate (Fig. 1 , lanes e,f). In contrast, E l protein showed a much more localised fluorescence pattern (Fig. 2b) . keywords: cells; golgi; oocytes; protein; reticulum; vplo cache: cord-272467-8heg5iql.txt plain text: cord-272467-8heg5iql.txt item: #256 of 541 id: cord-272986-ebgusf3o author: Cao, Yipeng title: Computational Study of Ions and Water Permeation and Transportation Mechanisms of the SARS-CoV-2 Pentameric E Protein Channel date: 2020-05-17 words: 4342 flesch: 48 summary: A new coronavirus associated with human respiratory disease in China Structure validation by Cα geometry: ϕ, ψ and Cβ deviation Molecular dynamics simulations of membrane channels and transporters A single polar residue and distinct membrane topologies impact the function of the infectious bronchitis coronavirus E protein SARS coronavirus E protein forms cation-selective ion channels MERS coronavirus envelope protein has a single transmembrane domain that forms pentameric ion channels Ion channels of excitable membranes Theoretical and computational models of biological ion channels Functional annotation of ion channel structures by molecular simulation Permeation process of small molecules across lipid membranes studied by molecular dynamics simulations Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants Effect of field direction on electrowetting in a nanopore Voltage gating of a biomimetic nanopore: Electrowetting of a hydrophobic barrier Viroporins: structure and biological functions Ion channel voltage sensors: structure, function, and pathophysiology Designing a hydrophobic barrier within biomimetic nanopores STIM1 activates CRAC channels through rotation of the pore helix to open a hydrophobic gate 376-Relaxation studies on cell membranes and lipid bilayers in the high electric field range CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures COVID-19 infection: origin, transmission, and characteristics of human coronaviruses The disintegration of the ion equilibrium of the intracellular area affect the charges coming from the cell through ion channels in the cell membrane, changing the pH and making it easier for the virus to fuse with the cell membrane. keywords: channel; coronavirus; e protein; ion; ions; pore; protein; sars; water cache: cord-272986-ebgusf3o.txt plain text: cord-272986-ebgusf3o.txt item: #257 of 541 id: cord-273019-hbpfz8rt author: Glingston, R. Sahaya title: Organelle dynamics and viral infections: at cross roads date: 2018-06-25 words: 9525 flesch: 30 summary: Current review briefly summarizes our knowledge of the various cell organelles/compartments following virus infection. caspase-independent cell death Lysosomal cell death at a glance A zinc finger protein Tsip1 controls cucumber mosaic virus infection by interacting with the replication complex on vacuolar membranes of the tobacco plant Visualization of assembly intermediates and budding vacuoles of Singapore grouper iridovirus in grouper embryonic cells Involvement of the vacuolar H(þ)-ATPase in animal virus entry Membrane and protein interactions of a soluble form of the semliki forest virus fusion protein The entry of reovirus into L cells is dependent on vacuolar proton-ATPase activity Cellular v-ATPase is required for virion assembly compartment formation in human cytomegalovirus infection Endocytosis via caveolae Endocytosis of simian virus 40 into the endoplasmic reticulum Cellular entry of ebola virus involves uptake by a macropinocytosis-like mechanism and subsequent trafficking through early and late endosomes Membrane dynamics associated with viral infection Biogenesis of the semliki forest virus RNA replication complex Fusion of SV40-induced endocytotic vacuoles with the nuclear membrane Interaction of endocytotic vacuoles with the inner nuclear membrane in simian virus 40 entry into CV-1 cell nucleus ESCRT complexes and the biogenesis of multivesicular bodies Involvement of vacuolar protein sorting pathway in ebola virus release independent of TSG101 interaction Identification of alpha-taxilin as an essential factor for the life cycle of hepatitis B virus Divergent roles of autophagy in virus infection keywords: cells; complex; degradation; expression; formation; golgi; hepatitis; host; human; infection; lipid; membrane; nuclear; nucleus; order; organelles; protein; replication; rna; virus; viruses cache: cord-273019-hbpfz8rt.txt plain text: cord-273019-hbpfz8rt.txt item: #258 of 541 id: cord-274056-9t3kneoo author: Abd Elwahaab, Marwa A. title: A Statistical Similarity/Dissimilarity Analysis of Protein Sequences Based on a Novel Group Representative Vector date: 2019-05-08 words: 3315 flesch: 55 summary: 2D and 3D amino acid adjacency matrices A new method to analyze protein sequence similarity using dynamic time warping A 2D graphical representation of protein sequence and its numerical characterization Graphical representation and similarity analysis of protein sequences based on fractal interpolation ADLD: a novel graphical representation of protein sequences and its application Comparative analysis of protein primary sequences with graph energy UC-curve: a highly compact 2D graphical representation of protein sequences The graphical representation of protein sequences based on the physicochemical properties and its applications F-curve, a graphical representation of protein sequences for similarity analysis based on physicochemical properties of amino acids A novel method of 2D graphical representation for proteins and its application 3D graphical representation of protein sequences and their statistical characterization Novel numerical characterization of protein sequences based on individual amino acid and its application Similarities/dissimilarities analysis of protein sequences based on PCA-FFT On novel representation of proteins based on amino acid adjacency matrix A sequence-segmented method applied to the similarity analysis of long protein sequence It is a figure which summarizes our approach. In our work, a representative of each of three groups of protein sequences is introduced. keywords: dissimilarity; group; protein; sequences; similarity; vector cache: cord-274056-9t3kneoo.txt plain text: cord-274056-9t3kneoo.txt item: #259 of 541 id: cord-274080-884x48on author: Rumlová, Michaela title: In vitro methods for testing antiviral drugs date: 2018-06-30 words: 18015 flesch: 26 summary: Virus-encoded methyltransferases have been identified and characterized in flaviviruses such as Zika virus Coutard et al., 2017; Duan et al., 2017; Munjal et al., 2017; Zhao et al., 2017) , West Nile virus, and dengue virus (Dong et al., 2012) ; rhabdoviruses such as vesicular stomatitis virus (VSV) (Rahmeh et al., 2009 ); coronaviruses such as SARS (Wang et al., 2015b) ; and roniviruses (Zeng et al., 2016) . Alternatively, cleavage products may be monitored by analysis of proteolytic products by mass spectrometric methods (Hu et al., 2015; Joshi et al., 2017; Lathia et al., 2011; Rumlová et al., 2003) , analytical HPLC (Teruya et al., 2016) , or electrochemical methods based on the difference in penetration of substrate and cleavage products through the membrane of a polyionselective sensor (Gemene and Meyerhoff, 2011; Han et al., 1996) . keywords: activity; assay; assembly; binding; capsid; cell; coronavirus; dna; drug; entry; envelope; et al; fluorescence; fusion; genome; hbv; hcv; helicase; hepatitis; host; human; infection; influenza; inhibitors; integrase; kinase; membrane; method; particles; polymerase; protease; protein; replication; rna; screening; specific; target; transcription; type; uncoating; viral; virus; viruses cache: cord-274080-884x48on.txt plain text: cord-274080-884x48on.txt item: #260 of 541 id: cord-274293-kzmch37j author: Yang, Li title: Tandem mass tag-based quantitative proteomic analysis of lycorine treatment in highly pathogenic avian influenza H5N1 virus infection date: 2019-10-02 words: 6751 flesch: 40 summary: Unlike the mechanism of oseltamivir, the vRNPs are retained in the nucleus by lycorine treatment instead of directly targeting viral proteins and RNA polymerase activity (He et al., 2013) . Therefore, we performed a comparative proteomic analysis to identify changes in protein expression in AIV-infected Madin-Darby Canine Kidney cells treated with lycorine. keywords: activity; analysis; buffer; cells; et al; group; infection; influenza; lycorine; min; nup93; proteins; study; treatment; virus cache: cord-274293-kzmch37j.txt plain text: cord-274293-kzmch37j.txt item: #261 of 541 id: cord-274366-t138l6px author: Benetti, Elisa title: ACE2 gene variants may underlie interindividual variability and susceptibility to COVID-19 in the Italian population date: 2020-07-17 words: 4534 flesch: 40 summary: Taking advantage of the Network of Italian Genomes (NIG), here we mined whole-exome sequencing data of 6930 Italian control individuals from five different centers looking for ACE2 variants. In order to shed light on the role of ACE2 variants on interindividual variability and susceptibility to COVID-19 in Italian population we performed WES analysis on a cohort of 131 patients and 258 controls who agreed in participating to the study (see Materials and methods). keywords: ace2; clinical; coronavirus; covid-19; data; disease; human; patients; population; protein; receptor; sars; spike; variants cache: cord-274366-t138l6px.txt plain text: cord-274366-t138l6px.txt item: #262 of 541 id: cord-274393-1geyuxtk author: Xie, Wenyan title: Mutations in the Leucine Zipper-Like Motif of the Human Parainfluenza Virus 3 Fusion Protein Impair Fusion Activity date: 2015-12-23 words: 6968 flesch: 46 summary: In the coimmunoprecipitation assay, all mutants resulted in decreased detection of the HN-F complexes compared with that of the wild-type F protein. The effects on the fusion activity, cell surface expression, and HN-F interactions of such mutated F proteins were examined. keywords: activity; cells; f protein; fusion; hpiv-3; leucine; motif; proteins; virus; wt f cache: cord-274393-1geyuxtk.txt plain text: cord-274393-1geyuxtk.txt item: #263 of 541 id: cord-274424-juj71nc5 author: Pulford, David J. title: Intracellular processing of the porcine coronavirus transmissible gastroenteritis virus spike protein expressed by recombinant vaccinia virus date: 1991-06-30 words: 4928 flesch: 41 summary: TGEV S protein steadily became Endo H resistant with time such that after a 4-hr chase virtually all S protein had been modified in the Golgi. The acquisition of Endo H resistance was significantly retarded for recombinant S protein compared to S protein expressed during a TGEV infection. keywords: barnhi; cells; coronavirus; endo; fig; gene; protein; recombinant; tgev; virus cache: cord-274424-juj71nc5.txt plain text: cord-274424-juj71nc5.txt item: #264 of 541 id: cord-275023-0z219rcy author: Cerofolini, Linda title: Orientation of immobilized antigens on common surfaces by a simple computational model: Exposition of SARS-CoV-2 Spike protein RBD epitopes date: 2020-07-29 words: 3488 flesch: 32 summary: Therefore, the possibility to control and manipulate the exposition of the relevant residues and protein surfaces plays an important role in the rational design of devices based on immobilized proteins. A more detailed experimental verification of the predictions of protein orientation at surfaces represents a significant challenge for the current biophysical methodologies. keywords: cov-2; gold; immobilization; interaction; orientation; protein; sars; state; structure; surface cache: cord-275023-0z219rcy.txt plain text: cord-275023-0z219rcy.txt item: #265 of 541 id: cord-275124-7l53bvp1 author: Yao, Minghui title: A potential treatment for COVID-19 based on modal characteristics and dynamic responses analysis of 2019-nCoV date: 2020-10-21 words: 2529 flesch: 60 summary: 3 Lumped parameter mechanical model of 2019-nCoV According to the mode shape of single spike protein as shown in Fig. 4 , the first-order bending mode shape is employed as the vibration form of spike proteins. Because of the relatively heavy mass of the sphere body compared to spike proteins, its modes are rigid body motion, which the sphere of COVID-19 model is fixed in modal analysis. keywords: 2019; model; ncov; spike; vibration cache: cord-275124-7l53bvp1.txt plain text: cord-275124-7l53bvp1.txt item: #266 of 541 id: cord-275993-isff6lp2 author: Han, Dong P title: Development of a safe neutralization assay for SARS-CoV and characterization of S-glycoprotein date: 2004-08-15 words: 5610 flesch: 42 summary: Antibodies against SARS proteins have been shown to appear as early as 9 days after the onset of illness (Hsueh et al., 2003) . Vesicular stomatitis virus G glycoprotein pseudotyped retroviral vectors: concentration to very high titer and efficient gene transfer into mammalian and nonmammalian cells Identification of the epitope region capable of inducing neutralizing antibodies against the porcine epidemic diarrhea virus Macrophage tropism of human immunodeficiency virus type 1 and utilization of the CC-CKR5 coreceptor Subunit protein vaccines: theoretical and practical considerations for HIV-1 Membrane rearrangement and vesicle induction by recombinant poliovirus 2C and 2BC in human cells Monoclonal antibodies to murine hepatitis virus-4 (strain JHM) define the viral glycoprotein responsible for attachment and cell -cell fusion Protection from lethal coronavirus infection by affinity-purified spike glycoprotein of murine hepatitis virus, strain A59 Assembly of coronavirus spike protein into trimers and its role in epitope expression Identification of a major co-receptor for primary isolates of HIV-1 Identification of a novel coronavirus in patients with severe acute respiratory syndrome The V5A13.1 envelope glycoprotein deletion mutant of mouse hepatitis virus type-4 is neuroattenuated by its reduced rate of spread in the central nervous system Antigenic relationships of murine coronaviruses: analysis using monoclonal antibodies to JHM (MHV-4) virus Aetiology: Koch's postulates fulfilled for SARS virus Eukaryotic transient-expression system based on recombinant vaccinia virus that synthesizes bacteriophage T7 RNA polymerase Alteration of the pH dependence of coronavirus-induced cell fusion: effect of mutations in the spike glycoprotein Major receptorbinding and neutralization determinants are located within the same domain of the transmissible gastroenteritis virus (coronavirus) spike protein Detection of SARS coronavirus in plasma by real-time RT-PCR Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China Microbiologic characteristics, serologic responses, and clinical manifestations in severe acute respiratory syndrome Location of antigenic sites defined by neutralizing monoclonal antibodies on the S1 avian infectious bronchitis virus glycopolypeptide Development of a safe and rapid neutralization assay using murine leukemia virus pseudotyped with HIV type 1 envelope glycoprotein lacking the cytoplasmic domain Protective immunity against murine hepatitis virus (MHV) induced by intranasal or subcutaneous administration of hybrids of tobacco mosaic virus that carries an MHV epitope A novel coronavirus associated with severe acute respiratory syndrome Neutralization and fusion inhibition activities of monoclonal antibodies specific for the S1 subunit of the spike protein of neurovirulent murine coronavirus JHMV c1-2 variant Localization of neutralizing epitopes and the receptor-binding site within the amino-terminal 330 amino acids of the murine coronavirus spike protein Coronviridae: the viruses and their replication A real-time PCR for SARS-coronavirus incorporating target gene pre-amplification The C12 mutant of MHV-A59 is very weakly demyelinating and has five amino acid substitutions restricted to the spike and replicase genes Role of pH in syncytium induction and genome uncoating of avian infectious bronchitis coronavirus (IBV) Coronavirus IBV-induced membrane fusion occurs at near-neutral pH Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus Virology: SARS virus infection of cats and ferrets New mammalian expression vectors Entry of mouse hepatitis virus into cells by endosomal and nonendosomal pathways Quantitative analysis and prognostic implication of SARS coronavirus RNA in the plasma and serum of patients with severe acute respiratory syndrome N-linked glycosylation sites adjacent to and within the V1/ V2 and the V3 loops of dualtropic human immunodeficiency virus type 1 isolate DH12 gp120 affect coreceptor usage and cellular tropism Initial events in bovine coronavirus infection: analysis through immunogold probes and lysosomotropic inhibitors Coronavirus as a possible cause of severe acute respiratory syndrome Foamy virus envelope glycoprotein-mediated entry involves a pH-dependent fusion process Early diagnosis of SARS Coronavirus infection by real time RT-PCR Rapid diagnosis of a coronavirus associated with severe acute respiratory syndrome (SARS) Identification of severe acute respiratory syndrome in Canada A role for carbohydrates in immune evasion in AIDS Characterization of a novel coronavirus associated with severe acute respiratory syndrome Targeted recombination demonstrates that the spike gene of transmissible gastroenteritis coronavirus is a determinant of its enteric tropism and virulence Pseudotyping of murine leukemia virus with the envelope glycoproteins of HIV generates a retroviral vector with specificity of infection for CD4-expressing cells Characterization of severe acute respiratory syndromeassociated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry Unique and conserved features of genome and proteome of SARScoronavirus, an early split-off from the coronavirus group 2 lineage Localization of major neutralizing epitopes on the S1 polypeptide of the murine coronavirus peplomer glycoprotein Interpretation of diagnostic laboratory tests for severe acute respiratory syndrome: the Toronto experience A 12-amino acid stretch in the hypervariable region of the spike protein S1 subunit is critical for cell fusion activity of mouse hepatitis virus Assessment of immunoreactive synthetic peptides from the structural proteins of severe acute respiratory syndrome coronavirus Summary of probable SARS cases with onset of illness from 1 The SARS-CoV S glycoprotein: expression and functional characterization Evaluation of reverse transcription-PCR assays for rapid diagnosis of severe acute respiratory syndrome associated with a novel coronavirus Requirement of proteolytic cleavage of the murine coronavirus MHV-2 spike protein for fusion activity We are grateful to CDC for providing plasmids encoding SARS-CoV S gene and convalescent sera, to Dr. Bernard Moss for vTF7-3, to Dr. Franc ßois-Loïc Cosset for TELCeB6 cell line, and to Drs. keywords: antibodies; cells; coronavirus; cov; et al; fig; glycoprotein; infection; protein; pseudoviruses; sars; virus cache: cord-275993-isff6lp2.txt plain text: cord-275993-isff6lp2.txt item: #267 of 541 id: cord-276456-oa6hh7ky author: Collins, R.N. title: 5.14 The Biophysics of Membrane Fusion date: 2012-05-03 words: 9190 flesch: 36 summary: hemagglutinin impair or abolish membrane fusion activity New insight into the spring-loaded conformational change of influenza virus hemagglutinin Leash in the groove mechanism of membrane fusion A host-guest system to study structure-function relationships of membrane fusion peptides Structural intermediates in influenza haemagglutinin-mediated fusion Composition and functions of the influenza fusion peptide Membrane fusion by influenza hemagglutinin Studies on the mechanism of membrane fusion: site-specific mutagenesis of the hemagglutinin of influenza virus Hypothesis: spring-loaded boomerang mechanism of influenza hemagglutinin-mediated membrane fusion Early endosomal SNAREs form a structurally conserved SNARE complex and fuse liposomes with multiple topologies The cytoplasmic tail slows the folding of human immunodeficiency virus type 1 Env from a late prebundle configuration into the six-helix bundle Fusion peptide of influenza hemagglutinin requires a fixed angle boomerang structure for activity Locking the kink in the influenza hemagglutinin fusion domain structure Membrane fusion mediated by the influenza virus hemagglutinin requires the concerted action of at least three hemagglutinin trimers Multiple local contact sites are induced by GPI-linked influenza hemagglutinin during hemifusion and flickering pore formation Secondary structure, orientation, oligomerization, and lipid interactions of the transmembrane domain of influenza hemagglutinin Endosome-to-cytosol transport of viral nucleocapsids Conformational changes and fusion activity of influenza virus hemagglutinin of the H2 and H3 subtypes: effects of acid pretreatment Reversible pH-dependent conformational change of reconstituted influenza hemagglutinin Amino acid sequence requirements of the transmembrane and cytoplasmic domains of influenza virus hemagglutinin for viable membrane fusion SNAREs-energies for membrane fusion Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 A resolution Energetics and dynamics of SNAREpin folding across lipid bilayers Single molecule probing of SNARE proteins by atomic force microscopy Is assembly of the SNARE complex enough to fuel membrane fusion Crystal structure of the endosomal SNARE complex reveals common structural principles of all SNAREs Structure and function of SNARE and SNARE-interacting proteins Structure of proteins involved in synaptic vesicle fusion in neurons Exocytosis requires asymmetry in the central layer of the SNARE complex SNARE complex zero layer residues are not critical for N-ethylmaleimide-sensitive factor-mediated disassembly Testing the 3Q:1R 'rule': mutational analysis of the ionic 'zero' layer in the yeast exocytic SNARE complex reveals no requirement for arginine Exocytotic mechanism studied by truncated and zero layer mutants of the C-terminus of SNAP-25 Dynamic structure of lipid-bound synaptobrevin suggests a nucleationpropagation mechanism for trans-SNARE complex formation The SNARE complex from yeast is partially unstructured on the membrane Structural basis for the inhibitory role of tomosyn in exocytosis Transmembrane segments of syntaxin line the fusion pore of Ca 2 þ -triggered exocytosis Single vesicle millisecond fusion kinetics reveals number of SNARE complexes optimal for fast SNARE-mediated membrane fusion Docking and fast fusion of synaptobrevin vesicles depends on the lipid compositions of the vesicle and the acceptor SNARE complex-containing target membrane Reconstitution of Rab-and SNARE-dependent membrane fusion by synthetic endosomes Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations Structural transitions in the synaptic SNARE complex during Ca 2 þ -triggered exocytosis Novel targets and catalytic activities of bacterial protein toxins Receptor and substrate interactions of clostridial neurotoxins X-ray structure of a neuronal complexin-SNARE complex from squid Three-dimensional structure of the complexin/SNARE complex The synaptic vesicle protein CSP alpha prevents presynaptic degeneration Ddi1, a eukaryotic protein with the retroviral protease fold Different domains of the UBL-UBA ubiquitin receptor, Ddi1/Vsm1, are involved in its multiple cellular roles A structure-based mechanism for vesicle capture by the multisubunit tethering complex Dsl1 A crucial interplay between protein conformations and lipid membrane energetics emerges as the guiding principle for the regulation and mechanism of membrane fusion in biological systems. keywords: complex; exocytosis; formation; fusion; fusion peptide; fusion pore; hemagglutinin; hemifusion; influenza; lipid; membrane; membrane fusion; pore; protein; snare; structure cache: cord-276456-oa6hh7ky.txt plain text: cord-276456-oa6hh7ky.txt item: #268 of 541 id: cord-276966-wmelyonk author: Roe, Kevin title: A proposed treatment for pathogenic enveloped viruses having high rates of mutation or replication date: 2020-07-08 words: 5244 flesch: 33 summary: All rights reserved 11 Viral mutation rates Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence Appendix -Structure, genome organization, and infectious cycles Viral escape from endosomes and host detection at a glance AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses The gamma interferon(IFN-gamma) mimetic peptide IFNgamma (95-133) prevents encephalomyocarditis virus infection both in tissue culture and in mice HIPdb: a database of experimentally validated HIV inhibiting peptides AVPpred: collection and prediction of highly effective antiviral peptides Pentraxins in the activation and regulation of innate immunity Protective immunity against Hepatitis C: many shades of gray Human Vδ2 versus non-Vδ2 γδ T cells in antitumor immunity Tissue adaptations of memory and tissue-resident gamma delta T cells Cytomegalovirus and tumor stress surveillance by binding of a human γδ T cell antigen receptor to endothelial protein C receptor Endothelial cell protein C receptor-dependent signaling Six-of-the-best: unique contributions of γδ T cells to immunology IgE repertoire and immunological memory: compartmental regulation and antibody function Disabling of lymphocyte immune response by Ebola virus Recent mass spectrometry-based techniques and considerations for disulfide bond characterization in proteins Antigen recognition by B-cell and T-cell receptors T cell receptor signaling for γδ T cell development Gamma-delta γδ T cells: friend or foe in cancer development Harnessing microglia and macrophages for the treatment of glioblastoma Innate immunity: the induced response to infection Role of hepatitis C virus envelope glycoprotein E1 in virus entry and assembly Identification of novel functions for hepatitis C virus envelope glycoprotein E1 in virus entry and assembly Conformational states of a soluble, uncleaved HIV-1 envelope trimer Measles virus fusion protein: structure, function, and inhibition Cryo-EM structures of eastern equine encephalitis virus reveal mechanisms of virus disassembly and antibody neutralization Protective antibodies against eastern equine encephalitis virus bind to epitopes 2 in domains A and B of the E2 glycoprotein Antigen-antibody interactions: principles and applications The humoral immune response Stopping untreatable pathogen infections using peptide ligands to sabotage pathogenic cell surface proteins Dual-peptide ligand masks: a proposed treatment approach to stop prion disease dementias Penetration of drugs through the blood-cerebrospinal fluid/bloodbrain barrier for treatment of central nervous system infections Accepted Article 20 In targeting specific viral pathogens, dual-protein ligand masks (for brevity, henceforth called dualprotein ligands) should be able to create a quick and powerful immune memory response with existing memory immune cells against some viral pathogens or virus infected cells, without some of the practical limitations of vaccines. keywords: cells; host; ligand; memory; mutation; pathogen; protein; surface; virus; viruses cache: cord-276966-wmelyonk.txt plain text: cord-276966-wmelyonk.txt item: #269 of 541 id: cord-276988-bvsz5q6d author: Neu, Carolin T. title: Post-Transcriptional Expression Control in Platelet Biogenesis and Function date: 2020-10-15 words: 11425 flesch: 33 summary: The complex transcriptional landscape of the anucleate human platelet Integration of proteomics and genomics in platelets: A profile of platelet proteins and platelet-specific genes Next generation sequencing analysis of human platelet PolyA+ mRNAs and rRNA-depleted total RNA Mapping and quantifying mammalian transcriptomes by RNA-Seq Uncovering the complexity of transcriptomes with RNA-Seq Platelet factor XI: Intracellular localization and mRNA splicing following platelet activation Signal-dependent splicing of tissue factor pre-mRNA modulates the thrombogenicity of human platelets Lipopolysaccharide signaling without a nucleus: Kinase cascades stimulate platelet shedding of proinflammatory IL-1beta-rich microparticles Lipopolysaccharide is a direct agonist for platelet RNA splicing Rigoutsos, I. These molecules, be they platelet proteins, lipids, growth factors, or cytokines, are mainly found in alpha (α) and dense (δ) granules [38] . keywords: activation; binding; cancer; cells; coding; control; expression; factor; function; human; mechanisms; megakaryocytes; mirnas; mks; mrna; patients; platelets; protein; rbps; rna; role; transcriptional; translation cache: cord-276988-bvsz5q6d.txt plain text: cord-276988-bvsz5q6d.txt item: #270 of 541 id: cord-277293-eo3bei9x author: Fondong, Vincent N. title: Geminivirus protein structure and function date: 2013-04-25 words: 10149 flesch: 28 summary: Except for a recent identification of mastreviruses in sweet potato in Peru (Kreuze et al., 2009) and in dragonflies (suborder Anisoptera) in Puerto Rico (Rosario et al., 2013) , these viruses have been found only in the Old World, where they infect a range of monocotyledonous plants (reviewed in Brown et al., 2012) and, from recent reports, dicotyledonous plants (Hadfield et al., 2012; Liu et al., 1999; Nahid et al., 2008) . The replication-associated protein A (RepA), the protein product of ORF C1, and Rep are the two complementary-sense proteins of the mastreviruses (Collin et al., 1996; Gutierrez et al., 2004; Hofer et al., 1992; Liu et al., 1997) , and are both required for virus replication. keywords: begomoviruses; binding; bipartite; cell; curl; dna; et al; geminivirus; gene; infection; interaction; leaf; monopartite; mosaic; movement; nsp; nuclear; plant; protein; replication; tomato; virus; yellow cache: cord-277293-eo3bei9x.txt plain text: cord-277293-eo3bei9x.txt item: #271 of 541 id: cord-277424-9aimvogs author: Criscitiello, Michael F. title: Deiminated proteins in extracellular vesicles and serum of llama (Lama glama)—Novel insights into camelid immunity date: 2019-11-13 words: 12807 flesch: 27 summary: Other histones that are known to undergo deimination include H3 and H4 (Chen et al., 2014; Kosgodage et al., 2018) . PADs have been identified throughout phylogeny from bacteria to mammals, with 5 tissue specific PAD isozymes in mammals, 3 in chicken, 1 in bony fish and arginine deiminase homologues in bacteria (Vossenaar et al., 2003; Rebl et al., 2010; Magnadóttir et al., 2018a, a; Kosgodage et al., 2019) . keywords: adiponectin; analysis; antibodies; binding; camelid; cancer; cells; chain; complement; deimination; disease; et al; evs; extracellular; f95; fig; functions; gene; human; immune; interactions; key; llama; llama serum; magnadóttir; metabolic; novel; pathway; prolidase; protein; regulation; response; roles; serum; shark cache: cord-277424-9aimvogs.txt plain text: cord-277424-9aimvogs.txt item: #272 of 541 id: cord-277811-j58qvyum author: Mehrani, Hossein title: Plasma proteomic profile of sulfur mustard exposed lung diseases patients using 2-dimensional gel electrophoresis date: 2011-01-07 words: 4100 flesch: 48 summary: Plasma proteins and peptides are from almost every tissue and cell, and their change in quantity and quality is specific not only to the tissue affected by disease, but also to the disease process itself. P50% S75% P75% Figure 1 SDS-PAGE of plasma proteins fractionated with different concentrations (v/v) of ethanol. keywords: analysis; controls; disease; ethanol; haptoglobin; lung; patients; plasma; proteins; spots cache: cord-277811-j58qvyum.txt plain text: cord-277811-j58qvyum.txt item: #273 of 541 id: cord-279106-3ffa9djf author: Syatila Ab Ghani, Nur title: Side chain similarity comparisons for integrated drug repositioning and potential toxicity assessments in epidemic response scenarios: the case for COVID-19 date: 2020-10-21 words: 6982 flesch: 40 summary: 33 34 3. Results and Discussion 35 In this study, sub-structural similarity searches and docking analyses were carried out to: (i) identify 36 potential targets and drug binding sites in SARS-CoV-2 proteins; (ii) identify off-targets for proposed drug 37 compounds for COVID-19; (iii) identify other approved drugs with similar structure to proposed drugs that 38 are potentially useful for COVID-19 treatment. In this work, the three-dimensional arrangements of amino acid side chains in known drug binding sites (substructures) were used to search for similarly arranged sites in SARS-CoV-2 protein structures in the Protein Data Bank for the potential repositioning of approved compounds. keywords: binding; compounds; cov-2; covid-19; docking; drug; pdbid; potential; protein; sars; similarity; sites; structures; target cache: cord-279106-3ffa9djf.txt plain text: cord-279106-3ffa9djf.txt item: #274 of 541 id: cord-279418-3r1ijafm author: Nevers, Quentin title: Negri bodies and other virus membrane-less replication compartments() date: 2020-08-21 words: 6446 flesch: 34 summary: These structures often referred as viral inclusions, viral factories or viroplasms, concentrate viral proteins, nucleic acids and specific cellular factors. Other DNA viruses belonging to Herpesviridae, Adenoviridae, Parvoviridae, Polyomaviridae and Papillomaviridae families induce the formation of membrane-less assemblies inside the nucleus termed viral replication compartments (or centers), hereafter referred as VRCs [65] , which concentrate viral proteins and nucleic acids, incoming viral genomes and host proteins. keywords: bodies; compartments; domain; factories; formation; liquid; membrane; phase; pml; protein; replication; rna; virus; viruses cache: cord-279418-3r1ijafm.txt plain text: cord-279418-3r1ijafm.txt item: #275 of 541 id: cord-279432-aik5bo6o author: Digard, Paul title: Complex formation between influenza virus polymerase proteins expressed in Xenopus oocytes date: 1989-07-31 words: 4856 flesch: 43 summary: Functions and movements of influenza P proteins during capped RNA-primed transcription Expression of a functional influenza viral cap-recognising protein by using a bovine papilloma virus vector An efficient ribosomal frame-shifting signal in the polymerase encoding region of the coronavirus IBV Translation of eukaryotic messenger RNA inXenopus oocytes The three influenza virus polymerase (P) proteins not associated with viral nucleocapsids in the infected cell are in the form of a complex The effect of capping and polyadenylation on the stability, movement and translation of synthetic messenger RNAs in Xenopus oocytes Influenza virus messenger RNAs are incomplete transcripts of the genome RNAs Transcription of the influenza virus genome Influenza virus, an RNA virus, synthesises its messenger RNA in the nucleus of infected cells Polypeptides specified by the influenza virus genome. key: cord-279432-aik5bo6o authors: Digard, Paul; Blok, Vivian C.; Inglis, Stephen C. title: Complex formation between influenza virus polymerase proteins expressed in Xenopus oocytes date: 1989-07-31 journal: Virology DOI: 10.1016/0042-6822(89)90523-0 sha: doc_id: 279432 cord_uid: aik5bo6o Abstract All three influenza virus polymerase (P) proteins were expressed in Xenopus oocytes from microinjected in vitro transcribed mRNA analogs, with yields of up to 100 ng per oocyte. keywords: complex; influenza; oocytes; pb2; pbl; polymerase; proteins; virus cache: cord-279432-aik5bo6o.txt plain text: cord-279432-aik5bo6o.txt item: #276 of 541 id: cord-279463-bli8hwda author: Lipp, Joachim title: The membrane-spanning segment of invariant chain (Iγ) contains a potentially cleavable signal sequence date: 1986-09-26 words: 6280 flesch: 59 summary: Membrane insertion might occur in a loop-like fashion as this scheme can most easily explain how the different membrane topologies of membrane proteins are achieved (Engelman and Steitz, 1981) . Membrane proteins are also inserted into the ER membrane by an SRP-mediated mechanism (Anderson et al., 1983; Rottier et al., 1985; Spiess and Lodish, 1986; Lipp and Dobberstein, 1986) . keywords: amino; insertion; membrane; protein; residues; segment; sequence; signal; terminal cache: cord-279463-bli8hwda.txt plain text: cord-279463-bli8hwda.txt item: #277 of 541 id: cord-279586-likfvwwj author: Jin, Jian title: Effects of Sonication on the In vitro Digestibility and Structural Properties of Buckwheat Protein Isolates date: 2020-09-17 words: 4837 flesch: 40 summary: Sonication mostly decreased the PDI, suggesting that the dispersion of proteins occurred in a narrower molecular weight distribution, possibly ascribed to the formation of aggregates or to swelling of protein particles. Taken together, sonication has proven to be a promising approach for improving the digestibility of buckwheat proteins, which can be explored as a source of plant-based alternative protein for food applications. keywords: amplitude; bpis; buckwheat; content; digestibility; min; protein; sonication; structure; surface; ultrasound cache: cord-279586-likfvwwj.txt plain text: cord-279586-likfvwwj.txt item: #278 of 541 id: cord-279598-xzionafe author: Chang, Chia-Yu title: Identification of Neutralizing Monoclonal Antibodies Targeting Novel Conformational Epitopes of the Porcine Epidemic Diarrhoea Virus Spike Protein date: 2019-02-21 words: 5407 flesch: 42 summary: As shown in Fig. 6 , the monomer of PEDV S protein was divided into S1 (a.a. 1-735, in light-blue) and S2 (a.a. 736-1378, in grey). A full-length homology model of the ectodomain of recombinant PEDV S protein was generated by SWISS-Model and built with ProMod3 version 1.0.0 (https://swissmodel.expasy. org). keywords: a.a; epidemic; epitope; pedv; pedv s; porcine; protein; spike; strain; virus cache: cord-279598-xzionafe.txt plain text: cord-279598-xzionafe.txt item: #279 of 541 id: cord-279629-t1xjy12y author: Nazneen Akhand, Mst Rubaiat title: Genome based Evolutionary study of SARS-CoV-2 towards the Prediction of Epitope Based Chimeric Vaccine date: 2020-04-15 words: 6731 flesch: 37 summary: ( Figure 10E ) indicated low chance of deformation of vaccine protein V3. Protein sequence of the spike, envelope, membrane and nucleocapsid were also retrieved from the corresponding genome sequences found in NCBI (Supplementary File 1). keywords: analysis; cell; coronavirus; covid-19; different; epitopes; et al; figure; novel; prediction; protein; sars; server; spike; study; table; vaccine cache: cord-279629-t1xjy12y.txt plain text: cord-279629-t1xjy12y.txt item: #280 of 541 id: cord-279691-v5kpmk0b author: Hagemeijer, Marne C. title: Biogenesis and Dynamics of the Coronavirus Replicative Structures date: 2012-11-21 words: 9053 flesch: 36 summary: [151] [152] [153] can all be applied to investigate the CoV RTCs and the membranous replicative structures at the ultrastructural level using fluorescently-tagged proteins, while EU-labeling of viral RNA in combination with correlative light-electron microscopy may provide the resolution to indisputably pinpoint the exact location of viral RNA synthesis [154] . Organelle-Like Membrane Compartmentalization of Positive-Strand RNA Virus Replication Factories Cytoplasmic Viral Replication Complexes Modification of Intracellular Membrane Structures for Virus Replication SARS-Coronavirus Replication is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum Identification of a Novel Coronavirus in Patients with Severe Acute Respiratory Syndrome A Novel Coronavirus Associated with Severe Acute Respiratory Syndrome Isolation and Characterization of Viruses Related to the SARS Coronavirus from Animals in Southern China Bats are Natural Reservoirs of SARS-Like Coronaviruses Evolving the Largest RNA Virus Genome A Contemporary View of Coronavirus Transcription Coronaviruses use Discontinuous Extension for Synthesis of Subgenome-Length Negative Strands Sequence Motifs Involved in the Regulation of Discontinuous Coronavirus Subgenomic RNA synthesis Coronavirus Minus-Strand RNA Synthesis and Effect of Cycloheximide on Coronavirus RNA Synthesis The RNA Structures Engaged in Replication and Transcription of the A59 Strain of Mouse Hepatitis Virus The Primary Structure and Expression of the Second Open Reading Frame of the Polymerase Gene of the Coronavirus MHV-A59; a Highly Conserved Polymerase is Expressed by an Efficient Ribosomal Frameshifting Mechanism Characterization of an Efficient Coronavirus Ribosomal Frameshifting Signal: Requirement for an RNA Pseudoknot Virus-Encoded Proteinases and Proteolytic Processing in the Nidovirales Processing of Open Reading Frame 1a Replicase Proteins nsp7 to nsp10 in Murine Hepatitis Virus Strain A59 Replication Functional and Genetic Analysis of Coronavirus Replicase-Transcriptase Proteins The RNA Polymerase Activity of SARS-Coronavirus nsp12 is Primer Dependent Non-Canonical RNA-Dependent RNA Superfamily 1 Helicase has RNA and DNA Duplex-Unwinding Activities with 5'-to-3' Polarity The Severe Acute Respiratory Syndrome (SARS) Coronavirus NTPase/helicase Belongs to a Distinct Class of 5' to 3' Viral Helicases Multiple Enzymatic Activities Associated with Severe Acute Respiratory Syndrome Coronavirus Helicase Human Coronavirus 229E Nonstructural Protein 13: Characterization of Duplex-Unwinding, Nucleoside Triphosphatase, and RNA 5'-Triphosphatase Activities Functional Screen Reveals SARS Coronavirus Nonstructural Protein nsp14 as a Novel Cap N7 Methyltransferase Coronavirus Nonstructural Protein 16 is a Cap-0 Binding Enzyme Possessing (Nucleoside-2'O)-Methyltransferase Activity In Vitro Reconstitution of SARS-Coronavirus mRNA Cap Methylation Molecular Mapping of the RNA Cap 2'-O-Methyltransferase Activation Interface between Severe Acute Respiratory Syndrome Coronavirus nsp10 and nsp16 Discovery of an RNA Virus 3'→5' Exoribonuclease that is Critically Involved in Coronavirus RNA Synthesis Major Genetic Marker of Nidoviruses Encodes a Replicative Endoribonuclease RNA Recognition and Cleavage by the SARS Coronavirus Endoribonuclease Infidelity of SARS-CoV Nsp14-Exonuclease Mutant Virus Replication is Revealed by Complete Genome Sequencing An RNA Proofreading Machine Regulates Replication Fidelity and Diversity RNA 3'-End Mismatch Excision by the Severe Acute Respiratory Syndrome Coronavirus Nonstructural Protein nsp10/nsp14 Exoribonuclease Complex Identification of Severe Acute Respiratory Syndrome Coronavirus Replicase Products and Characterization of Papain-Like Protease Activity Topology and Membrane Anchoring of the Coronavirus Replication Complex: keywords: cells; coronavirus; cov; dmvs; hepatitis; membrane; nsp3; nsp4; protein; replication; rna; rna synthesis; sars; sites; structures; synthesis; viruses cache: cord-279691-v5kpmk0b.txt plain text: cord-279691-v5kpmk0b.txt item: #281 of 541 id: cord-280360-rh37d5wc author: Gibson, David S. title: Comparative analysis of synovial fluid and plasma proteomes in juvenile arthritis – Proteomic patterns of joint inflammation in early stage disease date: 2009-05-02 words: 8306 flesch: 38 summary: The group of selected synovial fluid proteins fell within~10 to 100 KDa molecular weight range. This study is concerned with revealing protein markers to allow us to not only track the process of inflammation in detail, but more importantly to dissecting out synovial protein expression patterns which may identify more reliable predictors of JIA outcome. keywords: analysis; arthritis; disease; expression; fluid; gel; inflammation; jia; joint; levels; patients; plasma; proteins; proteome; spots; study; synovial cache: cord-280360-rh37d5wc.txt plain text: cord-280360-rh37d5wc.txt item: #282 of 541 id: cord-280429-4fota9rl author: Medvedev, Kirill E. title: Functional and evolutionary analysis of viral proteins containing a Rossmann‐like fold date: 2018-06-13 words: 7478 flesch: 42 summary: Given the relatively high number of viral protein families that contain a Rossmann-like fold (81 families), we sought to examine their evolutionary distributions among folds from the three major host kingdoms. This nearly equal distribution suggests the potential for viral protein families that derive from ancient origin, as the prevalence of HGT stems from bacterial origins. keywords: archea; bacteria; binding; core; dna; domains; families; family; fig; fold; helicase; host; protein; rossmann; structure; topology; viruses cache: cord-280429-4fota9rl.txt plain text: cord-280429-4fota9rl.txt item: #283 of 541 id: cord-280679-jj3wzojy author: Marblestone, Jeffrey G. title: Comparison of SUMO fusion technology with traditional gene fusion systems: Enhanced expression and solubility with SUMO date: 2006-01-01 words: 4862 flesch: 48 summary: The TRX tag did not enhance solubility for the difficult-toexpress proteins, while both SUMO and NUS A had pronounced soluble fusion protein expression. Numerous technological advancements have vastly improved recombinant protein expression in E. coli, including the development of strong promoters (Studier and Moffatt 1986) , coexpression with chaperones and foldases (Ikura et al. 2002) , and the use of protein fusions. keywords: egfp; expression; fusion; protease; protein; solubility; sumo; tag; tags cache: cord-280679-jj3wzojy.txt plain text: cord-280679-jj3wzojy.txt item: #284 of 541 id: cord-280878-1kt51viz author: To, Janet title: Targeting the Channel Activity of Viroporins date: 2016-01-07 words: 15340 flesch: 29 summary: Viral channel proteins in intracellular protein-protein communication: Vpu of HIV-1, E5 of HPV16 and p7 of HCV Mechanism of function of viral channel proteins and implications for drug development Structure-guided design affirms inhibitors of hepatitis C virus p7 as a viable class of antivirals targeting virion release Resistance mutations define specific antiviral effects for inhibitors of the hepatitis C virus p7 ion channel Function of the respiratory syncytial virus small hydrophobic protein Large-scale sequence analysis of M gene of influenza A viruses from different species: Mechanisms for emergence and spread of amantadine resistance Site-directed mutations in the Sindbis virus 6K protein reveal sites for fatty acylation and the underacylated protein affects virus release and virion structure Structure and ion channel activity of the human respiratory syncytial virus (hRSV) small hydrophobic protein transmembrane domain Two different conformations in hepatitis C virus p7 protein account for proton transport and dye release The small hydrophobic protein of the human respiratory syncytial virus forms pentameric ion channels Hepatitis C virus p7 is critical for capsid assembly and envelopment Agnoprotein of polyomavirus BK interacts with proliferating cell nuclear antigen and inhibits DNA replication Agnoprotein of mammalian polyomaviruses Development and validation of a high-throughput screening assay for the hepatitis C virus p7 viroporin TGEV corona virus ORF4 encodes a membrane protein that is incorporated into virions Development and application of hepatitis C reporter viruses with genotype 1 to 7 core-nonstructural protein 2 (NS2) expressing fluorescent proteins or luciferase in modified JFH1 NS5A A live, impaired-fidelity coronavirus vaccine protects in an aged, immunocompromised mouse model of lethal disease Influence of amantadine resistance mutations on the pH regulatory function of the M2 protein of influenza A viruses Maturation of influenza A virus hemagglutinin-Estimates of the pH encountered during transport and its regulation by the M2 protein The p7 protein of hepatitis C virus forms an ion channel that is blocked by the antiviral drug Genotype-dependent sensitivity of hepatitis C virus to inhibitors of the p7 ion channel Structural and energetic analysis of drug inhibition of the influenza A M2 proton channel Free energy calculations on the two drug binding sites in the M2 proton channel The p7 polypeptide of hepatitis C virus is critical for infectivity and contains functionally important genotype-specific sequences Triatoma virus recombinant VP4 protein induces membrane permeability through dynamic pores Semliki Forest virus 6K protein modifies membrane permeability after inducible expression in Escherichia coli cells Essential roles of Leu/Ile/Phe-rich domain of JC virus agnoprotein in dimer/ oligomer formation, protein stability and splicing of viral transcripts Infection by agnoproteinnegative mutants of polyomavirus JC and SV40 results in the release of virions that are mostly deficient in DNA content Protection and mechanism of action of a novel human respiratory syncytial virus vaccine candidate based on the extracellular domain of small hydrophobic protein Direct-acting antiviral agents and the path to interferon independence Structure and mechanism of the M2 proton channel of influenza A virus Identification of an ion channel activity of the Vpu transmembrane domain and its involvement in the regulation of virus release from HIV-1-infected cells Viroporins: Structure, function and potential as antiviral targets TLR2/MyD88/NF-kappa B pathway, reactive oxygen species, potassium efflux activates NLRP3/ASC inflammasome during respiratory syncytial virus infection Insight into the mechanism of the influenza A proton channel from a structure in a lipid bilayer Modular alpha-helical mimetics with antiviral activity against respiratory syncitial virus High frequency of resistant viruses harboring different mutations in amantadine-treated children with influenza The origin of Hepatitis C virus Mapping the interaction between the cytoplasmic domains of HIV-1 viral protein U and human CD4 with NMR spectroscopy The M, E, and N structural proteins of the severe acute respiratory syndrome coronavirus are required for efficient assembly, trafficking, and release of virus-like particles HIV-1 Vpu protein antagonizes innate restriction factor BST-2 via lipid-embedded helix-helix interactions Exacerbated innate host response to SARS-CoV in aged non-human primates Hepatitis C virus p7 protein is crucial for assembly and release of infectious virions Determinants of hepatitis C virus p7 ion channel function and drug sensitivity identified in vitro Inhibition of hepatitis C virus p7 membrane channels in a liposome-based assay system Structural basis for the function and inhibition of an influenza virus proton channel keywords: activity; am2; amt; binding; c virus; channel; channel activity; coronavirus; domain; drug; et al; hcv; hepatitis; human; influenza; inhibitors; ion; membrane; p7 protein; protein; release; residues; site; structure; syncytial; terminal; viroporins; virus; virus p7; viruses; vpu cache: cord-280878-1kt51viz.txt plain text: cord-280878-1kt51viz.txt item: #285 of 541 id: cord-281005-6gi18vka author: Singh, Praveen Kumar title: Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development date: 2020-09-01 words: 3164 flesch: 48 summary: 4, 5 In the present study, we found that although multiple genetic variants were identified in the same country, yet there were some unique mutations found in a particular country, which suggests that diversity of S protein mutations might have significant role in the pathogenicity of this virus in countries with high or low mortality rates, as proposed by others also. Conclusion S protein is the major target for vaccine development, but several mutations were predicted in the antigenic epitopes of S protein across all genomes available globally. keywords: antigenic; domain; genomes; mutations; protein; sars; spike; virus cache: cord-281005-6gi18vka.txt plain text: cord-281005-6gi18vka.txt item: #286 of 541 id: cord-281101-gv1sgbk1 author: Shin, Gu-Choul title: Preparation and characterization of a novel monoclonal antibody specific to severe acute respiratory syndrome-coronavirus nucleocapsid protein date: 2006-08-30 words: 5936 flesch: 42 summary: SARS N proteins exist as phosphorylated forms in mature viral particles, whereas, in host cells, this protein exists in both the dephosphorylated form and the phosphorylated form (Kalicharran and Dales, 1995; Surjit et al., 2005) . Three IgG(2b) mAbs were recognized within the N-terminus of N protein, whereas the epitope of two IgG(1) mAbs localized within the C-terminus. keywords: cells; coronavirus; cov; elisa; mabs; n protein; protein; sars cache: cord-281101-gv1sgbk1.txt plain text: cord-281101-gv1sgbk1.txt item: #287 of 541 id: cord-281124-4nhy35xn author: Soowannayan, Chumporn title: RNA-Binding Domain in the Nucleocapsid Protein of Gill-Associated Nidovirus of Penaeid Shrimp date: 2011-08-03 words: 5634 flesch: 41 summary: GAV N protein also bound to double-stranded (ds)RNAs prepared to GAV ORF1b gene regions and to bacteriophage M13 genomic ssDNA. GAV N protein binding to two dsRNAs was also assessed (Fig. 3B) . keywords: binding; fig; gav; gene; length; protein; rna; sequence; ssrna; virus cache: cord-281124-4nhy35xn.txt plain text: cord-281124-4nhy35xn.txt item: #288 of 541 id: cord-281528-xy8j5jiv author: Di Paola, Luisa title: The Discovery of a Putative Allosteric Site in the SARS-CoV-2 Spike Protein Using an Integrated Structural/Dynamic Approach date: 2020-06-17 words: 6724 flesch: 46 summary: Red triangles represent the position of AMR residues on the S1 protein sequence. Therefore, we propose that the different allosteric properties of AMR residues were due to mutations in the S-ACE2 interface. keywords: ace2; ace2 complex; affinity; allosteric; amr; complex; cov; cov-2; figure; protein; residues; s protein; sars; spike cache: cord-281528-xy8j5jiv.txt plain text: cord-281528-xy8j5jiv.txt item: #289 of 541 id: cord-281552-zfjy3m3i author: Alsaadi, Entedar A. J. title: Identification of a Membrane Binding Peptide in the Envelope Protein of MHV Coronavirus date: 2020-09-22 words: 4795 flesch: 42 summary: Retention of the avian coronavirus infectious bronchitis virus envelope protein in the pre-Golgi compartments and physical interaction between the envelope and membrane proteins Assembly of the coronavirus envelope: For many coronaviruses, including MHV, E protein also functions as an ion channel, a viroporin [14, 15] , affecting the trafficking of virions in the secretory pathways and membrane permeability, both of which are essential for virus growth [3, 16, 17] . keywords: binding; cells; coronavirus; expression; guvs; interaction; membrane; mhv; peptide; protein; region; sars cache: cord-281552-zfjy3m3i.txt plain text: cord-281552-zfjy3m3i.txt item: #290 of 541 id: cord-282604-xp71rkxc author: Nikolaev, EN title: Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein date: 2020-05-25 words: 2185 flesch: 47 summary: [6] , which has a structure similar to SARS-CoV-2 structure, it can be concluded that the number of copies of E, M, and N proteins is much larger than that of S, but the E and M are relatively short and tightly membrane-bound proteins, what makes them difficult to extract, detect, and identify. The detection of viral proteins in body fluids by mass-spectrometry based methods could serve as a complementary diagnostic tool. keywords: detection; mass; proteins; samples; sars; virus cache: cord-282604-xp71rkxc.txt plain text: cord-282604-xp71rkxc.txt item: #291 of 541 id: cord-282859-uxltqopq author: Rosati, A title: BAG3: a multifaceted protein that regulates major cell pathways date: 2011-04-07 words: 4448 flesch: 34 summary: In different tumor contexts, BAG3 protein was reported to sustain cell survival, resistance to therapy, and/or motility and metastatization. The origin of this doublet is currently unknown, but it could derive from post-translational modifications as phosphorylations, indeed BAG3 protein contains several serinerich motifs and 10 tyrosine residues. keywords: apoptosis; bag3; cancer; cell; chaperone; domain; expression; gene; protein; role; stress; tumor cache: cord-282859-uxltqopq.txt plain text: cord-282859-uxltqopq.txt item: #292 of 541 id: cord-283035-tpqf458q author: Thanthrige-Don, Niroshan title: Analyses of the spleen proteome of chickens infected with Marek's disease virus date: 2009-08-01 words: 7910 flesch: 38 summary: Arrows with accompanying spot numbers show successfully identified protein spots that were uniquely expressed (qualitative differences) in each group at corresponding time point. Comparison of total numbers of significantly differentially expressed protein spots in MDV-infected spleens at various sampling time points. keywords: cell; changes; chickens; disease; dpi; et al; expression; host; infection; marek; mdv; proteins; spleen; spots; study; time; virus cache: cord-283035-tpqf458q.txt plain text: cord-283035-tpqf458q.txt item: #293 of 541 id: cord-283096-qm7h4qui author: Jeon, Young Joo title: ISG15 and immune diseases date: 2010-02-12 words: 11213 flesch: 38 summary: Like ubiquitin, ISG15 proteins in some species are synthesized as precursors that need to be processed before conjugation to target proteins (Fig. 2) While ISG15 molecules in human, mouse, and rat are translated as precursors containing the extensions of5-8 amino acids in their C-termini, ISG15 proteins in most other species, including fish and bovine, are synthesized as matured forms [46] . keywords: cells; conjugation; ifn; ifns; interferon; isg15; isgylation; level; mice; protein; response; signaling; type; ubch8; ube1l; ubiquitin; ubp43; virus; −/− cache: cord-283096-qm7h4qui.txt plain text: cord-283096-qm7h4qui.txt item: #294 of 541 id: cord-284208-8fsqgkw5 author: Zolla, Lello title: Proteomics studies reveal important information on small molecule therapeutics: a case study on plasma proteins date: 2008-11-07 words: 6995 flesch: 30 summary: HUPO plasma proteome project: challenges and future directions The human proteome organization plasma proteome project pilot phase: reference specimens, technology platform comparisons, and standardized data submissions and analyses Characterization of the human blood plasma proteome Utilizing human blood plasma for proteomic biomarker discovery Oxidation of proteins: basic principles and perspectives for blood proteomics Proteomic analysis of RBC membrane protein degradation during blood storage Composition of the peptide fraction in human blood plasma: database of circulating human peptides Peptide and protein drug delivery to and into tumors: challenges and solutions Effects of genetic engineering on the pharmacokinetics of antibodies Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry Multi-component immunoaffinity subtraction chromatography: an innovative step towards a comprehensive survey of the human plasma proteome Differences among techniques for high-abundant protein depletion Immunoaffinity separation of plasma proteins by IgY microbeads: meeting the needs of proteomic sample preparation and analysis Evaluation of multiprotein immunoaffinity subtraction for plasma proteomics and candidate biomarker discovery using mass spectrometry A novel four-dimensional strategy combining protein and peptide separation methods enables detection of low-abundance proteins in human plasma and serum proteomes Two-dimensional separation of human plasma proteins using iterative free-flow electrophoresis The ProteoMiner in the proteomic arena: a non-depleting tool for discovering low-abundance species Prefractionation, enrichment, desalting and depleting of low volume and low abundance proteins and peptides using the MF10 An investigation into the human serum interactome Protein biomarker discovery and validation: the long and uncertain path to clinical utility Proteomics and disease -the challenges for technology and discovery Clinical proteomics: revolutionizing disease detection and patient tailoring therapy Mining the plasma proteome for cancer biomarkers Strategies for plasma proteomic profiling of cancers Proteomics-driven cancer biomarker discovery: looking to the future Dysregulation of retinoid transporters expression in body fluids of schizophrenia patients Comparative plasma proteome analysis of lymphoma-bearing SJL mice Proteomic characterization of inter-alpha inhibitor proteins from human plasma Proteomic strategies for Individualizing therapy of acute myeloid leukemia (AML) Pharmacogenomics and pharmacoproteomics in the evaluation and management of short stature From genomics to proteomics Mass spectrometry-based proteomics Mass spectrometry-based clinical proteomics Calorimetry outside the box: a new window into the plasma proteome The impact of systems approaches on biological problems in drug discovery Identifying pharmacodynamic protein markers of centrally active drugs in humans: a pilot study in a novel clinical model Alpha cell function in health and disease: influence of glucagon-like peptide-1 Technologies and methods for sample pretreatment in efficient proteome and peptidome analysis Quantitative phosphoproteomic analysis of signaling network dynamics Signaling -2000 and beyond Technology insight: pharmacoproteomics for cancerpromises of patient-tailored medicine using protein microarrays High-content single-cell drug screening with phosphospecific flow cytometry Antibody arrays in cancer research Protein chip technology Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front Progress in protein and antibody In the near future, pharmacoproteomics, the use of proteomic technologies in the field of drug discovery and development, and interactomics, the branch of proteomics which is concerned with identifying interactions between proteins, will allow researchers to (i) know the specific protein changes that occur in biological compartments in response to drug administration; (ii) design small novel therapeutic molecules that can have extended half-lives if carried by plasma protein in the blood stream. keywords: analysis; biomarkers; blood; cell; development; discovery; disease; drug; human; interactions; interactome; peptides; plasma; proteins; proteome; proteomic cache: cord-284208-8fsqgkw5.txt plain text: cord-284208-8fsqgkw5.txt item: #295 of 541 id: cord-284648-yznlgzir author: Varanko, Anastasia title: Recent trends in protein and peptide-based biomaterials for advanced drug delivery date: 2020-08-29 words: 33598 flesch: 36 summary: As researchers continue to make progress in adapting existing and developing new protein materials, there is also great opportunity for biological and materials science research that will maximize the clinical success of protein drug carriers. OVA was originally chosen as a carrier for drug delivery because of its availability, low cost, ability to form gel networks and stabilize emulsions and foams, and pH-and temperature-sensitive properties [128] . keywords: acid; albumin; applications; assembly; binding; cancer; cell; collagen; crosslinking; delivery; dox; drug; drug delivery; elastin; elp; figure; fold; fusion; gelatin; growth; half; helix; human; hydrogel; hydrophobic; keratin; life; materials; model; nanoparticles; peptide; phase; polypeptide; properties; protein; r n; release; residues; self; sequence; serum; silk; stability; structure; study; temperature; therapeutic; transferrin; tumor; u r; vivo; zein cache: cord-284648-yznlgzir.txt plain text: cord-284648-yznlgzir.txt item: #296 of 541 id: cord-284990-klsl1nzn author: Zhang, Dapeng title: A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems date: 2011-02-08 words: 13717 flesch: 33 summary: Phylogenetic analysis of each group, along with the phyletic patterns, strongly suggests that SUKH domain proteins have been widely disseminated both within and across the superkingdoms via extensive lateral transfer (Supplementary Data). Firstly, across the bacterial phylogenetic tree we found numerous genomic neighborhoods that linked two or more adjacent genes encoding SUKH domain proteins. keywords: analysis; bacteria; cdi; cell; conserved; domain; figure; fold; genes; immunity; like; neighborhoods; nuclease; proteins; sequence; sukh; sukh domain; sukh superfamily; superfamily; systems; terminal; toxins; versions cache: cord-284990-klsl1nzn.txt plain text: cord-284990-klsl1nzn.txt item: #297 of 541 id: cord-285180-32bxx94u author: Lee, Sunhee title: Functional characterization and proteomic analysis of the nucleocapsid protein of porcine deltacoronavirus date: 2015-10-02 words: 7663 flesch: 33 summary: These observations demonstrated that, like N proteins of other coronaviruses, PDCoV N protein is mostly distributed in the nucleolus along with the cytoplasm and has a conserved subcellular localization property. Similar to N proteins of other coronaviruses, the PDCoV N protein was found to interact with itself to form non-covalently linked oligomers and was mainly localized to the nucleolus. keywords: analysis; cells; expression; gene; host; infection; n cells; n protein; pdcov; pdcov n; porcine; protein; response; time; virus cache: cord-285180-32bxx94u.txt plain text: cord-285180-32bxx94u.txt item: #298 of 541 id: cord-285647-9tegcrc3 author: Estrada, Ernesto title: Fractional diffusion on the human proteome as an alternative to the multi-organ damage of SARS-CoV-2 date: 2020-08-17 words: 9192 flesch: 50 summary: Proteins mainly expressed outside the lungs are significantly perturbed during diffusive processes that have started at other proteins expressed in the lungs. A first step in understanding SARS pathogenesis A SARS-CoV-2-human protein-protein interaction map reveals drug targets and potential drug-repurposing Network medicine framework for identifying drug repurposing opportunities for COVID-19 Specificity and stability in topology of protein networks Perturbation waves in proteins and protein networks: Applications of percolation and game theories in signaling and drug design Predicting perturbation patterns from the topology of biological networks Modeling and simulating networks of interdependent protein interactions Network medicine: A networkbased approach to human disease Protein interaction networks in medicine and disease Human diseases through the lens of network biology Stochastic model of protein-protein interaction: Why signaling proteins need to be colocalized Accounting for conformational changes during protein-protein docking Inferring novel tumor suppressor genes with a protein-protein interaction network and network diffusion algorithms Information flow in interaction networks Sampling the cell with anomalous diffusion-The discovery of slowness Understanding biochemical processes in the presence of sub-diffusive behavior of biomolecules in solution and living cells Protein motion in the nucleus: From anomalous diffusion to weak interactions Random diffusivity from stochastic equations: Comparison of two models of Brownian yet non-Gaussian diffusion Anomalous protein diffusion in living cells as seen by fluorescence correlation spectroscopy Anomalous subdiffusion is a measure for cytoplasmic crowding in living cell Elucidating the origin of anomalous diffusion in crowded fluids In a mirror dimly: Tracing the movements of molecules in living cells Protein entrapment in polymeric mesh: Diffusion in crowded environment with fast process on short scales From continuous time random walks to fractional Fokker-Planck equation A mathematical analysis of obstructed diffusion within skeletal muscle Fractional Calculus and Waves in Linear Viscoelasticity. keywords: cov-2; diffusion; human; lungs; network; ppi; process; processes; proteins; sars; time cache: cord-285647-9tegcrc3.txt plain text: cord-285647-9tegcrc3.txt item: #299 of 541 id: cord-286217-3uklf2u2 author: Jiang, He-wei title: SARS-CoV-2 proteome microarray for global profiling of COVID-19 specific IgG and IgM responses date: 2020-07-14 words: 6841 flesch: 49 summary: One part of a sub-microarray showed the IgG responses of two controls, i.e., LC169 and NC96 against N proteins, N-Cter and N-Nter indicates the C-terminal and N-terminal of N protein, respectively. Indeed, a variety of protein microarrays have already been constructed and successfully applied to serum antibody profiling, such as the Mycobacterium tuberculosis proteome microarray 21 , the SARS-CoV protein microarray 12 , the Dengue virus protein microarray 22 and the influenza virus protein microarray 23 . keywords: antibody; convalescent; coronavirus; cov-2; fig; igg; igm; microarray; patients; proteins; responses; sars; serum; values cache: cord-286217-3uklf2u2.txt plain text: cord-286217-3uklf2u2.txt item: #300 of 541 id: cord-286219-qcx5ehnh author: Calistri, Arianna title: The Ubiquitin-Conjugating System: Multiple Roles in Viral Replication and Infection date: 2014-05-06 words: 10214 flesch: 35 summary: First of all, viral proteins have been described that can modify the substrate specificity of cellular Ub ligases. In addition to p53 and pRB, another protein complex involved in cell cycle control, the anaphase-promoting complex (APC) is emerging as a key target for viral proteins. keywords: budding; cells; cellular; complex; cycle; degradation; human; ligase; proteasome; protein; replication; role; tetherin; ubiquitin; ubiquitination; virus; viruses; vpr; vpu cache: cord-286219-qcx5ehnh.txt plain text: cord-286219-qcx5ehnh.txt item: #301 of 541 id: cord-286301-7sjw5ci7 author: Sadasivan, Jibin title: Cytoplasmic tail of coronavirus spike protein has intracellular targeting signals date: 2017-04-18 words: 6283 flesch: 41 summary: There is evidence to suggest that the localization signal in S protein is only active in the unfolded structure in ER, and its specific interactions in the folded form between the M protein leads to its incorporation into the virion, where the retention signals are no longer recognized causing excess S protein to go to the surface. A similar dibasic motif (KXHXX) in the cytoplasmic tail of S protein from alpha-coronavirus TGEV and from the newly emerging pathogen SARS, an outlier of beta-coronavirus, localizes the S protein in the ERGIC (Teasdale and Jackson 1996; keywords: cells; hcov; intracellular; localization; motif; oc43; protein; s protein; sars; signal; spike cache: cord-286301-7sjw5ci7.txt plain text: cord-286301-7sjw5ci7.txt item: #302 of 541 id: cord-286603-4p3t0vre author: Duan, Zhiqiang title: TMT-based quantitative proteomics analysis reveals the attenuated replication mechanism of Newcastle disease virus caused by nuclear localization signal mutation in viral matrix protein date: 2020-06-27 words: 10709 flesch: 31 summary: Taken together, our findings demonstrate that NDV replication is closely related to the nucleocytoplasmic trafficking of M protein, which accelerates our understanding of the molecular functions of NDV M protein. These results suggested that ubiquitin ligases might participate in the nucleocytoplasmic trafficking of M protein and the assembly and budding of NDV progeny virions, but whether NDV M protein interacts with some of these ubiquitin ligasesrelated DEPs and the exact role of their interaction in NDV budding are worth to be deeply studied. keywords: analysis; cells; deps; expression; figure; group; host; hpi; infection; m protein; ndv; nlsm; protein; replication; rna; rss1gfp; rss1gfp group; tifa; transcription; virus cache: cord-286603-4p3t0vre.txt plain text: cord-286603-4p3t0vre.txt item: #303 of 541 id: cord-286635-7aflpgxd author: YANG, Yong-xin title: Comparative Proteomic Analysis of Plasma from Clinical Healthy Cows and Mastitic Cows date: 2009-10-31 words: 2484 flesch: 38 summary: Protein spots were visualized with silver staining as previously described (Mortz et al. 2001) , and micropreparative gels were stained with Coomassie Blue. Gel images were conducted to remove backgrounds and to automatically detect protein spots. keywords: cows; gels; mastitis; plasma; protein; spots cache: cord-286635-7aflpgxd.txt plain text: cord-286635-7aflpgxd.txt item: #304 of 541 id: cord-286970-4pl95r0o author: Mamipour, Mina title: An overview on molecular chaperones enhancing solubility of expressed recombinant proteins with correct folding date: 2017-04-12 words: 4999 flesch: 50 summary: DsbA(thioredoxin-like thiol-disulphide oxido-reductase) and DsbB(cytoplasmic membrane protein) are two enzymes that help to disulphide bonds formation in periplasmic proteins [131, 132] . DsbG has negative charged surface, which is appropriate to interact with folded proteins [147, 148] . keywords: atp; bonds; chaperones; domain; expression; family; folding; hsp70; proteins cache: cord-286970-4pl95r0o.txt plain text: cord-286970-4pl95r0o.txt item: #305 of 541 id: cord-287266-sd5izamc author: Song, Zhenhui title: EIF4A2 interacts with the membrane protein of transmissible gastroenteritis coronavirus and plays a role in virus replication date: 2019-04-30 words: 4419 flesch: 47 summary: After blotting with 5% BSA (bovine serum albumin, BBI), the cells were incubated with TGEV M protein (1:100) mAb and rabbit pAb to EIF4A2 (1:50) overnight at 4°C. In addition, the gene of M protein is highly conserved and encoded a decisive protein for viral proliferation (ZHENHUI Song et al., 2015) . keywords: cells; eif4a2; pgbkt7; piecs; protein; replication; tgev; virus; yeast cache: cord-287266-sd5izamc.txt plain text: cord-287266-sd5izamc.txt item: #306 of 541 id: cord-287410-boxxlopy author: Devi, Arpita title: In silico designing of multi-epitope vaccine construct against human coronavirus infections date: 2020-08-10 words: 7221 flesch: 55 summary: The antigenicity of the epitopes and vaccine constructs was predicted using Vaxigen v2.0 (Doytchinova & Flower, 2007) webserver. The allergenicity of the epitopes and vaccine construct was predicted using AllerTOP v2.0 (Dimitrov et al., 2014) webserver. keywords: binding; cell; construct; coronavirus; cov; epitopes; level; protein; sars; score; server; structure; vaccine cache: cord-287410-boxxlopy.txt plain text: cord-287410-boxxlopy.txt item: #307 of 541 id: cord-287450-hydy874v author: Wendt, K Ulrich title: Structures and diseases date: 2008 words: 2774 flesch: 30 summary: Starting the session on viral diseases, Rolf Hilgenfeld (University of Lübeck) reviewed the work from his laboratory on proteases of RNA viruses, such as severe acute respiratory syndrome (SARS) coronavirus and coxsackievirus B3, and also highlighted recent structural data on falcipain-2 from Plasmodium falciparum, discussing implications for the design of active-site directed and allosteric inhibitors for these cysteine proteases 14 . Ryota Kuroki (Japan Atomic Energy Agency) presented recent structural studies on the complex of human granulocyte colony-stimulating factor (GCSF), a cytokine used for treatment of granulopenia, with its receptor. keywords: binding; cell; complex; data; diseases; institute; molecular; protein; session; structure; university cache: cord-287450-hydy874v.txt plain text: cord-287450-hydy874v.txt item: #308 of 541 id: cord-287477-aios0h8s author: Sicari, Daria title: Role of the early secretory pathway in SARS-CoV-2 infection date: 2020-07-28 words: 6498 flesch: 35 summary: Several protein disulfide isomerase inhibitors are available, including PACMA31, which specifically targets the cysteine residue present in the active site of protein disulfide isomerase proteins and blocking their capability to bind cargoes (Kaplan et al., 2015) . Among the 66 U.S. Food and Drug Administration-approved drugs, they suggested PS30613 (ER protein processing, Sec61 inhibitor); IHVR-19029 (ER protein processing); FK-506 (FKBP binder); zotatifin (EIF4E2/H, eiF4a inhibitor); rapamycin and rapalogs (LARP1, FKBP15, FKBP7/10, mammalian target of rapamycin inhibitor); diverse SIGMAR1/2 modulators, such as chloroquine, PB28, and haloperidol E-52862, PD-144418, and RS-PPCC; as well as diverse SIGMAR1/2 direct modulators, such as the antagonist PD-144418 and the agonist RS-PPCC (Gordon et al., 2020) . keywords: cell; coronavirus; cov-2; et al; golgi; host; infection; membrane; pathway; protein; sars; secretory; stress; table; virus cache: cord-287477-aios0h8s.txt plain text: cord-287477-aios0h8s.txt item: #309 of 541 id: cord-287729-pl88otue author: Gray, Stewart M. title: Plant virus proteins involved in natural vector transmission date: 1996-07-31 words: 2230 flesch: 52 summary: Both mechanisms probably involve conformational changes of virus proteins during their association with the vector. key: cord-287729-pl88otue authors: Gray, Stewart M. title: Plant virus proteins involved in natural vector transmission date: 1996-07-31 journal: Trends in Microbiology DOI: 10.1016/0966-842x(96)10040-8 sha: doc_id: 287729 cord_uid: pl88otue Abstract Plant viruses transmitted by invertebrate vectors either reversibly bind to vector mouthparts or are internalized by the vector and later secreted. keywords: aphid; coat; protein; transmission; vector; virus cache: cord-287729-pl88otue.txt plain text: cord-287729-pl88otue.txt item: #310 of 541 id: cord-288101-pij16jaa author: Li, Jun-Yu title: Proteomic analysis of the response of porcine adrenal gland to heat stress date: 2019-02-28 words: 5160 flesch: 36 summary: This conclusion follows directly from data suggesting that heat stress reduces the expression of heat shock proteins, handicapping their ability to induce a protective immune response when immunocytes are confronted with foreign entities. Among these 226 DEPs, tubulin and heat shock protein (HSP) such as HSP70, HSP60, HSP27, and Histone H2A might be involved in the regulation of heat stress. keywords: adrenal; analysis; cell; deps; fig; function; gland; heat; heat stress; pigs; proteins; response; stress cache: cord-288101-pij16jaa.txt plain text: cord-288101-pij16jaa.txt item: #311 of 541 id: cord-288673-ku3tmjd3 author: Sabotič, Jerica title: Microbial and fungal protease inhibitors—current and potential applications date: 2012-01-05 words: 14637 flesch: 17 summary: In medicine, protease inhibitors can be used as diagnostic or therapeutic agents for viral, bacterial, fungal and parasitic diseases as well as for treating cancer and immunological, neurodegenerative and cardiovascular diseases. Furthermore, protease inhibitors are indispensable in protein purification procedures to prevent undesired proteolysis during heterologous expression or protein extraction. keywords: activity; addition; bacteria; binding; cancer; cathepsin; cell; cysteine; cysteine protease; development; diseases; e.g.; et al; expression; families; family; fungal; fungi; host; inhibitors; metalloproteases; microbial; novel; origin; peptidase; peptide; plant; protease; protease inhibitors; protein; rawlings; resistance; role; serine; staphylococcus; structure; target; use; virulence cache: cord-288673-ku3tmjd3.txt plain text: cord-288673-ku3tmjd3.txt item: #312 of 541 id: cord-289026-v09m2fzw author: Sun, Yan-gang title: Characterization of the interaction between recombinant porcine aminopeptidase N and spike glycoprotein of porcine epidemic diarrhea virus date: 2018-10-01 words: 5243 flesch: 49 summary: Lane 1: PEDV S1 protein; Lane 2: pAPN ectodomain and PEDV S1 protein mixtures (1:1); Lane 3: pAPN ectodomain; Lane 4: pAPN ectodomain and PEDV S1t protein mixtures (1:5); Lane 5: PEDV S1t protein. Therefore, the recombinant proteins were heavily glycosylated compared to their calculated molecular masses (pAPN ectodomain: 104 kDa, PEDV S1 protein: 85.5 kDa, PEDV S1t protein: 15.1 kDa). keywords: binding; cells; coronavirus; diarrhea; ectodomain; fig; papn; pedv; pedv s1; porcine; protein; receptor; s1 t cache: cord-289026-v09m2fzw.txt plain text: cord-289026-v09m2fzw.txt item: #313 of 541 id: cord-289124-6w2zvvj1 author: Mok, Lawrence title: Proteomic analysis of Pteropus alecto kidney cells in response to the viral mimic, Poly I:C date: 2015-11-02 words: 5454 flesch: 48 summary: This study provides new insight into the antiviral response of bat cells, highlighting the importance of energy metabolism. Subsequent work will involve examining the proteomic response of bat cells using live viruses. keywords: analysis; bats; cells; hpt; itraq; pakit03; poly; proteins; samples; spots; virus cache: cord-289124-6w2zvvj1.txt plain text: cord-289124-6w2zvvj1.txt item: #314 of 541 id: cord-289710-ucguzgdm author: None title: Yeast Kex1p is a Golgi-associated membrane protein: deletions in a cytoplasmic targeting domain result in mislocalization to the vacuolar membrane date: 1992-12-02 words: 8024 flesch: 43 summary: This surprising result raises the possibility that the vacuole is the default destination for yeast Golgi membrane proteins. This unexpected finding is discussed in terms of models involving either the vacuole as a default destination for membrane proteins, or by endocytosis to the vacuole following their default localization to the plasma membrane. keywords: activity; cell; domain; et al; forms; golgi; hpa; kexlp; membrane; proteins; retention; targeting; vacuolar; vacuole; yeast cache: cord-289710-ucguzgdm.txt plain text: cord-289710-ucguzgdm.txt item: #315 of 541 id: cord-290088-g9559ux3 author: Loh, Hwei-San title: Using transgenic plants and modified plant viruses for the development of treatments for human diseases date: 2017-08-08 words: 2853 flesch: 26 summary: The initial strategy involved production of recombinant proteins using plant viruses by exploiting their natural ability to infect (full virus) plants. In addition to offering a versatile production platform for numerous plant-made proteins, plant viruses have been engineered to provide medical applications in other ways [22] . keywords: antigen; applications; expression; mice; plant; production; proteins; vaccine; virus cache: cord-290088-g9559ux3.txt plain text: cord-290088-g9559ux3.txt item: #316 of 541 id: cord-290290-wyx9ib7s author: Sinegubova, Maria V. title: High-level expression of the monomeric SARS-CoV-2 S protein RBD 320-537 in stably transfected CHO cells by the EEF1A1-based plasmid vector date: 2020-11-05 words: 6012 flesch: 43 summary: We developed a simple purification scheme that consistently yielded up to 30 mg of RBD protein per liter of the simple shake flask cell culture. This All cell populations, secreting RBD proteins, were analyzed by the quantitative PCR and it was found, that increased productivity of populations, adapted to higher concentrations of MTX corresponds to higher copy numbers of target gene (Fig 3C) . keywords: antigen; cell; cho; cov-2; culture; days; domain; expression; fig; protein; rbd; rbdv2; sars; spike; target; tests cache: cord-290290-wyx9ib7s.txt plain text: cord-290290-wyx9ib7s.txt item: #317 of 541 id: cord-290445-vb53bih9 author: Ahmed, Shiek SSJ title: Interplay of host regulatory network on SARS-CoV-2 binding and replication machinery date: 2020-04-23 words: 3796 flesch: 37 summary: This result confirms the hijack of host hub proteins and their molecular pathways for SARS-CoV2 machinery. For instance, eight differentially expressed hub proteins were noticed in the receptor-mediated network (S1 Table) . keywords: cov-2; cov2; host; hubs; network; proteins; receptor; replication; sars cache: cord-290445-vb53bih9.txt plain text: cord-290445-vb53bih9.txt item: #318 of 541 id: cord-290472-w77cmljm author: Sharon, Donald title: Systems Biology Approaches to Disease Marker Discovery date: 2010-06-09 words: 8676 flesch: 33 summary: Traditionally, discovery and detection of these disease markers relied on low throughput technologies such as Enzyme-Linked Immunosorbant Assay (ELISA) or 2D-gel plus Edman degradation for protein markers, Reverse Transcription-Polymerase Chain Reaction (RT-PCR) for mRNA markers, and restriction enzyme digestion, cloning and Sanger sequencing for DNA markers. Overall, this study demonstrated for the first time that protein microarrays could be used to diagnose and monitor human antibodies as protein markers that are generated during the course of a disease. keywords: autoantibodies; autoantibody; breast; cancer; detection; discovery; disease; genome; identification; markers; mass; microarrays; patients; protein; rna; samples; sequencing; serum; studies; technology cache: cord-290472-w77cmljm.txt plain text: cord-290472-w77cmljm.txt item: #319 of 541 id: cord-290638-7ro72sv3 author: Lenstra, Johannes A. title: Antigenicity of the peplomer protein of infectious bronchitis virus date: 1989-01-31 words: 3968 flesch: 46 summary: After adding concentrated SDS-containing lysis buffer (Laemmli and Favre, 1973) , hybrid proteins were spotted via a manifold on nitrocellulose membranes or fractionated by SDSpolyacrylamide gel electrophoresis (7.5%) followed by Western blotting. Hybrid proteins thus immobilized were analysed as described for the filters of the immunoscreening (see above). keywords: antisera; epitopes; et al; expression; fragments; ibv; pex; region cache: cord-290638-7ro72sv3.txt plain text: cord-290638-7ro72sv3.txt item: #320 of 541 id: cord-290904-ngvhk0qy author: Zheng, Zhiqiang title: Monoclonal antibodies for the S2 subunit of spike of SARS-CoV-1 cross-react with the newly-emerged SARS-CoV-2 date: 2020-07-16 words: 4490 flesch: 49 summary: In particular, mAb 1A9 was demonstrated to detect S protein in SARS-CoV-2-infected cells and is suitable for use in a sandwich ELISA format. Binding to S protein was observed for all four mAbs with 1A9 showing the strongest binding ( Figure 3B ). keywords: 1a9; antibodies; binding; cells; coronavirus; cov-2; mabs; protein; sars; sequence; subunit cache: cord-290904-ngvhk0qy.txt plain text: cord-290904-ngvhk0qy.txt item: #321 of 541 id: cord-291086-goidlh08 author: Walker, Peter J. title: Rhabdovirus accessory genes date: 2011-09-14 words: 12151 flesch: 33 summary: Is not required for viral replication Endogenous viral elements in animal genomes Antiviral immunity in drosophila Kotonkan, a new rhabdovirus related to Mokola virus of the rabies serogroup Complete nucleotide sequence of the hirame rhabdovirus, a pathogen of marine fish Matrix protein and another viral component contribute to induction of apoptosis in cells infected with vesicular stomatitis virus Normal replication of vesicular stomatitis virus without C proteins Molecular cloning of the six mRNA species of infectious hematopoietic necrosis virus, a fish rhabdovirus, and gene order determination by R-loop mapping Distribution and variation of NV genes in fish rhabdoviruses Characterization of infectious hematopoietic necrosis virus mRNA species reveals a nonvirion rhabdovirus protein Sendai virus C proteins are categorically nonessential gene products but silencing their expression severely impairs viral replication and pathogenesis Isolation and characterization of a tupaia rhabdovirus Phylogenetic relationships of seven previously unclassified viruses within the family Rhabdoviridae using partial nucleoprotein gene sequences Shimoni bat virus, a new representative of the Lyssavirus genus The rhabdoviruses: biodiversity, phylogenetics, and evolution Complete genomes of Aravan, Khujand Irkut and West Caucasian bat viruses, with special attention to the polymerase gene and non-coding regions Gene 2 of the sigma rhabdovirus genome encodes the P protein, and gene 3 encodes a protein related to the reverse transcriptase of retroelements The origins of defective interfering particles of the negative-strand RNA viruses Vesicular stomatitis Sigma viruses from three species of Drosophila form a major new clade in the rhabdovirus phylogeny Rhabdoviruses in two species of Drosophila: vertical transmission and a recent sweep Evidence for recombination in Crimean-Congo hemorrhagic fever virus Sequence of mouse hepatitis virus A59 mRNA 2 Indications for RNA recombination between coronaviruses and influenza C virus Analysis of nucleotide sequence of Iranian maize mosaic virus confirms its identity as a distinct nucleorhabdovirus Genome organization and transcription strategy in the complex GNS-L intergenic region of bovine ephemeral fever rhabdovirus The '30K' superfamily of viral movement proteins A host-factor interaction and localization map for a plant-adapted rhabdovirus implicates cytoplasm-tethered transcription activators in cell-to-cell movement Structure and transcription of the glycoprotein gene of attenuated HEP-Flury strain of rabies virus The glycoprotein of Thogoto virus (a tick-borne orthomyxo-like virus) is related to the baculovirus glycoprotein GP64 Nucleocytoplasmic distribution of rabies virus P protein is regulated by phosphorylation adjacent to C-terminal nuclear import and export signals Dual modes of rabies P-protein association with microtubules: a novel strategy to suppress the antiviral response Isolation of chikungunya virus from Aedes aegypti mosquitoes collected in the town of Yawat Lyssavirus P gene characterisation provides insights into the phylogeny of the genus and identifies structural similarities and diversity within the encoded phosphoprotein Accessory genes of the paramyxoviridae, a large family of nonsegmented negative-strand RNA viruses, as a focus of active investigation by reverse genetics Nucleocytoplasmic shuttling of the rabies virus P protein requires a nuclear localization signal and a CRM1-dependent nuclear export signal Vesicular stomatitis virus induces apoptosis primarily through Bak rather than Bax by inactivating Mcl-1 and Bcl-XL Identification of a set of proteins (C and C) encoded by the bicistronic P gene of the Indiana serotype of vesicular stomatitis virus and analysis of their effect on transcription by the viral RNA polymerase Origin and replication of defective interfering particles Translational termination-reinitiation in RNA viruses F gene recombination between genotype II and VII Newcastle disease virus A large outbreak of acute encephalitis with high fatality rate in children in Andhra Pradesh Rabies virus glycoprotein gene contains a long 3 noncoding region which lacks pseudogene properties Plant rhabdoviruses Shotgun sequencing of the negative-sense RNA genome of the rhabdovirus maize mosaic virus Taro vein chlorosis virus: characterization and variability of a new nucleorhabdovirus Genetic dissection of interferon-antagonistic functions of rabies virus phosphoprot inhibition of interferon regulatory factor 3 activation. Secondary structure predictions have shown that the SYNV sc4, LNYV 4b, LYMoV P3, MMV P3, MFSV P4, RYSV P3 and PYDV Y proteins have some structural similarities in common with those of the '30K' superfamily of plant virus movement proteins (Melcher, 2000) . keywords: accessory; alternative; amino; cell; et al; fig; fish; function; gene; genome; genus; kda; orf; orfs; proteins; rabies; region; replication; rhabdoviruses; sequence; species; stomatitis; virus cache: cord-291086-goidlh08.txt plain text: cord-291086-goidlh08.txt item: #322 of 541 id: cord-291210-ghjseynl author: Arbely, Eyal title: A Highly Unusual Palindromic Transmembrane Helical Hairpin Formed by SARS Coronavirus E Protein date: 2004-08-13 words: 5579 flesch: 48 summary: Retention of the avian coronavirus infectious bronchitis virus envelope protein in the pre-Golgi compartments and physical interaction between the envelope and membrane proteins Release of coronavirus E protein in membrane vesicles from virus-infected cells and E protein-expressing cells Analysis of constructed E gene mutants of mouse hepatitis virus confirms a pivotal role for E protein in coronavirus assembly Characterization of the coronavirus mouse hepatitis virus strain A59 small membrane protein E Induction of apoptosis in murine coronavirus-infected cultured cells and demonstration of E protein as an apoptosis inducer Induction of apoptosis in murine coronavirus-infected 17Cl-1 cells Statistical analysis of predicted transmembrane alpha-helices Membrane topology of coronavirus E protein Fourier transform infrared techniques for probing membrane protein structure Site-directed dichroism as a method for obtaining rotational and orientational constraints for oriented polymers X-ray reflectivity of solid supported, multilamellar membranes A structure for the trimeric MHC class II-associated invariant chain transmembrane domain Interhelical hydrogen bonding drives strong interactions in membrane proteins Asparagine-mediated self-association of a model transmembrane helix Computational searching and mutagenesis suggest a structure for the pentameric transmembrane domain of phospholamban The cytoplasmic tail of infectious bronchitis virus E protein directs Golgi targeting TGEV coronavirus ORF4 encodes a membrane protein that is incorporated into virions Internal Reflection Spectroscopy Infrared dichroism and molecular conformation of a-form poly-g-benzyl-L-glutamate Crystallography and NMR system: a new software suite for macromolecular structure determination Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins Do more complex organisms have a greater proportion of membrane proteins in their genomes? Here we describe the molecular characterization of SCoV E protein, a critical component of the virus responsible for virion envelope morphogenesis. keywords: bilayer; coronavirus; e protein; figure; hairpin; helices; hydrophobic; lipid; protein; residues; scov; scov e; transmembrane cache: cord-291210-ghjseynl.txt plain text: cord-291210-ghjseynl.txt item: #323 of 541 id: cord-291727-4wfhuvww author: Ketteler, Robin title: On programmed ribosomal frameshifting: the alternative proteomes date: 2012-11-19 words: 6683 flesch: 44 summary: However, it has been proposed that frameshifting may predominantly serve to modulate RNA levels rather than to produce frameshifted proteins (Plant et al., 2004) . Most commonly, an antibody that is specific to the out-of-frame sequence of the frameshifted protein is used to detect frameshifted proteins. keywords: et al; expression; frameshifting; gene; genome; peptides; proteins; pseudoknot; ribosomal; rna; sequence cache: cord-291727-4wfhuvww.txt plain text: cord-291727-4wfhuvww.txt item: #324 of 541 id: cord-292688-w4zvfkyl author: Tooze, Sharon A title: Biogenesis of secretory granules in the trans-Golgi network of neuroendocrine and endocrine cells date: 1998-08-14 words: 8178 flesch: 39 summary: Helper proteins for neuroendocrine secretion Chromogranin B (secretogranin I) promotes sorting to the regulated secretory pathway of processing intermediates derived from a peptide hormone precursor The primary structure of human secretogranin II, a widespread tyrosine-sulfated secretory granule protein that exhibits low pH-and calcium-induced aggregation Milieu-induced, selective aggregation of regulated secretory proteins in the trans-Golgi network Calcium-and pHdependent aggregation and membrane association of the precursor of the prohormone convertase PC2 Secretory granule content proteins and the luminal domains of granule membrane proteins aggregate in vitro at mildly acidic pH Conversion of proinsulin to insulin occurs coordinately with acidi¢cation of maturing secretory vesicles Clathrin-coated vesicular transport of secretory proteins during the formation of ACTH-containing secretory granules in AtT20 cells Chloroquine diverts ACTH from a regulated to a constitutive secretory pathway in AtT-20 cells However, in the absence of experiments to prove whether secretory proteins are also conveyed by this pathway, the question remains an open one. keywords: cells; formation; golgi; membrane; pathway; proteins; receptor; secretory; secretory granules; secretory proteins; sorting; tgn; vesicles cache: cord-292688-w4zvfkyl.txt plain text: cord-292688-w4zvfkyl.txt item: #325 of 541 id: cord-292958-k5d5fo3i author: Sekhon, Simranjeet Singh title: Porcine epidemic diarrhea (PED) infection, diagnosis and vaccination: A mini review date: 2017-01-04 words: 7442 flesch: 31 summary: This sequence is particularly rich in arginine (Arg), serine (Ser) and asparagine (Asp) residues, and presents in PED virus N protein with no counterpart in the remainder of Coronaviruses. The encoded polypeptides range of PEDV N protein is from 377 to 455 amino acids and has the similar physical properties with the other members of the family Coronaviridae 60 . keywords: cell; coronavirus; detection; diarrhea; diarrhea virus; elisa; epidemic; epidemic diarrhea; infection; pcr; pedv; porcine; porcine epidemic; protein; samples; study; virus cache: cord-292958-k5d5fo3i.txt plain text: cord-292958-k5d5fo3i.txt item: #326 of 541 id: cord-292985-w62xaa4f author: Römer, Rudolf A. title: Flexibility and mobility of SARS-CoV-2-related protein structures date: 2020-07-12 words: 5209 flesch: 54 summary: Molecular dynamics simulations and multiple X-ray structure analyses Structures of Two Coronavirus Main Proteases: Implications for Substrate Binding and Antiviral Drug Design Targeting the Dimerization of the Main Protease of Coronaviruses: A Potential Broad-Spectrum Therapeutic Strategy Structure of M pro from COVID-19 virus and discovery of its inhibitors Importance of protein dynamics in the structure-based drug discovery of class A G protein-coupled receptors (GPCRs Protein conformational flexibility modulates kinetics and thermodynamics of drug binding Rapid simulation of protein motion: merging flexibility, rigidity and normal mode analyses Protein flexibility and dynamics using constraint theory Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic Conformational change of proteins arising from normal mode calculations On the potential of normal mode analysis for solving difficult molecular replacement problems ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement Normal mode analysis and applications in biological physics Constrained geometric simulation of diffusive motion in proteins Docking of Photosystem I Subunit C Using a Constrained Geometric Simulation Protein flexibility is key to cisplatin crosslinking in calmodulin Inhibition of HIV-1 protease: the rigidity perspective Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions The flexibility and dynamics of protein disulfide isomerase Something in the way she moves': We have downloaded protein structure files as deposited on the Protein Data Bank, 35 including all PDB codes that came up when using SARS-CoV-2 and Covid-19 as search terms, as well as minor variations in spelling. keywords: cluster; cov-2; cut; domain; flexibility; motion; protein; rigidity; sars; structure cache: cord-292985-w62xaa4f.txt plain text: cord-292985-w62xaa4f.txt item: #327 of 541 id: cord-293798-qc22cps9 author: Gómez-Mascaraque, Laura G. title: Nanostructuring Biopolymers for Improved Food Quality and Safety date: 2018-04-06 words: 12561 flesch: 21 summary: Soy proteins Vegetal Polyphenols and anthocyanins from pomegranate (Robert et al., 2010) , w-3 fatty acids (Santhanam et al., 2015; α-Linolenic acid (Gómez-Mascaraque and Lopez-Rubio, 2016), lycopene (Pérez-Masiá et al., 2015) , cardamom essential oil (Mehyar et al., 2014) , folic acid (Pérez-Masiá et al., 2015) , probiotics (Gomez-Mascaraque et al., 2016; Lopez-Rubio et al., 2012 ) keywords: activity; angle; barrier; biopolymers; chitosan; drying; electrospun; encapsulation; et al; films; food; light; materials; matrices; microencapsulation; nanoparticles; oil; packaging; properties; proteins; release; sample; scattering; spray; stability; structure; systems; techniques cache: cord-293798-qc22cps9.txt plain text: cord-293798-qc22cps9.txt item: #328 of 541 id: cord-294125-v2dr4hm0 author: Albert, Manuel title: ISG15, a Small Molecule with Huge Implications: Regulation of Mitochondrial Homeostasis date: 2018-11-13 words: 8077 flesch: 28 summary: Dendritic Cells at the Site of Infection Link between the ubiquitin conjugation system and the ISG15 conjugation system: ISG15 conjugation to the UbcH6 ubiquitin E2 enzyme ISG15 inhibits Ebola VP40 VLP budding in an L-domain-dependent manner by blocking Nedd4 ligase activity Identification and characterization of a novel ISG15-ubiquitin mixed chain and its role in regulating protein homeostasis ISG15 governs mitochondrial function in macrophages following vaccinia virus infection ISG15 in antiviral immunity and beyond IFN-stimulated gene 15 functions as a critical antiviral molecule against influenza, herpes, and Sindbis viruses ISG15 Arg151 and the ISG15-conjugating enzyme UbE1L are important for innate immune control of Sindbis virus Identification of interferon-stimulated gene 15 as an antiviral molecule during Sindbis virus infection in vivo ISG15 is critical in the control of Chikungunya virus infection independent of UbE1L mediated conjugation The level of hepatitis B virus replication is not affected by protein ISG15 modification but is reduced by inhibition of UBP43 (USP18) expression Role of ISG15 protease UBP43 (USP18) in innate immunity to viral infection Reexamination of the role of ubiquitin-like modifier ISG15 in the phenotype of UBP43-deficient mice Respiratory syncytial virus (RSV) attachment and nonstructural proteins modify the type I interferon response associated with suppressor of cytokine signaling (SOCS) proteins and IFN-stimulated gene-15 (ISG15) Martinez, I. ISG15 Is Upregulated in Respiratory Syncytial Virus Infection and Reduces Virus Growth through Protein ISGylation Innate antiviral response targets HIV-1 release by the induction of ubiquitin-like protein ISG15 Zebrafish ISG15 exerts a strong antiviral activity against RNA and DNA viruses and regulates the interferon response Influenza B virus NS1 protein inhibits conjugation of the interferon (IFN)-induced ubiquitin-like ISG15 protein Vaccinia virus E3 protein prevents the antiviral action of ISG15 Consecutive Inhibition of ISG15 Expression and ISGylation by Cytomegalovirus Regulators Ovarian tumor domain-containing viral proteases evade ubiquitin-and ISG15-dependent innate immune responses A chimeric virus-mouse model system for evaluating the function and inhibition of papain-like proteases of emerging coronaviruses Hepatitis C virus reveals a novel early control in acute immune response The ISG15/USP18 ubiquitin-like pathway (ISGylation system) in hepatitis C virus infection and resistance to interferon therapy Influenza virus non-structural protein NS1: In the following sections, we discuss the antiviral mechanisms mediated by ISGylation of both viral and cellular proteins, with a focus on mitochondrial proteins, as we recently showed that ISG15 modulates essential mitochondrial metabolic processes such as respiration and mitophagy in macrophages, with important implications for innate immune responses [29] . keywords: cell; conjugation; ifn; infection; interferon; isg15; isgylation; mitochondria; proteins; regulation; response; role; signaling; targets; type; ubiquitin; virus cache: cord-294125-v2dr4hm0.txt plain text: cord-294125-v2dr4hm0.txt item: #329 of 541 id: cord-294575-kky8j9oy author: Li, Jieqiong title: Characterization of plasma proteins in children of different Mycobacterium tuberculosis infection status using label-free quantitative proteomics date: 2017-09-23 words: 4523 flesch: 42 summary: key: cord-294575-kky8j9oy authors: Li, Jieqiong; Sun, Lin; Xu, Fang; Xiao, Jing; Jiao, Weiwei; Qi, Hui; Shen, Chen; Shen, Adong title: Characterization of plasma proteins in children of different Mycobacterium tuberculosis infection status using label-free quantitative proteomics date: 2017-09-23 journal: Oncotarget DOI: 10.18632/oncotarget.21179 sha: doc_id: 294575 cord_uid: kky8j9oy Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), is an infectious disease found worldwide. We employed the label-free quantitative proteomic technology to identify and characterize differences in plasma proteins between ATB and latent TB infection (LTBI) in children. keywords: analysis; atb; binding; children; groups; infection; ltbi; mtb; plasma; proteins; sema4a; tuberculosis cache: cord-294575-kky8j9oy.txt plain text: cord-294575-kky8j9oy.txt item: #330 of 541 id: cord-294677-l1b4mw9d author: Prashantha, C.N. title: Molecular screening of antimalarial, antiviral, anti-inflammatory and HIV protease inhibitors against spike glycoprotein of Coronavirus date: 2020-10-13 words: 2414 flesch: 39 summary: SAVES is used to understand the complexity of protein structure based on atom-to-atom interaction of Ψ versus Φ conformational angels of 3D macromolecule measures the torsion angels of Cα (ideal) -N-Cβ (obs) and the results were represented in Ramachandran Plot. Prediction of protein structure is important in molecular docking, using I-TASSER to build three dimensional protein structure and used for homology modeling using SwissPDBViewer (SPDBV) software. keywords: amino; coronavirus; disease; docking; drugs; protein; receptor; structure; target cache: cord-294677-l1b4mw9d.txt plain text: cord-294677-l1b4mw9d.txt item: #331 of 541 id: cord-294712-kvvxmvqo author: Pelosse, Martin title: MultiBac: from protein complex structures to synthetic viral nanosystems date: 2017-10-30 words: 5382 flesch: 33 summary: A further posttranslational modification that can lead to heterogeneity is phosphorylation, which may or may not be authentic in insect cell expression. The introduced genome alterations resulted in a virus that exhibited delayed lysis of the insect cells, allowing the production of recombinant protein complexes at very high levels while the cells seemingly remained intact [11] . keywords: baculovirus; cells; complex; complexes; dna; expression; gene; genome; insect; multibac; multiprotein; production; protein; site; structure; system cache: cord-294712-kvvxmvqo.txt plain text: cord-294712-kvvxmvqo.txt item: #332 of 541 id: cord-294945-hcf7gsv8 author: Lin, K.H. title: Comparative proteomic analysis of cauliflower under high temperature and flooding stresses date: 2015-02-12 words: 8231 flesch: 40 summary: upon heat stress Drought-inhibition of photosynthesis in C3 plants: stomatal and non-stomatal limitations revisited Proteome analysis of wheat leaf under salt stress by two-dimensional difference gel electrophoresis (2D-DIGE) Comparative proteomic analysis of grain development in two spring wheat varieties under drought stress Physiology and proteome responses of two contrasting rice mutants and their wild type parent under salt stress conditions at the vegetative stage Comparative proteomic analysis of salt response proteins in seedling roots of two wheat varieties Proteome analysis of sugar beet leaves under drought stress Research on plant abiotic stress responses in the post-genome era: past, present and future Responses of antioxidative system to chilling stress in two rice cultivars differing in sensitivity Structural-functional state of thylakoid membranes of wheat genotypes under water stress Proteomic analysis of wheat embryos with 2-DE and liquid-phase chromatography (ProteomeLab PF-2D) -a For instance, proteomics approaches for the comparative analysis of protein abundance between untreated and stress-treated or tolerant and intolerant rice plants have greatly facilitated the study of plant cellular stress responses (Komatsu et al., 2003) . keywords: analysis; cauliflower; et al; flooding; h41; h69; h71; heat; peaks; plants; proteins; response; stress; stresses; table; temperature; treatments; water cache: cord-294945-hcf7gsv8.txt plain text: cord-294945-hcf7gsv8.txt item: #333 of 541 id: cord-295351-0zr2e8lh author: Mohd Ropidi, Muhammad Izzuddin title: Endoplasmic reticulum: a focal point of Zika virus infection date: 2020-01-20 words: 7858 flesch: 32 summary: ZIKV proteins localize to distinct subcellular compartments ZIKV proteins are primarily distributed within and in close proximity to several endomembrane compartments including the endoplasmic reticulum, Golgi apparatus, endosomes, lysosomes, autophagosomes, and nucleus The subcellular distribution of certain ZIKV proteins was corroborated in a separate study where interatomic analyses using proximity-dependent biotin-identification (BioID) labeling and FLAG-based immunoprecipitation (IP) coupled with mass spectrometry (MS) uncover indepth molecular interactions between ZIKV proteins with various host organelles and proteins. keywords: assembly; cells; complex; expression; genome; host; infection; ire1; membrane; protein; replication; response; rna; stress; upr; virus; zika; zikv cache: cord-295351-0zr2e8lh.txt plain text: cord-295351-0zr2e8lh.txt item: #334 of 541 id: cord-295381-0dqu3p3y author: Kamal, Adeela title: Therapeutic and diagnostic implications of Hsp90 activation date: 2004-06-01 words: 5168 flesch: 30 summary: Because of the wide array of Hsp90 client proteins, Hsp90 inhibitors can be used to target diverse cancers in which an Hsp90 client protein is necessary for cancer proliferation, survival or progression. The assembly of progesterone receptor-hsp90 complexes using purified proteins Inhibition of heat shock protein HSP90 -pp60v -src heteroprotein complex formation by benzoquinone ansamycins: essential role for stress proteins in oncogenic transformation Identification and structural characterization of the ATP/ADP-binding site in the Hsp90 molecular chaperone Crystal structure of an Hsp90 -geldanamycin complex: targeting of a protein chaperone by an antitumor agent In vivo function of Hsp90 is dependent on ATP binding and ATP hydrolysis ATP binding and hydrolysis are essential to the function of the Hsp90 molecular chaperone in vivo The importance of ATP binding and hydrolysis by hsp90 in formation and function of protein heterocomplexes Depletion of the erbB-2 gene product p185 by benzoquinoid ansamycins Polyubiquitination and proteasomal degradation of the p185c -erbB-2 receptor protein-tyrosine kinase induced by geldanamycin Preclinical pharmacologic evaluation of geldanamycin as an antitumor agent Inhibition of heat shock protein 90 function down-regulates Akt kinase and sensitizes tumors to Taxol Clinical development of 17-allylamino, 17-demethoxygeldanamycin A small molecule designed to bind to the adenine nucleotide pocket of Hsp90 causes Her2 degradation and the growth arrest and differentiation of breast cancer cells A high-affinity conformation of Hsp90 confers tumor selectivity on Hsp90 inhibitors Mammalian p50Cdc37 is a protein kinasetargeting subunit of Hsp90 that binds and stabilizes Cdk4 Cellular survival: a play in three Akts The Hsp90 inhibitor geldanamycin selectively sensitizes Bcr-Abl-expressing leukemia cells to cytotoxic chemotherapy Geldanamycin and its analogue 17-allylamino-17-demethoxygeldanamycin lowers Bcr-Abl levels and induces apoptosis and differentiation of Bcr-Abl-positive human leukemic blasts BCR-ABL point mutants isolated from patients with imatinib mesylate-resistant chronic myeloid leukemia remain sensitive to inhibitors of the BCR -ABL chaperone heat shock protein 90 ErbB2 overexpression in an ovarian cancer cell line confers sensitivity to the HSP90 inhibitor geldanamycin Physiologically-based pharmacokinetics and molecular pharmacodynamics of 17-(allylamino)-17-demethoxygeldanamycin and its active metabolite in tumor-bearing mice Unusual expression and localization of heatshock proteins in human tumor cells Differential expression of heat shock proteins in pancreatic carcinoma Expression and roles of heat shock proteins in human breast cancer Selective over-expression of mRNA coding for 90 KDa stress-protein in human ovarian cancer Heat shock protein-90, IL-6 and IL-10 in bladder cancer Repression of heat shock transcription factor HSF1 activation by HSP90 (HSP90 complex) that forms a stress-sensitive complex with HSF1 Regulation of the heat shock transcriptional response: cross talk between a family of heat shock factors, molecular chaperones, and negative regulators Induction of a heat shock factor 1-dependent stress response alters the cytotoxic activity of hsp90-binding agents Structural basis for inhibition of the Hsp90 molecular chaperone by the antitumor antibiotics radicicol and geldanamycin ATPases as drug targets: learning from their structure Development of a purine-scaffold novel class of Hsp90 binders that inhibit the proliferation of cancer cells and induce the degradation of Her2 tyrosine kinase Adenine derived inhibitors of the molecular chaperone HSP90 -SAR explained through multiple X-ray structures Cancer: the rules of attraction Crystal Structure and Molecular Modeling of 17-DMAG in Complex with Human Hsp90 Regulation of Hsp90 ATPase activity by tetratricopeptide repeat (TPR)-domain co-chaperones Stimulation of the weak ATPase activity of human hsp90 by a client protein The Mechanism of Hsp90 regulation by the protein kinase-specific cochaperone p50(cdc37) Activation of the ATPase activity of hsp90 by the stress-regulated cochaperone aha1 Structural and functional analysis of the middle segment of hsp90: implications for ATP hydrolysis and client protein and cochaperone interactions Quantitative immunohistochemical evaluation of HER2/neu expression with HercepTeste in breast carcinoma by image analysis Radicicol-sensitive peptide binding to the N-terminal portion of GRP94 Induction of heat shock proteins by tyrosine kinase inhibitors in rat cardiomyocytes and myogenic cells confers protection against simulated ischemia Geldanamycin provides posttreatment protection against glutamate-induced oxidative toxicity in a mouse hippocampal cell line Geldanamycin induces heat shock proteins in brain and protects against focal cerebral ischemia Hsp90 is required for the activity of a hepatitis B virus reverse transcriptase Host cell factor requirement for hepatitis C virus enzyme maturation Geldanamycin, a ligand of heat shock protein 90, inhibits the replication of herpes simplex virus type 1 in vitro Requirement for a kinase-specific chaperone pathway in the production of a Cdk9/cyclin T1 heterodimer responsible for P-TEFb-mediated tat stimulation of HIV-1 transcription Effects of geldanamycin, a heat-shock protein 90-binding agent, on T cell function and T cell nonreceptor protein tyrosine kinases Immunosuppressive effects of the heat shock protein 90-binding antibiotic geldanamycin Requirement for a hsp90 chaperonedependent MEK1/2-ERK pathway for B cell antigen receptor-induced cyclin D2 expression in mature B lymphocytes Stress management -heat shock protein-70 and the regulation of apoptosis Geldanamycin activates a heat shock response and inhibits huntingtin aggregation in a cell culture model of Huntington's disease Pharmacological prevention of Parkinson disease in Drosophila Hsp90 as a capacitor for morphological evolution We thank our colleagues at Conforma Therapeutics Corporation for useful comments and suggestions. keywords: activity; affinity; binding; cells; chaperone; geldanamycin; heat; hsp90; inhibitors; proteins; shock; tumor cache: cord-295381-0dqu3p3y.txt plain text: cord-295381-0dqu3p3y.txt item: #335 of 541 id: cord-296347-fanlvxqs author: Loureiro, Joana title: Antigen Presentation and the Ubiquitin‐Proteasome System in Host–Pathogen Interactions date: 2006-12-02 words: 29009 flesch: 29 summary: The knowledge that the TMD of US11 is essential for its function (Lilley et al., 2003) , led to the discovery of Derlins (Lilley and Ploegh, 2004) and of multiprotein complexes at the ER membrane that function in US11-mediated dislocation of HCs and US11-independent dislocation of a subset of ERAD substrates (Lilley and Ploegh, 2005a; Oda et al., 2006; Ye et al., 2005) . The US2 TMD, although dispensable for interaction with SPP, is also required for HC dislocation (Loureiro et al., 2006) . keywords: activation; activity; antigen; binding; cd4; cell; class; class ii; complex; complexes; control; cytomegalovirus; degradation; dislocation; domain; endoplasmic; et al; function; hcmv; host; human; ii mhc; immune; ligase; membrane; mhc; mhc class; molecules; nef; pathogen; pathway; peptide; presentation; proteasome; protein; receptor; recognition; response; reticulum; role; signal; signaling; spp; substrate; surface; system; t cells; type; ubiquitin; ubiquitination; us11; us2; virus cache: cord-296347-fanlvxqs.txt plain text: cord-296347-fanlvxqs.txt item: #336 of 541 id: cord-296794-ml2luc1t author: Sollner, Johannes title: Analysis and prediction of protective continuous B-cell epitopes on pathogen proteins date: 2008-01-07 words: 8023 flesch: 38 summary: Recently the usability of amino acid scales for the prediction of B-cell epitopes has been profoundly questioned [13] and common standards regarding the validation of epitope predictions have been discussed [14] . It may also be viable to suggest that conservation of posttranslational modification patterns may be different when comparing highly variable exposed loops and sites of functional relevance as modifications can play a major role in the masking of protective epitopes keywords: acid; amino; antigenicity; cell; epitopes; peptides; prediction; protective; protectivity; proteins; set; validation; variability cache: cord-296794-ml2luc1t.txt plain text: cord-296794-ml2luc1t.txt item: #337 of 541 id: cord-296928-wu14k7u9 author: Hofmann, Tim title: Greatest Hits—Innovative Technologies for High Throughput Identification of Bispecific Antibodies date: 2020-09-08 words: 7399 flesch: 23 summary: Similar to the bioconjugation methods described in later sections, (c)FAE serves as an ideal platform for bispecific antibody screening. In this respect, the advent of bispecific antibodies opened up new avenues for disease treatment such as effector cell redirection or the simultaneous blocking of two different disease mediators, with encouraging results in (mostly early stage) clinical trials [9] [10] [11] . keywords: antibodies; antibody; bioconjugation; bispecific; cell; format; generation; intein; peptide; production; protein; screening; split; spycatcher; spytag; system; throughput cache: cord-296928-wu14k7u9.txt plain text: cord-296928-wu14k7u9.txt item: #338 of 541 id: cord-297324-me5ff1pb author: Zeng, Rong title: Characterization of the 3a Protein of SARS-associated Coronavirus in Infected Vero E6 Cells and SARS Patients() date: 2004-07-30 words: 4582 flesch: 51 summary: In addition, there is a cysteine-rich region, overlapping the junction of the membrane-spanning region and the cytoplasmic region of S proteins, and this conserved structure of S protein exists in all three groups of coronaviruses. a) of 3a protein sequences from Himalayan palm civets was also only found in those three human SARS-CoV isolates. keywords: 3a protein; analysis; coronavirus; cov; figure; peptide; protein; region; sars cache: cord-297324-me5ff1pb.txt plain text: cord-297324-me5ff1pb.txt item: #339 of 541 id: cord-297960-4x1j0iqg author: Bösl, Korbinian title: Common Nodes of Virus–Host Interaction Revealed Through an Integrated Network Analysis date: 2019-10-04 words: 5491 flesch: 37 summary: Given that the viral proteins were interacting with a large number of host proteins, we analyzed the sub-cellular location of the host proteins. We binned the localization into 11 compartments and estimated the percent of host proteins in a given compartment as compared to the total number of host proteins targeted by a given FIGURE 3 | Clusters of hvPPI involved in core cellular processes. keywords: analysis; drug; evasion; figure; host; human; hvppi; network; novel; protein; targets; viral; virus; viruses cache: cord-297960-4x1j0iqg.txt plain text: cord-297960-4x1j0iqg.txt item: #340 of 541 id: cord-298242-iuskpoug author: Yu, Alvin title: A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion date: 2020-10-02 words: 3609 flesch: 34 summary: AA protein models (see discussion below) were subsequently simulated and coarsegrained to generate the CG models ( Figure 2 and see sections below). Several computational approaches have been developed to build or refine CG models using data from AA or fine-grained simulations. keywords: data; model; molecular; protein; sars; simulations; spike; structure; virion cache: cord-298242-iuskpoug.txt plain text: cord-298242-iuskpoug.txt item: #341 of 541 id: cord-298251-u36lb44w author: Donaldson, Julie G. title: Arf Family G Proteins and their regulators: roles in membrane transport, development and disease date: 2011-05-18 words: 10742 flesch: 35 summary: c | In primary cilia, ARL6 recruits the BBSome coat complex that facilitates the transport of membrane proteins into the cilium. Recycling endosomes return membrane proteins that are important for cell adhesion and migration back to the plasma membrane 34, 35 . keywords: activation; arf; arf1; arf6; binding; cells; complex; cytohesin; domain; exchange; family; gap; gefs; golgi; gtp; lipid; membrane; plasma; proteins; signalling; trafficking; transport cache: cord-298251-u36lb44w.txt plain text: cord-298251-u36lb44w.txt item: #342 of 541 id: cord-298301-p1zj6jg9 author: Dey, Lopamudra title: Machine Learning Techniques for Sequence-based Prediction of Viral-Host Interactions between SARS-CoV-2 and Human Proteins date: 2020-09-03 words: 6310 flesch: 46 summary: Choosing negative examples for the prediction of protein-protein interactions Prediction of interactions between viral and host proteins using supervised machine learning methods Sequence-based prediction of protein protein interaction using a deep-learning algorithm Human protein reference database-2009 update A human functional protein interaction network and its application to cancer data analysis Supervised classification algorithms in machine learning: A survey and review. We found a large number of predicted human proteins interact with more than one virus. keywords: amino; classifier; coronavirus; covid-19; dataset; features; human; interactions; learning; machine; prediction; proteins; sars; virus cache: cord-298301-p1zj6jg9.txt plain text: cord-298301-p1zj6jg9.txt item: #343 of 541 id: cord-298369-66ifwtlp author: Smith, Sherri A. title: Pharmacokinetic and Pharmacodynamic Considerations for Drugs Binding to Alpha-1-Acid Glycoprotein date: 2018-12-28 words: 10732 flesch: 37 summary: In human AAG levels are lower in the pregnant female and continue to decline throughout pregnancy until birth when they begin to climb back to pre-pregnancy values (53, 56, 57) . In the chronic, accelerated, and blast crisis phases of disease, 33, 83 and 75% of these patients, respectively, were increasingly likely to have higher AAG levels. keywords: aag; acid; affinity; albumin; alpha; binding; blood; drug; fold; free; glycoprotein; high; human; levels; plasma; serum; species; vismodegib cache: cord-298369-66ifwtlp.txt plain text: cord-298369-66ifwtlp.txt item: #344 of 541 id: cord-298736-9bvyp21d author: Gerold, Gisa title: Decoding protein networks during virus entry by quantitative proteomics date: 2016-06-15 words: 12175 flesch: 31 summary: With the discovery of CR2 as Epstein Barr virus (EBV) and CD4 as human immunodeficiency virus type 1 (HIV-1) receptor the hunt for virus receptors began (Fingeroth et al., 1984; Maddon et al., 1986) . Susceptible cell: cell that expresses virus receptors and entry factors and thus allows entry of a virus. keywords: analysis; binding; cell; complex; entry; et al; factors; hcv; hepatitis; host; human; identification; infection; interactions; label; mass; membrane; methods; protein; proteomics; receptor; signaling; silac; uptake; virus; virus entry; viruses cache: cord-298736-9bvyp21d.txt plain text: cord-298736-9bvyp21d.txt item: #345 of 541 id: cord-298759-j965t808 author: Jiang, Nan title: Development of a robust Escherichia coli-based cell-free protein synthesis application platform date: 2020-10-17 words: 5263 flesch: 49 summary: Based on E. coli which was the most widely used host background for protein expression, five commercially available types were tested in the initial screening experiment ( Table 2) . The results indicated that plasmid size could be an important parameter for protein expression in the CFPS system. keywords: cell; cfps; degfp; efficiency; expression; extract; protein; reaction; synthesis; system cache: cord-298759-j965t808.txt plain text: cord-298759-j965t808.txt item: #346 of 541 id: cord-298802-a5h91axf author: Ravindran, Madhu Sudhan title: Molecular chaperones: from proteostasis to pathogenesis date: 2018-06-22 words: 3200 flesch: 30 summary: Similar to soluble PQC compartments, increasing evidence indicates the existence of quality control structures for membrane proteins [24], but the formation and composition of these structures are poorly characterized. This article provides an overview of cellular proteostasis with emphasis on membrane protein substrates and suggests host–virus interaction as a tool to clarify outstanding questions in proteostasis. keywords: chaperones; control; factors; host; hsp70; membrane; protein; quality; virus cache: cord-298802-a5h91axf.txt plain text: cord-298802-a5h91axf.txt item: #347 of 541 id: cord-298922-k568hlf4 author: Sun, Dongbo title: Analysis of protein expression changes of the Vero E6 cells infected with classic PEDV strain CV777 by using quantitative proteomic technique date: 2015-06-15 words: 5207 flesch: 37 summary: In our study, the integrin recognized sequences of PEDV S protein was analyzed based on Ruoslahti's (1996) report. The CV777 strain of PEDV, kindly provided by Maurice Pensaert at Ghent University (Merelbeke, Belgium), was used in all of our experiments after being adapted to Vero E6 cells, as previously described (Hofmann and Wyler, 1988) . keywords: analysis; cells; deps; diarrhea; et al; groups; infection; pedv; porcine; proteins; vero; virus cache: cord-298922-k568hlf4.txt plain text: cord-298922-k568hlf4.txt item: #348 of 541 id: cord-299270-fwbz3t25 author: Lemieux, M. Joanne title: Structure and function of proteins in membranes and nanodiscs date: 2020-08-22 words: 3037 flesch: 33 summary: In order to address this, Muench and colleagues have developed a method to transfer membrane proteins from SMALPs into amphipols or detergents for downstream analysis [3] . Isolation of intramembrane proteases in membrane-like environments Factors influencing the solubilization of membrane proteins from Escherichia coli membranes by styrene-maleic acid copolymers Styrene maleic-acid lipid particles (SMALPs) into detergent or amphipols: An exchange protocol for membrane protein characterisation Microfluidic diffusional sizing probes lipid nanodiscs formation Detergent-free isolation of native red blood cell membrane complexes Dynamics and structural communication in the ternary complex of fully phosphorylated V2 vasopressin receptor, vasopressin, and beta-arrestin 1 Ligand-induced conformational changes in a SMALP-encapsulated GPCR Detergent-free extraction of a functional low-expressing GPCR from a human cell line Intrinsically disordered regions regulate the activities of ATP binding cassette transporters Application of fluorescence correlation spectroscopy to study substrate binding in styrene maleic acid lipid copolymer encapsulated ABCG2 Expression and detergent free purification and reconstitution of the plant plasma membrane Na(+)/H(+) antiporter SOS1 Solution structure of the cytoplasmic domain of NhaP2 a K(+)/H(+) antiporter from Vibrio cholera Characterization of multimeric daptomycin bound to lipid nanodiscs formed by calcium-tolerant styrene-maleic acid co-polymer Solution structure and oligomeric state of the E. coliglycerol facilitator Lipid dynamics in nanoparticles formed by maleic acid-containing copolymers: EPR spectroscopy and molecular dynamics simulations The effect of hydrophobic alkyl sidechains on size and solution behaviors of nanodiscs formed by alternating styrene maleamic copolymer SLC26A7 protein is a chloride/bicarbonate exchanger and its abundance is osmolarity-and pH-dependent in renal epithelial cells HPLC reveals novel features of nucleoside and nucleobase homeostasis, nucleoside metabolism and nucleoside transport Diversity and sequence motifs of the bacterial SecA protein motor Solution NMR spectroscopy of membrane proteins Expression, purification, and functional reconstitution of (19)F-labeled cytochrome b5 in peptide nanodiscs for NMR studies where he serves as Director of NANUC, Canada's national NMR centre. keywords: binding; copolymer; detergent; dynamics; lipid; membrane; nanodiscs; protein cache: cord-299270-fwbz3t25.txt plain text: cord-299270-fwbz3t25.txt item: #349 of 541 id: cord-299413-3o6mdx3e author: Wang, Hui title: Advantages of mRNA display selections over other selection techniques for investigation of protein–protein interactions date: 2014-01-09 words: 7950 flesch: 38 summary: • mRNA display has many advantages over other widely used peptide or protein-selection techniques, including: -Easy and robust recovery of the selected polypeptide sequences -Freedom of using arbitrary selection conditions -Making use of very large libraries of candidate sequences -Minimizing context dependence in both expression and selection -Easy removal of the abundant sequences from the candidate pools -Applicable to the selection of protein sequences of long length -Compatible with most diversity-generation methods • Researchers have used mRNA display to study various protein-protein interactions from both natural protein and synthetic peptide libraries, including: -Generation of affinity molecules against target proteins from synthetic polypeptide libraries -Mapping protein-protein interactions network from proteomic libraries -Mapping DNA-protein interactions network from proteomic libraries -Studying the specificity of antibodies -Mapping the consensus-binding motifs of proteins -Identifying the downstream substrates of kinases and proteases -Evolution of enzymes from partially randomized protein scaffolds mRNA display has also been used to identify the natural downstream substrates of enzymes such as kinases and proteases. While performing protein selection using these techniques under in vitro conditions provides great flexibility, in vitro selections could generate false positives that do not function inside the cells due to degradation, loss of solubility and conditions different from the physiological environment. keywords: affinity; binding; colleagues; display; interactions; libraries; library; mrna; mrna display; peptide; protein; selection; sequences; target; vitro cache: cord-299413-3o6mdx3e.txt plain text: cord-299413-3o6mdx3e.txt item: #350 of 541 id: cord-300418-s4wt5gim author: Bedford, Lynn title: Ubiquitin-like protein conjugation and the ubiquitin–proteasome system as drug targets date: 2010-12-10 words: 13164 flesch: 30 summary: For example, pathogens can code for orthologues of enzymes of the UPS, such as an E2 (REF. 76 ), or express their own novel analogues of UPS enzymes, such as ubiquitin protein ligases 77 . The roles of NF-κB in inflammation and the immune response, and therefore the usefulness of ubiquitin pathway inhibitors, could be extended to osteolytic disorders. keywords: activation; activity; autophagy; binding; cell; chains; complex; disease; enzyme; example; inhibition; inhibitors; pathways; proteasome; protein; ring; substrate; system; ubiquitin; ubl; ups cache: cord-300418-s4wt5gim.txt plain text: cord-300418-s4wt5gim.txt item: #351 of 541 id: cord-300429-b0zev8zb author: Sobocińska, Justyna title: Protein Palmitoylation and Its Role in Bacterial and Viral Infections date: 2018-01-19 words: 13448 flesch: 31 summary: + channels Activation of the protein deacetylase SIRT6 by long-chain fatty acids and widespread deacylation by mammalian sirtuins SIRT6 regulates TNF-α secretion through hydrolysis of long-chain fatty acyl lysine Lysine fatty acylation promotes lysosomal targeting of TNF-α A Salmonella typhimurium effector protein SifA is modified by host cell prenylation and S-acylation machinery Geranylgeranylation but not GTP-loading of Rho GTPases determines T cell function Inhibition of protein geranylgeranylation specifically interferes with CD40-dependent B cell activation, resulting in a reduced capacity to induce T cell immunity Local palmitoylation cycles define activity-regulated postsynaptic subdomains Analysis of S-acylation of proteins Chemical probes for the rapid detection of fatty-acylated proteins in mammalian cells Robust fluorescent detection of protein fatty-acylation with chemical reporters Large-scale profiling of protein palmitoylation in mammalian cells Assays of protein palmitoylation Visualization and identification of fatty acylated proteins using chemical reporters Nonradioactive analysis of dynamic protein palmitoylation Palmitoylome profiling reveals S-palmitoylation-dependent antiviral activity of IFITM3 Global profiling of dynamic protein palmitoylation Proteomic analysis of fatty-acylated proteins in mammalian cells with chemical reporters reveals S-acylation of histone H3 variants Global analysis of palmitoylated proteins in Toxoplasma gondii A single protein S-acyl transferase acts through diverse substrates to determine cryptococcal morphology, stress tolerance, and pathogenic outcome Purification of biotinylated proteins on streptavidin resin: a protocol for quantitative elution Comparative analysis of cleavable azobenzene-based affinity tags for bioorthogonal chemical proteomics Systems analysis of protein fatty acylation in herpes simplex virus-infected cells using chemical proteomics Single-cell in situ imaging of palmitoylation in fattyacylated proteins Method for cellular imaging of palmitoylated proteins with clickable probes and proximity ligation applied to Hedgehog, tubulin, and Ras Analysis of protein palmitoylation reveals a pervasive role in Plasmodium development and pathogenesis Global profiling of co-and post-translationally N-myristoylated proteomes in human cells Proteomic identification of palmitoylated proteins Palmitoylated proteins: purification and identification Site-specific analysis of protein S-acylation by resin-assisted capture Proteomic analysis of fatty-acylated proteins Mass-tag labeling reveals site-specific and endogenous levels of protein S-fatty acylation Proteomic analysis of palmitoylated platelet proteins Proteomic analysis of S-acylated proteins in human B cells reveals palmitoylation of the immune regulators CD20 and CD23 Quantitative analysis of the human T cell palmitome Global analysis of protein palmitoylation in African trypanosomes Identification of new palmitoylated proteins in Toxoplasma gondii Neural palmitoyl-proteomics reveals dynamic synaptic palmitoylation Role of S-palmitoylation by ZDHHC13 in mitochondrial function and metabolism in liver Tracking brain palmitoylation change: predominance of glial change in a mouse model of Huntington's Disease protein palmitoylation database. Recently, substantial progress in the understanding of protein palmitoylation was made possible by the development of methods allowing high-throughput analysis of cellular/tissue palmitoyl proteomes. keywords: acid; activity; acylation; analysis; bacteria; cells; chemistry; click; cysteine; fatty; host; influenza; lipid; localization; membrane; modification; palmitate; palmitic; palmitoylation; plasma; protein palmitoylation; proteins; rafts; receptor; signaling; transmembrane; virus cache: cord-300429-b0zev8zb.txt plain text: cord-300429-b0zev8zb.txt item: #352 of 541 id: cord-300625-fvirvpyl author: Srinivasan, Suhas title: Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins date: 2020-03-25 words: 5912 flesch: 32 summary: The SARS-CoV intra-viral interactome was created using the published data where the SARS-CoV ORFeome was cloned, and a genome-wide analysis of viral protein interactions was performed through yeast-two-hybrid (Y2H) matrix screens [61] . Next, using comparative modeling, we structurally characterized protein interaction complexes for both intra-viral interactions (homo-and hetero-oligomers) and host-viral interactions, where the host proteins were exclusively human. keywords: binding; coronavirus; cov-2; host; human; interactions; protein; sars; sequence; sites; structure cache: cord-300625-fvirvpyl.txt plain text: cord-300625-fvirvpyl.txt item: #353 of 541 id: cord-300796-rmjv56ia author: None title: The signal sequence of the p62 protein of Semliki Forest virus is involved in initiation but not in completing chain translocation date: 1990-09-01 words: 8108 flesch: 49 summary: However, the typical cytoplasmic orientation of the NH2-termini of membrane protein chains carrying a combined signal sequence-anchoring peptide suggests that signal sequences in general might direct their function in translocation through the insertion of their hydrophobic and uncharged stretch of amino acid residues into the membrane in such an orientation that the NHEterminus of the signal remains on the outside of the ER mem- The possibility that our results about p62 protein translocation would be unique to the viral system .and different from the general translocation process in the ER we find most unlikely. keywords: chain; dhfr; et al; fig; glycosylation; membrane; p62; p62 protein; p62 signal; protein; region; sequence; signal; signal sequence; time; translocation cache: cord-300796-rmjv56ia.txt plain text: cord-300796-rmjv56ia.txt item: #354 of 541 id: cord-300884-rqfxe0x1 author: Zhang, Jianqiang title: Genomic characterization of equine coronavirus date: 2007-12-05 words: 6808 flesch: 45 summary: Improved tools for biological sequence comparison Coronavirus as a possible cause of severe acute respiratory syndrome Identification of a novel coronavirus in bats ADPribose-1ʺ-monophosphatase: a conserved coronavirus enzyme that is dispensable for viral replication in tissue culture Identification of protease and ADP-ribose 1ʺ-monophosphatase activities associated with transmissible gastroenteritis virus non-structural protein 3 Stem-loop IV in the 5′ untranslated region is a cis-acting element in bovine coronavirus defective interfering RNA replication Stem-loop III in the 5′ untranslated region is a cis-acting element in bovine coronavirus defective interfering RNA replication Full-length genome sequences of two SARS-like coronaviruses in horseshoe bats and genetic variation analysis A contemporary view of coronavirus transcription Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements Selective replication of coronavirus genomes that express nucleocapsid protein Murine coronavirus nonstructural protein ns2 is not essential for virus replication in transformed cells The human coronavirus 229E superfamily 1 helicase has RNA and DNA duplex-unwinding activities with 5′-to-3′ polarity A complex zinc finger controls the enzymatic activities of nidovirus helicases Comparison of the genome organization of toro-and coronaviruses: evidence for two nonhomologous RNA recombination events during Berne virus evolution Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage A hidden Markov model for predicting transmembrane helices in protein sequences Single-amino-acid substitutions in open reading frame (ORF) 1b-nsp14 and ORF 2a proteins of the coronavirus mouse hepatitis virus are attenuating in mice The severe acute respiratory syndrome (SARS) coronavirus NTPase/helicase belongs to a distinct class of 5′ to 3′ viral helicases On the basis of antigenic and genetic analyses, coronaviruses are divided into three groups (Gonzalez et al., 2003; Gorbalenya et al., 2004; Snijder et al., 2003) . keywords: amino; analysis; bcov; coronavirus; ecov; et al; genome; hcov; mrna; nc99; oc43; protein; rna; sequence cache: cord-300884-rqfxe0x1.txt plain text: cord-300884-rqfxe0x1.txt item: #355 of 541 id: cord-301128-woe6knpv author: Joyeux, Marc title: Requirements for DNA-bridging proteins to act as topological barriers of the bacterial genome date: 2020-08-12 words: 4508 flesch: 37 summary: Marcel Dekker Use of site-specific recombination as a probe of DNA structure and metabolism in vivo Structure and reactions of closed duplex DNA DNA gyrase: structure and function Transcription-coupled hypernegative supercoiling of plasmid DNA by T7 RNA polymerase in Escherichia coli topoisomerase I-deficient strains Potent stimulation of transcription-coupled DNA supercoiling by sequence-specific DNA-binding proteins Large-scale conformational transitions in supercoiled DNA revealed by coarse-grained simulation Hyperplectonemes: A higher order compact and dynamic DNA self-organization Viscous nonlinear dynamics of twist and writhe Twist and writhe dynamics of stiff polymers Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins Domain organization and oligomerization among H-NS like nucleoid-associated proteins in bacteria Protein occupancy landscape of a bacterial genome Fis protein forms DNA topological barriers to confine transcription-coupled DNA supercoiling in Escherichia coli Genes on a wire: The nucleoid-associated protein HU insulates transcription units in Escherichia coli Shape and compaction of Escherichia coli nucleoids DNA condensation in bacteria: Interplay between macromolecular crowding and nucleoid proteins Physical descriptions of the bacterial nucleoid at large scales, and their biological implications From structure to function of bacterial chromosomes: Evolutionary perspectives and ideas for new experiments Polymer solutions: An introduction to physical properties A combined wormlike-chain and bead model for dynamic simulations of long linear DNA Conformational and thermodynamic properties of supercoiled DNA References (70,71) The role of high affinity nonspecific DNA binding by Lrp in transcriptional regulation and DNA organization DNA supercoiling, a critical signal regulating the basal expression of the lac operon in Escherichia coli bp LacI-mediated, negatively supercoiled DNA loop by atomic force microscope Description of non-specific DNA-protein interaction and facilitated diffusion with a dynamical model Dynamical model of DNA protein interaction: effect of protein charge distribution and mechanical properties Comparison of kinetic and dynamical models of DNA-protein interaction and facilitated diffusion A model of H-NS mediated compaction of bacterial DNA Equilibration of complexes of DNA and H-NS proteins on charged surfaces: A coarse-grained model point of view Role of salt valency in the switch of H-NS proteins between DNAbridging and DNA-stiffening modes Compaction of bacterial genomic DNA: keywords: barriers; dna; domains; model; proteins cache: cord-301128-woe6knpv.txt plain text: cord-301128-woe6knpv.txt item: #356 of 541 id: cord-301827-a7hnuxy5 author: Uversky, Vladimir N title: A decade and a half of protein intrinsic disorder: Biology still waits for physics date: 2013-04-29 words: 20990 flesch: 37 summary: Why these proteins are intrinsically disordered Caseins as rheomorphic proteins: interpretation of primary and secondary structures of the as1-, b-, and k-caseins The relation of polypeptide hormone structure and flexibility to receptor binding: the relevance of X-ray studies on insulins, glucagon and human placental lactogen High-resolution proton-magnetic-resonance studies of chromatin core particles Protein structure and enzyme activity Structural studies of tau protein and Alzheimer paired helical filaments show no evidence for beta-structure NACP, a protein implicated in Alzheimer's disease and learning, is natively unfolded Protein structure protection commits gene expression patterns A protein-chameleon: conformational plasticity of alpha-synuclein, a disordered protein involved in neurodegenerative disorders Malleable machines take shape in eukaryotic transcriptional regulation Operational definition of intrinsically unstructured protein sequences based on susceptibility to the 20S proteasome Drugs for 'protein clouds': targeting intrinsically disordered transcription factors Protein dynamics: dancing on an ever-changing free energy stage Protein flexibility, not disorder, is intrinsic to molecular recognition TOP-IDP-scale: a new amino acid scale measuring propensity for intrinsic disorder Intrinsic disorder and functional proteomics Sequence complexity of disordered protein Predicting disordered regions from amino acid sequence: common themes despite differing structural characterization The protein non-folding problem: amino acid determinants of intrinsic order and disorder Composition Profiler: a tool for discovery and visualization of amino acid composition differences Comparing predictors of disordered protein A practical overview of protein disorder prediction methods Predicting protein disorder and induced folding: from theoretical principles to practical applications Prediction of protein disorder at the domain level Prediction of protein disorder Predicting intrinsic disorder in proteins: an overview Inherent relationships among different biophysical prediction methods for intrinsically disordered proteins Intrinsic protein disorder in complete genomes Prediction and functional analysis of native disorder in proteins from the three kingdoms of life The mysterious unfoldome: structureless, underappreciated, yet vital part of any given proteome Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life Thousands of proteins likely to have long disordered regions Norton RS (2006) This study showed that the fraction of protein disorder was positively correlated with both measured RNA expression levels of E. coli genes in three different growth media and with predicted abundance levels of E. coli proteins. keywords: acid; amino; analysis; binding; cell; complex; diseases; disorder; disordered proteins; disordered regions; domains; evolution; fact; folding; function; idps; interactions; membrane; molten; p53; partners; protein structure; proteins; regions; regulation; residues; sequence; signaling; state; structure cache: cord-301827-a7hnuxy5.txt plain text: cord-301827-a7hnuxy5.txt item: #357 of 541 id: cord-302009-oqc21fah author: Geng, Xindu title: Protein folding liquid chromatography and its recent developments() date: 2007-04-15 words: 6673 flesch: 48 summary: As it is well known that there is no obvious interaction between denatured protein and the stationary phase of SEC, but there are strong interactions between denatured proteins and the stationary phase in the other three chromatographic methods, therefore for convenience, the latter are referred to as adsorption liquid chromatography. Protein refolding by liquid chromatography can be simply named as protein folding liquid chromatography. keywords: chromatography; column; et al; folding; pflc; phase; protein; recovery; refolding cache: cord-302009-oqc21fah.txt plain text: cord-302009-oqc21fah.txt item: #358 of 541 id: cord-302414-g5onwhg1 author: Tahir ul Qamar, Muhammad title: Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2 date: 2020-09-16 words: 6792 flesch: 43 summary: Interaction and binding patterns between receptor and vaccine protein were stable and higher. The quality score beyond the usual range of native proteins indicates a possible error in protein structure. keywords: analysis; cell; construct; coronavirus; cov-2; covid-19; epitopes; file; immune; mesv; prediction; protein; sars; server; structure; vaccine cache: cord-302414-g5onwhg1.txt plain text: cord-302414-g5onwhg1.txt item: #359 of 541 id: cord-302490-em1tiz7s author: Cañadas, Olga title: Lipid–Protein and Protein–Protein Interactions in the Pulmonary Surfactant System and Their Role in Lung Homeostasis date: 2020-05-25 words: 16704 flesch: 27 summary: Front Surfactant protein A binds Mycoplasma pneumoniae with high affinity and attenuates its growth by recognition of disaturated phosphatidylglycerols Characteristics of surfactant protein A and D binding to lipoteichoic acid and peptidoglycan, 2 major cell wall components of gram-positive bacteria respiratory fungal infections: Their role in the inflammatory response Surfactant Proteins A and D: Trimerized Innate Immunity Proteins with an Affinity for Viral Fusion Proteins Collectins and fungal pathogens: Roles of surfactant proteins and mannose binding lectin in host resistance Surfactant protein D binding to terminal alpha1-3-linked fucose residues and to Schistosoma mansoni Opsonic activities of surfactant proteins A and D in phagocytosis of gram-negative bacteria by alveolar macrophages Surfactant protein A (SP-A)-mediated clearance of Staphylococcus aureus involves binding of SP-A to the staphylococcal adhesin eap and the macrophage receptors SP-A receptor 210 and scavenger receptor class A Purification of a cell-surface receptor for surfactant protein A Lung surfactant proteins (SP-A and SP-D) in non-adaptive host responses to infection Glycoprotein-340 binds surfactant protein-A (SP-A) and stimulates alveolar macrophage migration in an SP-A-independent manner Collectin surfactant protein D binds antibodies and interlinks innate and adaptive immune systems By binding SIRPalpha or calreticulin/CD91, lung collectins act as dual function surveillance molecules to suppress or enhance inflammation Natural Anti-Infective Pulmonary Proteins: In Vivo Cooperative Action of Surfactant Protein SP-A and the Lung Antimicrobial Peptide SP-BN Pulmonary surfactant protein A up-regulates activity of the mannose receptor, a pattern recognition receptor expressed on human macrophages Pulmonary collectins enhance phagocytosis of Mycobacterium avium through increased activity of mannose receptor Pulmonary surfactant protein A augments the phagocytosis of Streptococcus pneumoniae by alveolar macrophages through a casein kinase 2-dependent increase of cell surface localization of scavenger receptor A Ten Haken, B.; et al. A inhibits influenza A virus infection of A549 lung epithelial cells: A recombinant form containing neck and lectin domains promotes infectivity Interactions of surfactant protein A with influenza A viruses: Binding and neutralization Impact of ozone exposure on the phagocytic activity of human surfactant protein A (SP-A) and SP-A variants Evidence for a protective role of pulmonary surfactant protein D (SP-D) against influenza A viruses Mechanisms of anti-influenza activity of surfactant proteins A and D: Comparison with serum collectins Collectin-mediated antiviral host defense of the lung: keywords: activity; ae2c; alveolar; binding; cells; cholesterol; collectins; homeostasis; interaction; lipid; lps; lung; macrophages; membrane; protein; protein sp; pulmonary; receptor; role; structure; surface; surfactant; surfactant protein; virus cache: cord-302490-em1tiz7s.txt plain text: cord-302490-em1tiz7s.txt item: #360 of 541 id: cord-302514-rstvf3mc author: Abbas, Wasim title: The eEF1A Proteins: At the Crossroads of Oncogenesis, Apoptosis, and Viral Infections date: 2015-04-07 words: 5156 flesch: 26 summary: Additionally, resveratrol suppresses growth of human ovarian cancer cells in culture and in a murine xenograft model with reduced expression of proliferating cell nuclear antigen and increased TUNEL staining (61) . 1/2 correlate with cell growth but not apoptosis in hepatocellular carcinoma cell lines with different differentiation grade Etiology-dependent molecular mechanisms in human hepatocarcinogenesis Amplification of chromosomal region 20q13 in invasive breast cancer: prognostic implications Elongation factor-1 alpha is an overexpressed actin binding protein in metastatic rat mammary adenocarcinoma Expression profile of eukaryotic translation factors in human cancer tissues and cell lines Up-regulation of eEF1A2 promotes proliferation and inhibits apoptosis in prostate cancer iTRAQ identification of candidate serum biomarkers associated with metastatic progression of human prostate cancer Elongation factor-1 alpha gene determines susceptibility to transformation Ovarian cancer: strategies for overcoming resistance to chemotherapy Ovarian cancer metastasis: integrating insights from disparate model organisms Ovarian cancer Therapeutic strategies in epithelial ovarian cancer Expression of eEF1A2 is associated with clear cell histology in ovarian carcinomas: overexpression of the gene is not dependent on modifications at the eEF1A2 locus The prognostic significance of elongation factor eEF1A2 in ovarian cancer eEF1A2 as a putative oncogene The eukaryotic translation elongation factor eEF1A2 induces neoplastic properties and mediates tumorigenic effects of ZNF217 in precursor cells of human ovarian carcinomas Cancer chemopreventive and therapeutic potential of resveratrol: mechanistic perspectives Resveratrol, a sirtuin 1 activator, increases IL-6 production by peripheral blood mononuclear cells of patients with knee osteoarthritis Resveratrol suppresses growth of human ovarian cancer cells in culture and in a murine xenograft model: eukaryotic elongation factor 1A2 as a potential target Cancer statistics Comparison of time trends in lung cancer mortality (1990-2006) in the world, from the WHO mortality database Establishment and expression profiling of new lung cancer cell lines from Chinese smokers and lifetime keywords: akt; apoptosis; cancer; cell; eef1a2; elongation; expression; factor; gene; human; lines; protein; translation; virus cache: cord-302514-rstvf3mc.txt plain text: cord-302514-rstvf3mc.txt item: #361 of 541 id: cord-303494-tofch4j7 author: Bai, Juan title: Identification of VP1 peptides diagnostic of encephalomyocarditis virus from swine date: 2014-12-30 words: 3864 flesch: 51 summary: Immunization of mice with recombinant VP1 protein (plasmids or recombinant adenoviruses expressing small hairpin RNAs targeted to VP1 protein genes of EMCV), which could provide protective efficacy against EMCV [26, 27] . EMCV VP1 protein was one of the most important structural proteins and played an important role in the protective immunity. keywords: amino; cells; emcv; encephalomyocarditis; epitopes; figure; mcabs; protein; results; virus; vp1 cache: cord-303494-tofch4j7.txt plain text: cord-303494-tofch4j7.txt item: #362 of 541 id: cord-303555-mwu72q7w author: Dent, Paul title: Cell Signaling and Translational Developmental Therapeutics date: 2020-10-06 words: 8900 flesch: 37 summary: Lessons From the Old Testament of Glycogen Metabolism and the New Testament of Molecular Biology D-chiro-inositol glycans in insulin signaling and insulin resistance Insulin and a Putative Insulin Metabolic Mediator Fraction From Liver and Muscle Stimulate p33 Messenger Ribonucleic Acid Accumulation by Apparently Different Mechanisms Insulin-Mediated Effect on the Activity of UDPG-Glycogen Transglucosylase of Muscle Molecular Basis for the Substrate Specificity of Protein Kinase B; Comparison With MAPKAP Kinase-1 and p70 S6 Kinase Mechanism of Activation of Protein Kinase B by Insulin and IGF-1 Characterization of a 3-Phosphoinositide-Dependent Protein Kinase Which Phosphorylates and Activates Protein Kinase B alpha Inhibition of Glycogen Synthase Kinase-3 by Insulin Mediated by Protein Kinase B Specific Binding of the Akt-1 Protein Kinase to Phosphatidylinositol 3,4,5-Trisphosphate Without Subsequent Activation Mechanism of Activation and Function of Protein Kinase B The Molecular Mechanism by Which Insulin Stimulates Glycogen Synthesis in Mammalian Skeletal Muscle Facts and New Hopes on Selective FGFR Inhibitors in Solid Tumors Membrane Phosphorylation: Activator From Rabbit Skeletal Muscle Molecular Structure of a Protein-Tyrosine/Threonine Kinase Activating p42 Mitogen-Activated Protein (MAP) Kinase: MAP Kinase Kinase Identification and Characterization of a New Mammalian Mitogen-Activated Protein Kinase Kinase, MKK2 A Conserved Kinase Cascade for MAP Kinase Activation in Yeast The MAP Kinase Cascade Is Essential for Diverse Signal Transduction Pathways The Pheromone Response Pathway in Saccharomyces cerevisiae Regulation of the MAP Kinase Cascade Activation of Mitogen-Activated Protein Kinase Kinase by v-Raf in NIH 3T3 Cells and In Vitro Raf-1 Activates MAP Kinase-Kinase Raf-1 Is a Potential Substrate for Mitogen-Activated Protein Kinase In Vivo Stimulation of the Stress-Activated Mitogen-Activated Protein Kinase Subfamilies in Perfused Heart. keywords: activation; autophagy; cancer; cells; drug; factor; glycogen; growth; insulin; kinase; neratinib; pathway; phosphorylation; protein; ras; receptor; regulation; signaling; studies; tumor; tyrosine cache: cord-303555-mwu72q7w.txt plain text: cord-303555-mwu72q7w.txt item: #363 of 541 id: cord-304040-64obh7i3 author: Sande, Charles J. title: Untargeted analysis of the airway proteomes of children with respiratory infections using mass spectrometry based proteomics date: 2018-09-14 words: 5045 flesch: 35 summary: With the exception of milk proteins, no systematic changes in protein expression level could be associated with increasing age. It is additionally notable that mass spectrometry platforms used to investigate protein expression in these studies may have previously lacked sufficient sensitivity necessary for extensive proteome coverage that would be helpful in elucidating important biomarkers of mechanisms or prognosis. keywords: airway; analysis; cells; children; expression; fig; levels; proteins; proteome; protocol; samples cache: cord-304040-64obh7i3.txt plain text: cord-304040-64obh7i3.txt item: #364 of 541 id: cord-304306-rxjahqwh author: Vlachakis, Dimitrios title: Molecular mechanisms of the novel coronavirus SARS-CoV-2 and potential anti-COVID19 pharmacological targets since the outbreak of the pandemic date: 2020-10-08 words: 8538 flesch: 33 summary: A different function of the N protein is its interaction with the protease subunit p42, which degrades viral proteins . Specifically, this interaction may impair proteolysis of viral proteins and their presentation to Cytotoxic T-Lymphocytes, thus promoting viral evasion from immune effectors . keywords: activity; binding; cell; coronavirus; cov-2; covid-19; domain; drug; et al; helicase; inhibitors; membrane; polymerase; protease; protein; replication; rna; sars; spike; structure; target cache: cord-304306-rxjahqwh.txt plain text: cord-304306-rxjahqwh.txt item: #365 of 541 id: cord-304343-m7tbdfri author: Khandia, Rekha title: A Comprehensive Review of Autophagy and Its Various Roles in Infectious, Non-Infectious, and Lifestyle Diseases: Current Knowledge and Prospects for Disease Prevention, Novel Drug Design, and Therapy date: 2019-07-03 words: 20405 flesch: 25 summary: Autophagic degradation of inhibitor of apoptosis dBruce controls DNA fragmentation during late oogenesis in Drosophila Suppression of T cell autophagy results in decreased viability and function of T cells through accelerated apoptosis in a murine sepsis model Combination of TRAIL and Chal-24 synergistically induces autophagy-mediated apoptosis in lung cancer cells Induction of autophagy-dependent necroptosis is required for childhood acute lymphoblastic leukemia cells to overcome glucocorticoid resistance FADD and caspase-8 control the outcome of autophagic signaling in proliferating T cells Identification of small molecule inhibitors of phosphatidylinositol 3-kinase and autophagy Fas-associated death domain (FADD) is a negative regulator of T-cell receptor-mediated necroptosis Caspase inhibition prevents tumor necrosis factor-α-induced apoptosis and promotes necrotic cell death in mouse hepatocytes in vivo and in vitro An ursolic acid derived small molecule triggers cancer cell death through hyperstimulation of macropinocytosis L929 cells depends on autocrine production of TNFα mediated by the PKC-MAPKs-AP-1 pathway The sirtuin family, therapeutic targets to treat diseases of aging Antineoplastic activity of the cytosolic FoxO1 results from autophagic cell death RIP3, a molecular switch for necrosis and inflammation Knockout of Atg5 inhibits proliferation and promotes apoptosis of DF-1 cells The autophagy machinery controls cell death switching between apoptosis and necroptosis Sorafenib-induced defective autophagy promotes cell death by necroptosis NAD+ depletion triggers macrophage necroptosis, a cell death pathway exploited by Mycobacterium tuberculosis ADP-ribose) polymerase 1, PARP1, modifies EZH2 and inhibits EZH2 histone methyltransferase activity after DNA damage Receptor interacting protein kinase-3 determines cellular necrotic response to TNF-alpha AMP-activated protein kinase, an emerging drug target to regulate imbalances in lipid and carbohydrate metabolism to treat cardio-metabolic diseases Role of AMPK-mTOR-Ulk1/2 in the regulation of autophagy: Cross talk, shortcuts, and feedbacks ATM signals to TSC2 in the cytoplasm to regulate mTORC1 in response to ROS Autophagy recognizes intracellular Salmonella enterica serovar Typhimurium in damaged vacuoles Listeria monocytogenes ActA is a key player in evading autophagic recognition Interactions between Shigella flexneri and the autophagy machinery NOD proteins: Regulators of inflammation in health and disease Similarly, components were found to be degraded by autophagy during developmental apoptosis [185] , whilst it was recently shown that inhibiting autophagy increased apoptosis and accelerated mortality in murine sepsis models with inadequate autophagy pathways in CD4 + T cells, indicating that autophagy has a functional role against apoptosis and immunosuppression in T cells in sepsis [186] . keywords: accumulation; activation; apoptosis; atg5; autophagosome; autophagy; beclin; cancer; cells; complex; death; degradation; disease; expression; formation; genes; human; immunity; infection; inhibit; intracellular; iron; lc3; levels; lysosomal; lysosome; mechanisms; membrane; mice; mtor; novel; pathway; promote; protein; rapamycin; replication; response; role; starvation; stress; tumor; virus cache: cord-304343-m7tbdfri.txt plain text: cord-304343-m7tbdfri.txt item: #366 of 541 id: cord-304607-td0776wj author: Paszkiewicz, Konrad H. title: Omics, Bioinformatics, and Infectious Disease Research date: 2010-12-24 words: 7023 flesch: 39 summary: In addition, 21 nonannotated regions had clear levels of transcription and should therefore be considered as genes (Passalacqua et al., 2009) . Indeed, the first bacterial genomes sequenced were those from pathogens Fraser et al., 1995; Tomb et al., 1997) , and these were preceded by many bacteriophage genomes such as bacteriophage MS2 (Fiers et al., 1976) and ϕX174 (Sanger et al., 1977) and viral genomes (Fiers et al., 1978) . keywords: analysis; assembly; bioinformatics; data; disease; et al; genes; genome; genomics; proteins; sequence; sequencing; species; vaccine cache: cord-304607-td0776wj.txt plain text: cord-304607-td0776wj.txt item: #367 of 541 id: cord-304616-k92fa15l author: Izes, Aaron M. title: Assay validation and determination of in vitro binding of mefloquine to plasma proteins from clinically normal and FIP-affected cats date: 2020-08-05 words: 4213 flesch: 44 summary: A simple, high pressure liquid chromatography assay was developed to detect mefloquine plasma concentrations in feline plasma. In vitro hepatic metabolism of mefloquine using microsomes from cats, dogs and the common brush-tailed possum (Trichosurus vulpecula) Predicting plasma protein binding of drugs: a new approach Drug-protein binding: a critical review of analytical tools Clinical pharmacokinetics of mefloquine Positive predictive value of albumin: globulin ratio for feline infectious peritonitis in a mid-western referral hospital population A high performance liquid chromatographic assay of mefloquine in saliva after a single oral dose in healthy adult Africans Defining limit of detection and limit of quantitation as applied to drug of abuse testing: striving for a consensus International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use Prevalence of feline immunodeficiency virus infection in domesticated and feral cats in eastern Australia Risk factors for feline infectious peritonitis in Australian cats pH adjustment of human blood plasma prior to bioanalytical sample preparation Chemistry (cobas) reference intervals In vitro hepatic metabolism of mefloquine using microsomes from cats, dogs and the common brush-tailed possum Clinical application of mefloquine pharmacokinetics in the treatment of P. falciparum malaria In vitro binding of cefovecin to plasma proteins in Australian marsupials and plasma concentrations of cefovecin following single subcutaneous administration to koalas (Phascolarctos cinereus) Species differences in drug plasma protein binding Selective plasma protein binding of antimalarial drugs to α1-acid glycoprotein Plasma protein binding and blood-free concentrations: which studies are needed to develop a drug? Serum protein concentrations in Plasmodium falciparum malaria Critical assessment of the diagnostic value of feline α1-acid glycoprotein for feline infectious peritonitis using the likelihood ratios approach Protein binding of antimicrobials: methods for quantification and for investigation of its impact on bacterial killing Errors in estimating the unbound fraction of drugs due to the volume shift in equilibrium dialysis Clinical pharmacology: plasma protein binding of drugs What is the true clinical significance of plasma protein binding displacement interactions? keywords: binding; cats; concentrations; feline; fip; mefloquine; plasma; protein; samples cache: cord-304616-k92fa15l.txt plain text: cord-304616-k92fa15l.txt item: #368 of 541 id: cord-304953-ntg8w5k4 author: Modis, Yorgo title: Relating structure to evolution in class II viral membrane fusion proteins date: 2014-02-11 words: 3706 flesch: 38 summary: Class II fusion proteins have a conserved three-domain architecture and are found in many important viral pathogens. Class II fusion proteins are a structurally unrelated class found in flaviviruses, alphaviruses, and most recently in rubella virus (sole member of the rubivirus genus) and Rift Valley fever virus (from the phlebovirus genus) keywords: class; envelope; fusion; membrane; proteins; rubella; virus cache: cord-304953-ntg8w5k4.txt plain text: cord-304953-ntg8w5k4.txt item: #369 of 541 id: cord-305143-mqd4ioj4 author: Zmasek, Christian M. title: Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO) date: 2019-01-06 words: 7272 flesch: 36 summary: Protein domains were analyzed using hmmscan from HMMER v3.1b2 (Eddy, 2011) and the Pfam 31.0 database (Finn et al., 2016) . The ortholog conjecture is untestable by the current gene ontology but is supported by RNA sequencing data ICP27 interacts with the Cterminal domain of RNA polymerase II and facilitates its recruitment to herpes simplex virus 1 transcription sites, where it undergoes proteasomal degradation during infection Herpesvirus systematics Evolution of the herpesviruses Fast and accurate phylogeny minimum-evolution principle Specific inhibition of herpes simplex virus DNA polymerase by helical peptides corresponding to the subunit interface Accelerated profile HMM searches Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis The Pfam protein families database: towards a more sustainable future Distinguishing homologous from analogous proteins Construction and properties of a mutant of herpes simplex virus type 1 with glycoprotein H coding sequences deleted Multiple functions of DNA polymerases Transcriptional analysis of the murine cytomegalovirus HindIII-I region: identification of a novel immediate-early gene region Human herpesvirus 6 open reading frame U12 encodes a functional beta-chemokine receptor Evolutionary history and functional implications of protein domains and their combinations in eukaryotes Orthologs and paralogs -we need to get it right MAFFT multiple sequence alignment software version 7: improvements in performance and usability A comparative study of uracil-DNA glycosylases from human and herpes simplex virus type 1 aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity A herpes simplex virus mutant in which glycoprotein D sequences are replaced by beta-galactosidase sequences binds to but is unable to penetrate into cells Characterization of the protease and other products of aminoterminus-proximal cleavage of the herpes simplex virus 1 UL26 protein Intranuclear delivery of an antiviral peptide mediated by the B subunit of Escherichia coli heatlabile enterotoxin keywords: analysis; architecture; dna; domain; gene; herpesviridae; herpesviruses; human; members; pfam; polymerase; protein; species cache: cord-305143-mqd4ioj4.txt plain text: cord-305143-mqd4ioj4.txt item: #370 of 541 id: cord-305602-yzc4bosn author: Llano, Manuel title: Chapter Seven Defining Pharmacological Targets by Analysis of Virus–Host Protein Interactions date: 2018-12-31 words: 5925 flesch: 30 summary: In this study, 35% of the 1745 genes initially found to be involved in viral protein interactions were demonstrated to influence viral replication by subsequent RNAi screening. Due to the dependency on host factors for viral replication, pharmacological disruption of the host-pathogen protein–protein interactions (PPIs) is an important therapeutic alternative to block viral replication. keywords: analysis; binding; complexes; et al; host; human; interactions; ppis; protein; replication; viral; virus; viruses cache: cord-305602-yzc4bosn.txt plain text: cord-305602-yzc4bosn.txt item: #371 of 541 id: cord-306111-wn1gxhk9 author: Dommett, R. M. title: Mannose‐binding lectin in innate immunity: past, present and future date: 2006-09-01 words: 9072 flesch: 33 summary: Therapeutic potential of MBL MBL replacement was first attempted (without any knowledge of the deficiency) when fresh frozen plasma was given to patients and found to correct the opsonic defect (28, 29) . The mannose-binding protein A but not C is an acute phase reactant Structure of a C-type mannose-binding protein complexed with an oligosaccharide Human mannose-binding protein is identical to a component of Ra-reactive factor Association of mutations in mannose binding protein gene with childhood infection in consecutive hospital series Cutting edge: complementactivating complex of ficolin and mannose-binding lectin-associated serine protease Mannose-binding lectin accelerates complement activation and increases serum killing of Neisseria meningitidis serogroup C Activation of the lectin complement pathway by H-ficolin (Hakata antigen) Differential recognition of obligate anaerobic bacteria by human mannose-binding lectin Differential binding of mannose-binding lectin to respiratory pathogens in cystic fibrosis Human mannose-binding protein inhibits infection of HeLa cells by Chlamydia trachomatis Binding of mannan-binding protein to various bacterial pathogens of meningitis Interaction of human mannose-binding protein with Mycobacterium avium Interaction of mannose-binding lectin with primary isolates of human immunodeficiency virus type 1 High mannose glycans and sialic acid on gp120 regulate binding of mannose-binding lectin (MBL) to HIV type 1 Mannose binding lectin (MBL) and HIV Mannan-binding protein and bovine conglutinin mediate enhancement of herpes simplex virus type 2 infection in mice Mannan-binding lectin modulates the response to HSV-2 infection Mannose binding protein is involved in first-line host defence: evidence from transgenic mice Binding of host collectins to the pathogenic yeast Cryptococcus neoformans: human surfactant protein D acts as an agglutinin for acapsular yeast cells Mannose-binding lectin is a component of innate mucosal defense against Cryptosporidium parvum in AIDS Recognition of plasmodium falciparum proteins by mannan-binding lectin, a component of the human innate immune system The major surface glycoprotein of Trypanosoma cruzi amastigotes are ligands of the human serum mannose-binding protein Novel MASP2 variants detected among North African and Sub-Saharan individuals Analysis of mannose-binding lectin 2 (MBL2) genotype and the serum protein levels in the Korean population Association of mannose-binding lectin gene haplotype LXPA and LYPB with interferon-resistant hepatitis C virus infection in Japanese patients keywords: binding; complement; deficiency; gene; hiv; human; infection; lectin; levels; mannan; mannose; mbl; pathway; patients; protein; role; studies cache: cord-306111-wn1gxhk9.txt plain text: cord-306111-wn1gxhk9.txt item: #372 of 541 id: cord-306261-yc2y2xak author: van Tricht, Ewoud title: Fast, selective and quantitative protein profiling of adenovirus-vector based vaccines by ultra-performance liquid chromatography date: 2018-12-28 words: 5817 flesch: 42 summary: This suggests that temperature stress resulted in loss of virus particles rather than specific degradation of adenovirus proteins. 91% overall chromatogram peak area decrease) and a number of new peaks were observed in the chromatogram, which were tentatively assigned to oxidized adenovirus proteins. keywords: adenovirus; analysis; areas; concentration; method; min; peak; proteins; sample; tfa; uplc cache: cord-306261-yc2y2xak.txt plain text: cord-306261-yc2y2xak.txt item: #373 of 541 id: cord-306624-1mjmttec author: Wodrich, Harald title: A Capsid-Encoded PPxY-Motif Facilitates Adenovirus Entry date: 2010-03-19 words: 11673 flesch: 48 summary: U2OS cells were transfected with protein VI fused to mRFP, either using wt protein VI (VI-wt, top row), with mutated protein VI (VI-M1, middle row) or with deleted amphipathic helix (VI-DW, bottom row). We show that protein VI, an internal capsid protein, is rapidly exposed after cell surface attachment and internalization and remains partially associated with the capsid during intracellular transport. keywords: ad5; adenovirus; capsid; cells; entry; figure; gfp; ligases; motif; mtoc; mutant; nedd4.2; particles; ppxy; protein; protein vi; row; ubiquitin; ubiquitylation; virus cache: cord-306624-1mjmttec.txt plain text: cord-306624-1mjmttec.txt item: #374 of 541 id: cord-306733-df36w6l7 author: Rosales-Mendoza, Sergio title: What Does Plant-Based Vaccine Technology Offer to the Fight against COVID-19? date: 2020-04-14 words: 8607 flesch: 34 summary: Another approach to express heterologous protein in plants relies on the use of viral-based vectors, which exploit the efficient promoters, UTRs, and DNA/RNA replication mechanisms found in plant viruses. A recent review revealed that at least 97 vaccine candidates have been developed based on plant viruses covering infectious agents, cancer, and autoimmune disorders [78] . keywords: antigen; approach; cells; coronavirus; cov-1; covid-19; development; expression; immune; mice; plant; production; protein; sars; vaccines; virus; vlps cache: cord-306733-df36w6l7.txt plain text: cord-306733-df36w6l7.txt item: #375 of 541 id: cord-306904-8iteddug author: Uversky, Vladimir N title: Unreported intrinsic disorder in proteins: Building connections to the literature on IDPs date: 2014-12-12 words: 18448 flesch: 37 summary: Digested disorder: quarterly intrinsic disorder digest Digested disorder, issue #2: quarterly intrinsic disorder digest Digested disorder, issue #3: quarterly intrinsic disorder digest Comprehensive comparative assessment of in-silico predictors of disordered regions eIF4B and eIF4G jointly stimulate eIF4A ATPase and unwinding activities by modulation of the eIF4A conformational cycle New initiation factor activity required for globin mRNA translation The mechanism of eukaryotic translation initiation and principles of its regulation Molecular mechanism of scanning and start codon selection in eukaryotes mRNA helicases: the tacticians of translational control The DEAD-box helicase eIF4A: paradigm or the odd one out Exploiting heterogeneous sequence properties improves prediction of protein disorder Predicting intrinsic disorder from amino acid sequence Sequence complexity of disordered protein PONDR-FIT: a meta-predictor of intrinsically disordered amino acids Prediction of protein binding regions in disordered proteins ANCHOR: web server for predicting protein binding regions in disordered proteins Remarkable stabilization of plasminogen activator inhibitor 1 in a molecular sandwich complex Interaction of T4 Furthermore, based on the combination of literature mining and a brief computational analysis 20 hidden gems were found; i.e., papers that missed protein disorder. keywords: activity; analysis; binding; cell; complex; disordered; disordered protein; disordered regions; dna; domain; factor; family; figure; functions; human; interaction; lgn; membrane; papers; phosphorylation; protein; regions; regulation; replication; residues; role; shock; sites; structure; tail; terminal; transcription; uniprot cache: cord-306904-8iteddug.txt plain text: cord-306904-8iteddug.txt item: #376 of 541 id: cord-307227-x6xketcn author: Martin, William R. title: Repurposing of FDA-Approved Toremifene to Treat COVID-19 by Blocking the Spike Glycoprotein and NSP14 of SARS-CoV-2 date: 2020-09-10 words: 4008 flesch: 42 summary: 6 Indeed, a crystal structure of the Ebola virus with bound toremifene indicates the interaction lies between the attachment (GP1) and fusion (GP2) protein subunits. 13 Further studies have been done using large databases, such as ZINC, 14 to test large compound libraries across multiple viral proteins. keywords: binding; cov-2; docking; interaction; potential; protein; sars; spike; structure; toremifene cache: cord-307227-x6xketcn.txt plain text: cord-307227-x6xketcn.txt item: #377 of 541 id: cord-307731-a2fqmaly author: Vázquez, Javier title: Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches date: 2020-10-15 words: 11917 flesch: 33 summary: RSC Adv Discovery of cyanopyridine scaffold as novel indoleamine-2,3-dioxygenase 1 (IDO1) inhibitors through virtual screening and preliminary hit optimisation Virtual screening for potential allosteric inhibitors of cyclin-dependent kinase 2 from traditional chinese medicine Identification of novel CDK2 inhibitors by a multistage virtual screening method based on SVM, pharmacophore and docking model Ligand-based and e-pharmacophore modeling, 3D-QSAR and hierarchical virtual screening to identify dual inhibitors of spleen tyrosine kinase (Syk) and janus kinase 3 (JAK3) New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations: A cross-docking study Molecular dynamics simulations and kinetic measurements to estimate and predict protein-ligand residence times Structural stability predicts the binding mode of protein-ligand complexes OpenEye Scientic Software. SIFt is included in Arpeggio [142] , a web server for the analysis of protein interactions with small-molecule ligands, proteins, and DNA. keywords: binding; chemical; compounds; design; docking; drug; interaction; ligand; methods; performance; protein; screening; similarity; structure; target cache: cord-307731-a2fqmaly.txt plain text: cord-307731-a2fqmaly.txt item: #378 of 541 id: cord-307811-6e3j0pn7 author: Hao, Wei title: Binding of the SARS-CoV-2 Spike Protein to Glycans date: 2020-07-02 words: 5709 flesch: 47 summary: Binding of the subunits and S proteins of SARS-CoV-2, SARS-CoV, and MERS-CoV to a HS microarray. Additionally, we found that the binding preferences of the RBDs, S1 subunits and full-length S proteins of SARS-CoV and MERS-CoV are similar to those of the subunits and S protein of SARS-CoV-2, although small differences are observed (Fig. keywords: acid; binding; cell; cov-2; microarray; protein; sars; sulfate; surface; virus cache: cord-307811-6e3j0pn7.txt plain text: cord-307811-6e3j0pn7.txt item: #379 of 541 id: cord-308043-h0knm8y4 author: Hussey, Séamus title: Autophagy as an emerging dimension to adaptive and innate immunity date: 2009-08-31 words: 6956 flesch: 31 summary: A morphometric approach to the kinetics of intracellular degradation by autophagy Quantitative characterization of dense body, autophagic vacuole, and acid phosphatase-bearing particle populations during the early phases of glucagon-induced autophagy in rat liver 3-Methyladenine: specific inhibitor of autophagic/lysosomal protein degradation in isolated rat hepatocytes A unified nomenclature for yeast autophagy-related genes Cis1/Atg31 is required for autophagosome formation in Saccharomyces cerevisiae Molecular machinery of autophagosome formation in yeast, Saccharomyces cerevisiae ATG genes involved in nonselective autophagy are conserved from yeast to man, but the selective Cvt and pexophagy pathways also require organism-specific genes Toward unraveling membrane biogenesis in mammalian autophagy Ultrastructural characterization of the delimiting membranes of isolated autophagosomes and amphisomes by freeze-fracture electron microscopy Studies on the mechanisms of autophagy: formation of the autophagic vacuole Autophagy: a forty-year search for a missing membrane source Studies on induced cellular autophagy. Other essential groups of autophagy proteins participate in isolation membrane formation. keywords: activation; autophagosome; autophagy; cells; class; complex; degradation; formation; immune; kinase; lc3; membrane; mhc; mtor; protein; role cache: cord-308043-h0knm8y4.txt plain text: cord-308043-h0knm8y4.txt item: #380 of 541 id: cord-308641-vqiipbo8 author: Jankauskaitė, Justina title: SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation date: 2019-02-01 words: 5461 flesch: 29 summary: Understanding the relationship between the sequence, structure, binding energy, binding kinetics and binding thermodynamics of protein–protein interactions is crucial to understanding cellular signaling, the assembly and regulation of molecular complexes, the mechanisms through which mutations lead to disease, and protein engineering. We present SKEMPI 2.0, a major update to our database of binding free energy changes upon mutation for structurally resolved protein–protein interactions. keywords: affinity; binding; data; et al; interactions; kcal; mol; mutant; mutations; protein; skempi cache: cord-308641-vqiipbo8.txt plain text: cord-308641-vqiipbo8.txt item: #381 of 541 id: cord-309043-dlmx12vt author: von Brunn, Albrecht title: Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome date: 2007-05-23 words: 6742 flesch: 48 summary: We therefore cloned the SARS-CoV ORFeome by recombinatorial cloning (GATEWAY technology) and performed a genome-wide analysis for viral protein interactions by yeast-two-hybrid (Y2H) matrix screen. Known virus-host and intraviral interactions of SARS proteins were identified by a literature screen (see Tables S1 and S2). keywords: accessory; cells; coronavirus; cov; interactions; network; nsp2; nsp8; number; orf9b; proteins; replication; rna; sars; virus; y2h cache: cord-309043-dlmx12vt.txt plain text: cord-309043-dlmx12vt.txt item: #382 of 541 id: cord-309384-vlk8cebh author: Kolter, Thomas title: Ganglioside Biochemistry date: 2012-12-19 words: 16942 flesch: 31 summary: I integral membrane protein of the endoplasmic reticulum Zebrafish and mouse α2,3-sialyltransferases responsible for synthesizing GM4 ganglioside Prevention of experimental allergic encephalomyelitis by ganglioside G(M4) Purification and characterization of UDP-glucose:ceramide glucosyltransferase from rat liver Golgi membranes Expression cloning of a cDNA for human ceramide glucosyltransferase that catalyzes the first glycosylation step of glycosphingolipid synthesis Oligomerization and topology of the Golgi 28 ISRN Biochemistry membrane protein glucosylceramide synthase Identification of active site residues in glucosylceramide synthase: a nucleotide-binding/catalytic motif conserved with processive β-glycosyltransferases Topology of glucosylceramide synthesis in Golgi membranes from porcine submaxillary glands Lactosylceramide is synthesized in the lumen of the Golgi apparatus MDR1 Pglycoprotein is a lipid translocase of broad specificity, while MDR3 P-glycoprotein specifically translocates phosphatidylcholine ABC lipid transporters: extruders, flippases, or flopless activators? Pre-and post-Golgi translocation of glucosylceramide in glycosphingolipid synthesis Reconstitution of glucosylceramide flip-flop across endoplasmic reticulum: implications for mechanism of glycosphingolipid biosynthesis Glycosphingolipid synthesis requires FAPP2 transfer of glucosylceramide Mutation of βglucosidase 2 causes glycolipid storage disease and impaired male fertility Biosynthesis of glycolipids cDNA cloning and expression of human lactosylceramide synthase Isolation and characterization of extremely minor gangliosides, G(M1b) and G(D1α), in adult bovine brains as developmentally regulated antigens Enhanced insulin sensitivity in mice lacking ganglioside GM3 Tissue-specific expression of cseries gangliosides in the extraneural system Structural characterization of a novel cholinergic neuron-specific ganglioside in bovine brain Biosynthetic pathway for a new series of gangliosides, GT1aα and GQ1bα Biosynthesis of the major brain gangliosides GD1a and GT1b Glycosphingolipid functions: insights from engineered mouse models A mouse B16 melanoma mutant deficient in glycolipids Complex gangliosides are essential in spermatogenesis of mice: possible roles in the transport of testosterone Mice lacking complex gangliosides develop Wallerian degeneration and myelination defects A functional role for complex gangliosides: motor deficits in GM2/GD2 synthase knockout mice Attenuation of interleukin 2 signal in the spleen cells of complex gangliosidelacking mice CD4 and CD8 T cells require different membrane gangliosides for activation Mice lacking major brain gangliosides develop parkinsonism G(M1) ganglioside rescues substantia nigra pars compacta neurons and increases dopamine synthesis in residual nigrostriatal dopaminergic neurons in MPTP-treated mice GM1 specifically interacts with α-synuclein and inhibits fibrillation Mice expressing only monosialoganglioside GM3 exhibit lethal audiogenic seizures Interruption of ganglioside synthesis produces central nervous system degeneration and altered axon-glial interactions Sphingolipid synthetic pathways are major regulators of lipid homeostasis Membranes in balance: mechanisms of sphingolipid homeostasis Regulation of ganglioside biosynthesis in the nervous system The cytoplasmic tail of GM3 synthase defines its subcellular localization, stability, and in vivo activity Multi-enzyme kinetic analysis of glycolipid biosynthesis Golgi localization of glycosyltransferases involved in ganglioside biosynthesis Regulation of ganglioside biosynthesis by enzyme complex formation of glycosyltransferases The synthesis of complex carbohydrates by multiglycosyltransferase systems and their potential function in intercellular adhesion Glycosyltransferase complexes improve glycolipid synthesis Physical and functional association of glycolipid N-acetylgalactosaminyl and galactosyl transferases in the Golgi apparatus Ganglioside glycosyltransferases organize in distinct multienzyme complexes in CHO-K1 cells Identification and expression of NEU3, a novel human sialidase associated to the plasma membrane A close association of the ganglioside-specific sialidase Neu3 with caveolin in membrane microdomains Membrane sialidase NEU3 is highly expressed in human melanoma cells promoting cell growth with minimal changes in the composition of gangliosides Sialidase occurs in both membranes of the nuclear envelope and hydrolyzes endogenous GD1a Degradation of glycolipids Lysosomal degradation of membrane lipids Activator proteins and topology of lysosomal sphingolipid catabolism Regulation of apoptosis-associated lysosomal membrane permeabilization Recycling compartments and the internal vesicles of multivesicular bodies harbor most of the cholesterol found in the endocytic pathway Biological function of the cellular lipid BMP-BMP as a key activator for cholesterol sorting and membrane digestion Metabolism, function and mass spectrometric analysis of bis(monoacylglycero)phosphate and cardiolipin Separation and characterization of late endosomal membrane domains Lysosome biogenesis and lysosomal membrane proteins: trafficking meets function Lysosomal membrane proteins: life between acid and neutral conditions Hoppe-Seyler's Zeitschrift für Physiologische Chemie The human G(M2) activator protein. Secondary storage of gangliosides GM2 and GM3 occurs also in Hurler disease [290] (mucopolysaccharidosis type I; α-Liduronidase deficiency). keywords: acid; activator; binding; biosynthesis; brain; carbohydrate; cell; ceramide; complex; degradation; disease; example; figure; form; function; gangliosides; glycosphingolipid; glycosyltransferases; gm1; gm2; gm3; golgi; gsls; hexosaminidase; human; lipid; lysosomal; membrane; mice; protein; series; sialic; storage; structure; synthase; system; type; variant cache: cord-309384-vlk8cebh.txt plain text: cord-309384-vlk8cebh.txt item: #383 of 541 id: cord-310680-klywz85w author: Li, Qihan title: The interaction of the SARS coronavirus non-structural protein 10 with the cellular oxido-reductase system causes an extensive cytopathic effect date: 2005-04-06 words: 4412 flesch: 47 summary: The observation of nsp10-GFP fusion protein expressed in KMB-17 cells shows that nsp10 protein is accumulated as a distributed cluster in the cytoplasm (Fig. 2c) . Approximately 4 ug expressed and purified GST-nsp10 fusion protein and GST protein were respectively mixed with the 500 ul labeled extract of KMB-17 cells (5 × 10 6 cells), which were lysed in lysis buffer at 4 • C overnight. keywords: cells; cov; effect; kmb-17; kmb-17 cells; nsp10; protein; sars; virus cache: cord-310680-klywz85w.txt plain text: cord-310680-klywz85w.txt item: #384 of 541 id: cord-310847-63gh2tg4 author: Uversky, Vladimir N title: The alphabet of intrinsic disorder: II. Various roles of glutamic acid in ordered and intrinsically disordered proteins date: 2013-04-01 words: 19457 flesch: 42 summary: In fact, glutamic acid residue has a nonpolar surface of 69 Å 2 , and the estimated hydrophobic effect associated with the burial of this residue is 1.74 kcal/mol. + selectivity of Na,K-ATPase relies on the strategic positioning of glutamic acid residues. keywords: acid; acid residues; acidic; amino; amino acid; analysis; binding; cell; chain; channels; charge; disorder; domain; fact; function; glutamate; glutamic; glutamic acid; helix; human; idps; interactions; membrane; motif; pga; protein; region; repeat; residues; role; sequence; site; structure; terminal cache: cord-310847-63gh2tg4.txt plain text: cord-310847-63gh2tg4.txt item: #385 of 541 id: cord-310909-nc82a70n author: Qiu, Maofeng title: Antibody responses to individual proteins of SARS coronavirus and their neutralization activities date: 2005-04-13 words: 4524 flesch: 40 summary: Among the rabbit antisera to recombinant proteins S3, N, 3a and 9b, only anti-S3 serum showed significant neutralizing activity to the SARS-CoV infection in Vero E6 cells. In order to investigate the kinetics of the IgG antibodies to recombinant proteins S3, 3a, N and 9b in humans after onset of SARS, a group of serial sera collected from 13 people from weeks 2 to 30 were analyzed. keywords: antibodies; cov; proteins; recombinant; sars; sera cache: cord-310909-nc82a70n.txt plain text: cord-310909-nc82a70n.txt item: #386 of 541 id: cord-310947-aqau2n7q author: Pan, Ji'An title: Genome-Wide Analysis of Protein-Protein Interactions and Involvement of Viral Proteins in SARS-CoV Replication date: 2008-10-01 words: 6850 flesch: 39 summary: In our screen, 1.4 protein interactions per viral protein on the average was detected, and this result is in the upper range of the detection rates of viral protein interactions obtained by yeast two-hybrid systems Nsp11 is a small polypeptide containing only 13 amino acids and no interaction was detected with it in various assays but nsp11 in the fusion with nsp10 (nsp10/ 11) could significantly enhance the binding capability of nsp10 with either nsp14 or nsp16, indicating that the small nsp11 may also play important roles in viral protein interactions and replication. keywords: activity; coronavirus; cov; genome; hybrid; interactions; nsp10; protein; replication; rna; sars; syndrome; system; transcription cache: cord-310947-aqau2n7q.txt plain text: cord-310947-aqau2n7q.txt item: #387 of 541 id: cord-312332-rwmuucsp author: Dicker, Kate title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity date: 2020-09-10 words: 9241 flesch: 41 summary: The human RNA-Binding proteome and its dynamics during translational arrest Purification of cross-linked RNA-protein complexes by phenol-toluol extraction Comprehensive identification of RNA-Binding domains in human cells High-resolution mapping of RNA-Binding regions in the nuclear proteome of embryonic stem cells The new (dis)order in RNA regulation Two RNA polymerase complexes from vesicular stomatitis virus-infected cells that carry out transcription and replication of genome RNA Identification of cellular interaction partners of the influenza virus ribonucleoprotein complex and polymerase complex using proteomic-based approaches Comprehensive proteomic analysis of influenza virus polymerase complex reveals a novel association with mitochondrial proteins and RNA polymerase accessory factors Discovery of widespread host protein interactions with the prereplicated genome of CHIKV using VIR-CLASP Fields Virology Diverse roles of host RNA binding proteins in RNA virus replication https://doi.org/10.1016/j.semcdb.2020.08.002. Thiouracil cross-linking mass spectrometry: a cell-based method to identify host factors involved in viral amplification Identification of proteins bound to dengue viral RNA in vivo reveals new host proteins important for virus replication Identification of RNA binding proteins associated with dengue virus RNA in infected cells reveals temporally distinct host factor requirements Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry Unconventional RNA-binding proteins step into the virus-host battlefront Identification and characterization of sindbis virus RNA-Host protein interactions System-wide profiling of RNA-Binding proteins uncovers key regulators of virus infection An RNA-centric dissection of host complexes controlling flavivirus infection Viruses seen by our cells: the role of viral RNA sensors Intracellular sensing of viral genomes and viral evasion To translate, or not to translate: viral and host mRNA regulation by interferon-stimulated genes The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts Insights into RNA biology from an atlas of mammalian mRNAbinding proteins A brave new world of RNAbinding proteins Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS) keywords: assembly; binding; cell; hiv-1; host; human; infection; particles; proteins; rbps; replication; rna; role; transcription; virion; virus; viruses; vrna cache: cord-312332-rwmuucsp.txt plain text: cord-312332-rwmuucsp.txt item: #388 of 541 id: cord-312489-ywep0c08 author: Andoh, Kiyohiko title: Decreased neutralizing antigenicity in IBV S1 protein expressed from mammalian cells date: 2015-10-02 words: 5052 flesch: 35 summary: These results indicated that while recombinant S1 protein retained antigenicity (the ability to induce antibodies against S1 protein), the resulting antibodies was decreased its neutralizing activity, in contrast to those induced by inactivated virus. Results showed that the recombinant S1 protein was highly glycosylated, and the neutralizing antigenicity of recombinant S1 protein was lower than that of inactivated virus. keywords: antibodies; bronchitis; cells; chickens; et al; ibv; infectious; protein; virus cache: cord-312489-ywep0c08.txt plain text: cord-312489-ywep0c08.txt item: #389 of 541 id: cord-312741-0au4nctt author: Lin, Panpan title: Coronavirus in human diseases: Mechanisms and advances in clinical treatment date: 2020-10-01 words: 14692 flesch: 30 summary: The 9-kDa hydrophobic protein encoded at the 3' end of the porcine transmissible gastroenteritis coronavirus genome is membrane-associated Mouse hepatitis virus gene 5b protein is a new virion envelope protein Infectious bronchitis virus E protein is targeted to the Golgi complex and directs release of virus-like particles A comprehensive comparison of transmembrane domains reveals organelle-specific properties Subcellular location and topology of severe acute respiratory syndrome coronavirus envelope protein Induction of apoptosis in murine coronavirus-infected cultured cells and demonstration of E protein as an apoptosis inducer Assembly of the coronavirus envelope: homotypic interactions between the M proteins SARS coronavirus E protein forms cation-selective ion channels Differential maturation and subcellular localization of severe acute respiratory syndrome coronavirus surface proteins S, M and E Bcl-xL inhibits T-cell apoptosis induced by expression of SARS coronavirus E protein in the absence of growth factors The transmembrane domain of the infectious bronchitis virus E protein is required for efficient virus release Biochemical evidence for the presence of mixed membrane topologies of the severe acute respiratory syndrome coronavirus envelope protein expressed in mammalian cells Role of the coronavirus E viroporin protein transmembrane domain in virus assembly Severe acute respiratory syndrome coronavirus envelope protein regulates cell stress response and apoptosis Heterologous gene expression from transmissible gastroenteritis virus replicon particles Generation of a replication-competent, propagation-deficient virus vector based on the transmissible gastroenteritis coronavirus genome The small envelope protein E is not essential for murine coronavirus replication A severe acute respiratory syndrome coronavirus that lacks the E gene is attenuated in vitro and in vivo Absence of E protein arrests transmissible gastroenteritis coronavirus maturation in the secretory pathway Characterization of severe acute respiratory syndrome coronavirus membrane protein Sequence and topology of a model intracellular membrane protein, E1 glycoprotein, from a coronavirus Genetic evidence for a structural interaction between the carboxy termini of the membrane and nucleocapsid proteins of mouse hepatitis virus The molecular biology of coronaviruses A structural analysis of M protein in coronavirus assembly and morphology Envelope glycoprotein interactions in coronavirus assembly Efficient assembly and release of SARS coronavirus-like particles by a heterologous expression system Coronaviruses: an overview of their replication and pathogenesis Nucleocapsidindependent assembly of coronavirus-like particles by co-expression of viral envelope protein genes Coronavirus pseudoparticles formed with recombinant M and E proteins induce alpha interferon synthesis by leukocytes The cytoplasmic tails of infectious bronchitis virus E and M proteins mediate their interaction The missing link in coronavirus assembly. syndrome coronavirus nucleocapsid protein modulates its multimerization, translation inhibitory activity and cellular localization Identification of in vivointeracting domains of the murine coronavirus nucleocapsid protein Glycogen synthase kinase-3 regulates the phosphorylation of severe acute respiratory syndrome coronavirus nucleocapsid protein and viral replication Oligomerization of the carboxyl terminal domain of the human coronavirus 229E nucleocapsid protein Solution structure of the c-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method High affinity interaction between nucleocapsid protein and leader/intergenic sequence of mouse hepatitis virus RNA The nucleocapsid protein of SARS coronavirus has a high binding affinity to the human cellular heterogeneous nuclear ribonucleoprotein A1 Theoretical aspects of virus capsid assembly Analysis of multimerization of the SARS coronavirus nucleocapsid protein Mass spectroscopic characterization of the coronavirus infectious bronchitis virus nucleoprotein and elucidation of the role of phosphorylation in RNA binding by using surface plasmon resonance Mapping of the coronavirus membrane protein domains involved in interaction with the spike protein Envelope protein palmitoylations are crucial for murine coronavirus assembly The hydrophobic domain of infectious bronchitis virus E protein alters the host secretory pathway and is important for release of infectious virus The coronavirus E protein: assembly and beyond Mouse hepatitis virus replicase proteins associate with two distinct populations of intracellular membranes The intracellular sites of early replication and budding of SARS-coronavirus Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer Glycan shield and epitope masking of a coronavirus spike protein observed by cryoelectron microscopy Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains A human homolog of angiotensin-converting enzyme. keywords: binding; cells; coronavirus; cov; covid-19; covs; domain; east; entry; fusion; host; human; infection; inhibitors; membrane; mers; middle; novel; patients; protein; receptor; replication; rna; sars; sars coronavirus; spike; syndrome; syndrome coronavirus; treatment cache: cord-312741-0au4nctt.txt plain text: cord-312741-0au4nctt.txt item: #390 of 541 id: cord-312996-qzu8pkyt author: Iles, R. K. title: A clinical MALDI-ToF Mass spectrometry assay for SARS-CoV-2: Rational design and multi-disciplinary team work. date: 2020-08-22 words: 6852 flesch: 41 summary: Viral envelope protein peak intensities were clearly elevated in the spiked samples ( Figure 5 ). Viral envelope proteins (VEPs) became more prevalent in live virus culture and Ig light chains and IgA heavy chain were additional peaks found in gargle/saliva samples. keywords: covid-19; envelope; gargle; levels; maldi; mass; pcr; preprint; proteins; saliva; samples; sars; spectrometry; tof; virus cache: cord-312996-qzu8pkyt.txt plain text: cord-312996-qzu8pkyt.txt item: #391 of 541 id: cord-313694-p2sgaypq author: West, Christopher M. title: Current ideas on the significance of protein glycosylation date: 1986 words: 10925 flesch: 29 summary: The role of protein glycosylation in the compartmentalization and processing of mouse mammary tumor virus glycoproteins in mouse mammary tumor virus-infected rat hepatoma cells The formation of vesicular stomatitis virus (San Juan strain) becomes temperature-sensitive when glucose residues are retained on the oligosaccharides of the glycoprotein Deletions into a NI-I2-terrninal hydrophobic domain result in secretion of Rotavirus VP7, a resident endoplasmic reticulum membrane glycoprotein Glycoantigen expression is regulated both temporally and spatially during development in the cellular slime molds Dictyostelium discoideum and D. mucoroides The identification of N-linked oligosaccharides on the human CR2/Epstein-Barr virus receptor and their function in receptor metabolism, plasma membrane expression, and ligand binding Glycosylation and secretion of surfactant-associated glycoprotein A Complete glycosylation of the insulin and insulin-like growth factor 1 receptors is not necessary for their biosynthesis and function Chemistry, metabolism, and biological functions of sialic acids Effect of size and location of the oligosaccharide chain on protease degradation of bovine pancreatic ribonuclease Swainsonine inhibits glycoprotein degradation by isolated rat liver lysosomes Slime mold lectins Bacterial glycoconjugates are natural ligands for the carbohydrate binding site of discoidin I and influence its cellular compartmentalization Carbohydrate-specific receptors of the liver Hepatic clearance of serum glycoproteins The repair of the surface structure of animal cells Carbohydrate-mediated clearance of immune complexes from the circulation Carbohydrate-mediated clearance of antibody-antigen complexes from the circulation Surface carbohydrates and surface lectins are recognition determinants in phagocytosis The carbohydrate structure of porcine uteroferrin and the role of the high mannose chains in promoting uptake by the reticuloendothelial cells of the fetal liver Intracellular movement of cell surface receptors after endocytosis: resialylation of asialotransferrin receptor in human erythroleukemia cells Hyaluronic acid bonded to cell culture surfaces stimulated chondrogenesis in stage 24 limb mesenchyme cell cultures Lectin activation in Giardia lamblia by host protease: A novel hostparasite interaction Carbohydrates as recognition determinants in phagocytosis and in lectin-mediated killing of target cells Specificity of binding of a strain of uropathogenic Escherichia coli to Galcd-4Gal-containing glycosphingolipids Evidence for a malarial parasite interaction site on the major transmembrane protein of the human erythrocyte Adherent bacterial colonization in the pathogenesis of osteomyelitis Mucoproteins in relation to virus action The synthesis of complex carbohydrates by multiglycosyltransferase systems and their potential function in intercellular adhesion The receptor function of galactosyltransferase during cellular interactions The Biology of Glycoproteins A multivalent lacto-N-fucopentaose III-lysyllysine conjugate decompacts preimplantation mouse embryos, while the free oligosaccharide is ineffective Receptor function of mouse sperm surface galactosyltransferase during fertilization O-linked oligosaccharides of mouse egg ZP3 account for its sperm receptor activity Differential cell adhesion may result from nonspecific interactions between cell surface glycoproteins Specific alteration of N-CAM-mediated cell adhesion by an endoneuraminidase A heparin-bindifig domain from N-CAM is involved in neural cell-substratum adhesion Recognition of IgG by Fc receptor and complement: effects of glycosidase digestion Cell surface carbohydrates in cell recognition and response Feizi T: Cell interactions in preimplantation embryos: evidence for involvement of saccharides of the poly-Nacetyllactosamine series Mitochondrial synthesis of glycoproteins and surface properties of mitochondrial membranes Cell membranes in sponges The phosphomannosyl recognition system for intracellular and intercellular transport of lysosomal enzymes Cell-cell recognition in yeast, characterization of the sexual agglutination factors from Saccharomyces kluyveri Lymphocyte attachement to high endothelial venules during recirculation: a possible role for carbohydrates as recognition determinants Lymphocyte adhesion to immobolized polysaccharides suggests multiple carbohydrate receptors for recirculation Spontaneous glycosylation of glycosaminoglycan substrates by adherent fibroblasts Immunocytochemical demonstration of ecto-galactosyltransferase in absorptive intestinal cells Soluble lectins: a new class of extraeellular proteins Effect of choroquine on the degradation of L-fucose and the polypeptide moiety of plasma membrane glycoproteins Different half-lives of the carbohydrate and protein moieties of a 110000 dalton glycoprotein isolated from plasma membraned of rat liver Structural determinants of the capacity of heparin to inhibit the proliferation of vascular smooth muscle cells. This observation has led to the suggestion that cell surface carbohydrate might also establish a convection and diffusionqimited region around the cell in an area thick enough to be named, in certain cell types, the glycocalyx or fuzz. keywords: adhesion; binding; carbohydrate; cell; cell surface; function; glycoproteins; glycosylation; golgi; interactions; lysosomal; mannose; membrane; non; oligosaccharides; protein; receptor; recognition; role; structures; studies; surface cache: cord-313694-p2sgaypq.txt plain text: cord-313694-p2sgaypq.txt item: #392 of 541 id: cord-313932-f0a1qh7p author: Chen, Peng title: Establishment and validation of a drug-target microarray for SARS-CoV-2 date: 2020-07-21 words: 2492 flesch: 43 summary: The basic principle of protein microarray is to fix proteins on solid-phase carriers such as silicon and glass substrates. Compared with affinity purification and separation based on mass spectrometry, protein microarray has been widely used in the field of drug target screening. keywords: drug; human; microarray; protein; research; targets; virus cache: cord-313932-f0a1qh7p.txt plain text: cord-313932-f0a1qh7p.txt item: #393 of 541 id: cord-313988-3xjnpkqp author: Ferraz, Rosa María title: Insertional protein engineering for analytical molecular sensing date: 2006-04-03 words: 3519 flesch: 17 summary: Protein engineering allows the modification of the receptor in a way in which the interaction with the analyte promotes profound conformational modifications. Electrochemical biosensors: recommended definitions and classification Survey of the year 2004 commercial optical biosensor literature Biosensor profiling of molecular interactions in pharmacology New methodologies for measuring protein interactions in vivo and in vitro Using the yeast interaction trap and other two-hybrid-based approaches to study protein-protein interactions Analysis of protein interactions using fluorescence technologies K+ channel interactions detected by a genetic system optimized for systematic studies of membrane protein interactions Insertional gene fusion technology Engineering allosteric protein switches by domain insertion Engineering a regulatable enzyme for homogeneous immunoassays Creation of an allosteric enzyme by domain insertion Engineering of solvent-exposed loops in Escherichia coli beta-galactosidase Mapping of unit boundaries of a protein: exhaustive search for permissive sites for duplication by complementation analysis of random fragment libraries of tryptophan synthase alpha subunit Permissive sites and topology of an outer membrane protein with a reporter epitope Expression of heterologous peptides at two permissive sites of the MalE protein: antigenicity and immunogenicity of foreign B-cell and T-cell epitopes A simple screen for permissive sites in proteins: analysis of Escherichia coli lac permease Antigenicity and immunogenicity of the HIV-1 gp41 epitope ELDKWA inserted into permissive sites of the MalE protein Modular protein engineering for non-viral gene therapy Characterization of an internal permissive site in the cholera toxin B-subunit and insertion of epitopes from human immunodeficiency virus-1, hepatitis B virus and enterotoxigenic Escherichia coli Proteolysis as a regulatory mechanism Complete and limited proteolysis in cell cycle progression Hilt W: Targets of programmed destruction: a primer to regulatory proteolysis in yeast Improved mimicry of a footand-mouth disease virus antigenic site by a viral peptide displayed on beta-galactosidase surface Green fluorescent protein rendered susceptible to proteolysis: positions for protease-sensitive insertions beta-Galactosidase containing a human immunodeficiency virus protease cleavage site is cleaved and inactivated by human immunodeficiency virus protease Engineering the E. coli beta-galactosidase for the screening of antiviral protease inhibitors Autoinhibitory domains: modular effectors of cellular regulation Rational design of p53, an intrinsically unstructured protein, for the fabrication of novel molecular sensors A protease assay for two-photon crosscorrelation and FRET analysis based solely on fluorescent proteins Design of FRET-based GFP probes for detection of protease inhibitors A high-throughput method for development of FRET-based indicators for proteolysis Rational design of green fluorescent protein mutants as biosensor for bacterial endotoxin keywords: activity; allosteric; binding; biosensors; engineering; enzyme; protease; protein; signal cache: cord-313988-3xjnpkqp.txt plain text: cord-313988-3xjnpkqp.txt item: #394 of 541 id: cord-314039-qkrmxvaj author: Houdebine, Louis-Marie title: Production of pharmaceutical proteins by transgenic animals date: 2008-02-19 words: 4774 flesch: 44 summary: Expression in milk is achieved successfully with promoters from milk protein genes. This includes monoclonal antibodies, vaccines, blood factors, hormones, growth factors, cytokines, enzymes, milk proteins, collagen, fibrinogen and others. keywords: animals; cells; gene; human; milk; plants; production; proteins; transgenic cache: cord-314039-qkrmxvaj.txt plain text: cord-314039-qkrmxvaj.txt item: #395 of 541 id: cord-314321-klb8oe9q author: Chen, Serena H. title: Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets date: 2020-04-18 words: 3176 flesch: 46 summary: Here, to obtain deeper insights into S protein structure for biological understanding and therapeutic targeting, we employ a combined molecular dynamics (MD) simulation and artificial intelligence (AI) methodology on a series of coronavirus S proteins. To better understand S protein structure keywords: coronavirus; cov-2; domain; fig; protein; protomer; sars; structures cache: cord-314321-klb8oe9q.txt plain text: cord-314321-klb8oe9q.txt item: #396 of 541 id: cord-314567-purplsjn author: Fernández-Ponce, Cecilia title: Ultrastructural Localization and Molecular Associations of HCV Capsid Protein in Jurkat T Cells date: 2018-01-04 words: 7982 flesch: 24 summary: Among them, HCV core protein has been widely associated with pathogenicity, virulence, immune evasion and immune regulation (Dominguez-Villar et al., 2007 , 2012a Waggoner et al., 2007; However, the underlying molecular processes, as well as the behavior of HCV core protein or its interactions with host cell components, remain unclear. keywords: c virus; cd4; cells; core; core protein; cycle; et al; figure; gfp; hcv; hcv core; hepatitis; jurkat; localization; nucleolar; nucleolus; protein; rna; t cells; virus; virus core cache: cord-314567-purplsjn.txt plain text: cord-314567-purplsjn.txt item: #397 of 541 id: cord-314642-oobbdgzh author: Campbell, Allan title: The future of bacteriophage biology date: 2003 words: 5949 flesch: 48 summary: The dodecameric portal protein rotates in the protein shell of the phage, in steps of 12 °, which reel in phage DNA and are powered by ATP hydrolysis (FIG. 2) . The insertion of phage DNA into the chromosome during lysogenization is a good example. keywords: bacteria; bacteriophage; cell; dna; genes; host; lambdoid; phage; protein; recombination; repressor; site; viruses cache: cord-314642-oobbdgzh.txt plain text: cord-314642-oobbdgzh.txt item: #398 of 541 id: cord-314746-1o0rf0ii author: Bergasa-Caceres, Fernando title: Interdiction of Protein Folding for Therapeutic Drug Development in SARS CoV-2 date: 2020-08-10 words: 5040 flesch: 47 summary: The proposed strategy is based on a drug binding to the contact location, thereby aiming to prevent protein folding. This therapeutic drug development strategy based on folding interdiction of target regions (FITRs) is similar to an earlier proposal to develop drugs to interfere in protein folding. keywords: acids; amino; contact; cov-2; domain; folding; loop; protein; sars; scm; structure cache: cord-314746-1o0rf0ii.txt plain text: cord-314746-1o0rf0ii.txt item: #399 of 541 id: cord-314751-i9rxesrg author: Oh, Jongsuk title: Immunogenicity and protective efficacy of recombinant S1 domain of the porcine epidemic diarrhea virus spike protein date: 2014-07-10 words: 6085 flesch: 40 summary: However, immunizations involving at least one dose of PEDV S1 protein vaccine (groups 2 and 3) were more efficacious than immunization of sows with two doses of PEDV live and killed vaccines (group 1) in reducing the overall degree of diarrhea, in terms of the duration and severity, in the suckling piglets. In contrast, sows immunized with two doses of PEDV live and S1 protein vaccines (group 2) or three doses of S1 protein vaccine (group 3) at 2-week intervals produced relatively lower neutralizing antibody titers of 1:16 to 1:32 compared to those in group 1. keywords: antibody; cells; diarrhea; epidemic; pedv; porcine; protein; rs1; sows; vaccine; virus cache: cord-314751-i9rxesrg.txt plain text: cord-314751-i9rxesrg.txt item: #400 of 541 id: cord-315531-2gc2dc46 author: McGarvey, Peter B. title: Systems Integration of Biodefense Omics Data for Analysis of Pathogen-Host Interactions and Identification of Potential Targets date: 2009-09-25 words: 7018 flesch: 33 summary: Callable Personal Librarian (CPL) (version 65) UniRef: comprehensive and non-redundant UniProt reference clusters A data integration methodology for systems biology: experimental verification From bytes to bedside: data integration and computational biology for translational cancer research Integration of metabolomic and proteomic phenotypes: analysis of data covariance dissects starch and RFO metabolism from low and high temperature compensation response in Arabidopsis thaliana Comparative proteomics of human monkeypox and vaccinia intracellular mature and extracellular enveloped virions The utility of accurate mass and LC elution time information in the analysis of complex proteomes Cytoscape: a software environment for integrated models of biomolecular interaction networks Exploring biological networks with Cytoscape software Comparative assessment of large-scale data sets of protein-protein interactions A direct comparison of protein interaction confidence assignment schemes A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae Protein interactions: two methods for assessment of the reliability of high throughput observations Assessment of the reliability of protein-protein interactions and protein function prediction Gaining confidence in high-throughput protein interaction networks Vaccinia virus induces cell fusion at acid pH and this activity is mediated by the N-terminus of the 14-kDa virus envelope protein A 14K envelope protein of vaccinia virus with an important role in virus-host cell interactions is altered during virus persistence and determines the plaque size phenotype of the virus The oligomeric structure of vaccinia viral envelope protein A27L is essential for binding to heparin and heparan sulfates on cell surfaces: a structural and functional approach using site-specific mutagenesis Vaccinia virus envelope H3L protein binds to cell surface heparan sulfate and is important for intracellular mature virion morphogenesis and virus infection in vitro and in vivo Vaccinia virus envelope D8L protein binds to cell surface chondroitin sulfate and mediates the adsorption of intracellular mature virions to cells Vaccinia virus F9 virion membrane protein is required for entry but not virus assembly, in contrast to the related L1 protein The vaccinia virus gene I2L encodes a membrane protein with an essential role in virion entry Blockade of chemokine activity by a soluble chemokine binding protein from vaccinia virus Monkeypox virus viral chemokine inhibitor (MPV vCCI), a potent inhibitor of rhesus macrophage inflammatory protein-1 Identification of a peptide derived from vaccinia virus A52R protein that inhibits cytokine secretion in response to TLR-dependent signaling and reduces in vivo bacterial-induced inflammation A46R and A52R from vaccinia virus are antagonists of host IL-1 and toll-like receptor signaling The poxvirus protein A52R targets Toll-like receptor signaling complexes to suppress host defense Molecular characterization and expression of the stratification-related cytokeratins 4 and 15 Mouse keratin 4 is necessary for internal epithelial integrity Clumping factor B, a fibrinogen-binding MSCRAMM (microbial surface components recognizing adhesive matrix molecules) adhesin of Staphylococcus aureus, also binds to the tail region of type I cytokeratin 10 The surface protein Srr-1 of Streptococcus agalactiae binds human keratin 4 and promotes adherence to epithelial HEp-2 cells Vaccinia virus entry, exit, and interaction with differentiated human airway epithelia Protective effect of Toll-like receptor 4 in pulmonary vaccinia infection Computational identification of strain-, species-and genus-specific proteins A search method for homologs of small proteins. The MPD is built on the data and capabilities of iProClass [6] a warehouse of protein information, which in turn is built around UniProtKB keywords: analysis; anthracis; bacillus; data; gene; host; information; integration; interactions; mpd; pathogen; protein; proteomics; research; results; search; virus cache: cord-315531-2gc2dc46.txt plain text: cord-315531-2gc2dc46.txt item: #401 of 541 id: cord-315570-khm1veuv author: González-Mora, Alejandro title: Bacteriophage-Based Vaccines: A Potent Approach for Antigen Delivery date: 2020-09-04 words: 9972 flesch: 36 summary: Until now, phage display vaccines have been used for preventing or treating several diseases including cancer, viral, parasitic and fungal infection as well as their use in immunocontraception and drug abuse, among others [2, [15] [16] Until now, phage display vaccines have been used for preventing or treating several diseases including cancer, viral, parasitic and fungal infection as well as their use in immunocontraception and drug abuse, among others [2, [15] [16] keywords: antigen; bacteriophage; cells; development; display; dna; expression; identification; particles; peptides; phage; phage display; protein; response; systems; use; vaccines cache: cord-315570-khm1veuv.txt plain text: cord-315570-khm1veuv.txt item: #402 of 541 id: cord-315984-5gbhobw8 author: Isaacson, Marisa K. title: Ubiquitination, Ubiquitin-like Modifiers, and Deubiquitination in Viral Infection date: 2009-06-18 words: 8923 flesch: 34 summary: Viral proteins themselves can be directly modified by ubiquitin or ubiquitin-like proteins, and some viruses even encode their own ubiquitinating or deubiquitinating enzymes. It is therefore a challenge to distinguish between adventitious modification of viral proteins by host ubiquitination machinery without immediate consequences for virus lifestyle and those events that are required for virus replication and viral gene transcription. keywords: activity; cell; degradation; domain; et al; infection; isg15; ligase; pathway; protein; replication; role; ubiquitin; ubiquitination; virus; viruses cache: cord-315984-5gbhobw8.txt plain text: cord-315984-5gbhobw8.txt item: #403 of 541 id: cord-316258-7hucqcaj author: Henriques, Elsa S title: Modeling of the Toll-like receptor 3 and a putative Toll-like receptor 3 antagonist encoded by the African swine fever virus date: 2011-01-28 words: 4112 flesch: 40 summary: 14 Other possible similarities/homologies were investigated using PHYRE, the Protein Fold Recognizer Server, 15 which predicts protein structures by detecting remote homology to known structures. In conjunction with the experimental evidence, the present modeling exercise allowed us to gain further insight into the strategies used by the ASF-virus to evade the host immune response and the role of the nonassigned I329L gene encoded viral protein in this process. keywords: domain; modeling; pi329l; protein; receptor; signaling; structure; tir; tlr3; viral cache: cord-316258-7hucqcaj.txt plain text: cord-316258-7hucqcaj.txt item: #404 of 541 id: cord-316273-vo6j8zb0 author: Cosset, François-Loic title: Cell Entry of Enveloped Viruses date: 2011-02-08 words: 23445 flesch: 28 summary: Vectors derived from HIV pseudotyped with Sendai virus fusion protein F (Kowolik and Yee, 2002) or E1E2 from hepatitis C virus (Bartosch et al., 2003) , and such vectors are able to transduce human hepatoma cells and primary human hepatocytes efficiently, although they are unable to enter nonliver cells. Both p62 and prM are cleaved by the cellular protease furin late in the secretory pathway, in a maturation reaction that is a crucial regulatory step for subsequent virus fusion (Salminen et al., 1992; Stadler et al., 1997; Wengler, 1989; Zhang et al., 2003a) . keywords: activation; binding; c virus; cell; cell fusion; changes; class; cleavage; domain; ebola; endocytosis; entry; envelope; envelope glycoprotein; envgp; et al; fusion; fusion peptide; fusion proteins; glycoprotein; hepatitis; hiv; hiv-1; host; human; infection; inhibitors; membrane fusion; pathway; process; receptor; structure; surface; transmembrane; type; virus; virus entry; virus fusion; virus glycoprotein; viruses cache: cord-316273-vo6j8zb0.txt plain text: cord-316273-vo6j8zb0.txt item: #405 of 541 id: cord-316745-n10ia3j3 author: Liu, HongDe title: A new approach to the prediction of transmembrane structures date: 2008-05-23 words: 1831 flesch: 54 summary: (3) The prediction accuracy of membrane protein sequences Once all the transmembrane regions of a membrane protein sequence are predicted properly, the whole membrane protein sequence is considered to be predicted correctly. The prediction accuracy of membrane ARTICLES CHEMICAL BIOLOGY protein sequences is: Q t = (N TT /N TOR ) ×100%, where N TT is the number of correctly predicted membrane protein sequences and N TOR is the number of membrane protein sequences in the test sets. keywords: membrane; mscwt; prediction; protein; tmhs cache: cord-316745-n10ia3j3.txt plain text: cord-316745-n10ia3j3.txt item: #406 of 541 id: cord-316983-h4mtpcyc author: Mathé-Hubert, Hugo title: Comparative venomics of Psyttalia lounsburyi and P. concolor, two olive fruit fly parasitoids: a hypothetical role for a GH1 β-glucosidase date: 2016-10-25 words: 8298 flesch: 44 summary: In the absence of VLPs and PDVs, secreted venom proteins are likely the main maternal actors of parasitism success of Psyttalia species. Identified venom proteins. keywords: concolor; ervi; family; fig; function; host; lounsburyi; parasitoid; proteins; psyttalia; role; species; tables; unisequences; venom; wasp cache: cord-316983-h4mtpcyc.txt plain text: cord-316983-h4mtpcyc.txt item: #407 of 541 id: cord-317675-s1ac5vcx author: de Marco, Ario title: Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli date: 2009-05-14 words: 11539 flesch: 25 summary: Protein disulfide bond formation in prokaryotes Pathways of disulfide bond formation in Escherichia coli Thioredoxins and glutaredoxins as facilitators of protein folding Increased yield and activity of soluble singlechain antibody fragments by combining high-level expression and the Skp peripasmic chaperonin Translational level is a critical factor for the secretion of the heterologous proteins in Escherichia coli Secretion of active kringle-2-serine protease in Escherichia coli Fed-batch production of recombinant beta-galactosidase using the universal stress promoters uspA and uspB in high cell density cultivations Secretory production of human leptin in Escherichia coli Evaluation of inducible promoters on the secretion of a ZZ-proinsulin fusion protein in Escherichia coli Medium and copy number effects on the secretion of human proinsulin in Escherichia coli using the universal stress promoters uspA and uspB Broad-host-range plasmid pJB658 can be used for industrial-level production of a secreted hosttoxic single-chain antibody fragment in Escherichia coli A novel Ecotin-Ubiquitin-Tag (ECUT) for efficient, soluble peptide production in the periplasm of Escherichia coli Sec-dependent preprotein translocation in bacteria SRP-mediated protein targeting: structure and function revisited Using secretion to solve a solubility problem: High-yield expression in Escherichia coli and purification of the bacterial glycoamidase PNGase F Expression of full-length immunoglobulins in Escherichia coli: rapid and efficient production of aglycosylated antibodies TolAIII co-overexpression facilitates the recovery of periplasmic recombinant proteins into the growth medium of Escherichia coli Identification of factors impeding the production of a singlechain antibody fragment in Escherichia coli by comparing in vivo and in vitro expression A novel fusion protein system for the production of native human pepsinogen in the bacterial periplasm The presence of N-terminal secretion signal sequences leads to strong stimulation of the total expression levels of three tested medically important proteins during high-density cultivations of Escherichia coli SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli The DsbA signal sequence directs efficient, cotranslational export of passenger proteins to the Escherichia coli periplasm via the signal recognition particle pathway Improvement of post-translational bottlenecks in the production of penicillin amidase in recombinant Escherichia coli strains Use of thioredoxin as a reporter to identify a subset of Escherichia coli signal sequences that promote signal recognition particle-dependent translocation Signal sequences directing cotranslational translocation expand the range of proteins amenable to phage display Efficient selection of DARPins with sub-nanomolar affinities using SRP phage display Investigation of the DsbA mechanism through the synthesis and analysis of an irreversible enzyme-ligand complex Expression of eukaryotic proteins in soluble form in Escherichia coli Identification of a protein required for disulfide bond formation in vivo A pathway for disulfide bond formation in vivo Identification and characterization of the Escherichia coli gene dsbB, whose product is involved in the formation of disulfide bonds in vivo Two cysteines in each periplasmic domain of the membrane protein DsbB are required for its function in protein disulfide bond formation Characterization of DsbC, a periplasmic protein of Erwinia chrysantemi and Escherichia coli with disulfide isomerase activity Chaperone activity of DsbC A new Escherichia coli gene, dsbG, encodes a periplasmic protein involved in disulphide bond formation, required for recycling DsbA/DsbB and DsbC redox proteins In vivo and in vitro function of the Escherichia coli periplasmic cysteine oxidoreductase DsbG Identification and characterization of a new disulfide isomerase-like protein (DsbD) in Escherichia coli Six conserved cysteines of the membrane protein DsbD are required for the transfer of electrons from the cytoplasm to the periplasm of Escherichia coli Transmembrane electron transfer by the membrane protein DsbD occurs via a disulfide bond cascade Beckwith : Reduction of the periplasmic disulfide bond isomerase, DsbC, occurs by passage of electrons from cytoplasmic thioredoxin nDsbD: a redox interaction hub in the Escherichia coli periplasm DsbG, a protein disulfide isomerase with chaperone activity The disulphide isomerase DsbC cooperates with the oxidase DsbA in a DsbD-independent manner Engineered DsbC chimeras catalyze both protein oxidation and disulfide-bond isomerization in Escherichia coli: reconciling two competing pathways De novo design and evolution of artificial disulfide isomerase enzymes analogous to the bacterial DsbC Combination of Dsb co-expression and an addition of sorbitol markedly enhanced soluble expression of single-chain Fv in Escherichia coli Improvement of productivity of active horseradish peroxidase in Escherichia coli by coexpression of Dsb proteins A system for concomitant overexpression of four periplasmic folding catalists to improve secretory protein production in Escherichia coli Production of recombinant bovine enterokinase catalytic subunit in Escherichia coli using the novel secretory fusion partner DsbA Increased production of human proinsulin in the periplasmic space of Escherichia coli by fusion to DsbA DsbA and DsbCcatalyzed oxidative folding of proteins with complex disulfide bridge patterns in vitro and in vivo Overproduction of bacterial protein disulfide isomerase (DsbC) and its modulator (DsbD) markedly inhances periplasmic production of human nerve growth factor in Escherichia coli Overexpression of protein disulfide isomerase DsbC stabilizes multiple-disulfidebonded recombinant protein produced and transported to the periplasm in Escherichia coli Production of brainderived neurotrophic in Escherichia coli by co-expression of Dsb proteins Expression of active human tissuetype plasminogen activator in Escherichia coli Optimisation of production of domoic acid-binding scFv antibody fragment in Escherichia coli using molecular chaperones and functional immobilization on a mesoporous silicate support In vitro and in vivo redox states of the Escherichia coli periplasmic oxidoreductases DsbA and DsbC secretion Escherichia coli alkaline phosphatase fails to acquire disulfide bonds when retained in the cytoplasm Mutations that allow disulfide bond formation in the cytoplasm of Escherichia coli The role of the thioredoxin and glutaredoxin pathways in reducing protein disulfide bonds in the Escherichia coli cytoplasm Disufide bond formation in the Escherichia coli cytoplasm: an in vivo role reversal for the thioredoxins The thioredoxin superfamily: redundancy, specificity, and gray-area genomics The reductive enzyme thioredoxin 1 acts as an oxidant when it is exported to the Escherichia coli periplasm Complementation of DsbA deficiency with secreted thioredoxin variants reveals the crucial role of an efficient dithiol oxidant for catalyzed protein folding in the bacterial periplasm Disulfide bond formation by exported glutaredoxin indicates glutathione's presence in the E. coli periplasm Monitoring disulfide bond formation in the eukaryotic cytosol Mutant AhpC peroxiredoxins suppress thiol-disulfide redox deficiencies and acquire deglutathionylating activity Functional plasticity of a peroxidase allows evolution of diverse disulfide-reducing pathways Functional antibody single-chain fragments from the cytoplasm of Escherichia coli: influence of thioredoxin reductase (TrxB) Efficient folding of proteins with multiple disulfide bonds in the Escherichia coli cytoplasm High-level production of human collagen prolyl 4-hydroxylase in Escherichia coli Expression and characterization of recombinant C-terminal biotynilated extracellular domain of human receptor for the advanced glycation end products (hsRAGE) in Escherichia coli Expression and purification of neurolin immunoglobulin domain 2 from Carrassius auratus (goldfish) in Escherichia coli Effect of folding factors in rescuing unstable heterologous lipase B to enhance its overexpres Expression of active human C1 inhibitor serpin domain in Escherichia coli Leishmania donovani: expression and characterization of Escherichia coliexpressed recombinant chitinase LdCHT1 Characterization of soluble, disulfide-bond stabilized, prokaryotically expressed human thyrotropin receptor ectodomain Jararhagin ECD-containing disintegrin domain: expression in Escherichia coli and inhibition of the platelet-collagen interaction Fusion expression of human pro-urokinase with E. coli thioredoxin Evolution rescues folding of human immunodeficiency virus-1 envelope glycoprotein GP120 lacking a conserved disulfide bond Antibody scFv fragments without disulfide bonds made by molecular evolution In vitro folding and thermodynamic stability of an antibody fragment selected in vivo for high expression levels in Escherichia coli cytoplasm A semi-synthetic repertoire of intrinsically stable antibody fragments derived from a singleframework scaffold Identification of a universal VHH framework to graft non-canonical antigen-binding loops of camel single domain antibodies A focused antibody library for selecting scFvs expressed at high levels in the cytoplasm Immunomodulation of enzyme function in plants by singledomain antibody fragments Targeting and tracing antigens in live cells with fluorescent nanobodies Intracellular immunization with cytosolic recombinant antibodies Intrabodies: turning the humoral immune system outside in for intracellular immunization Engineered turns of a recombinant antibody improve its in vivo folding Expression studies of catalytic antibodies Engineering antibodies for stability and efficient folding Biotechnological applications for surfaceengineered bacteria Protection of guinea-pigs against foot-and-mouth disease virus by immunization with PhoE-FMDV hybrid protein Surface expression of maliaria antigens in Salmonella typhimurium: induction of serum antibody response upon oral vaccination of mice Oral vaccination with attenuated Salmonella typhimurium strain expressing Borrelia burgdorferi OspA prevents murine lyme borreliosis Outer membrane PhoE protein of Escherichia coli as a carrier for foreign antigenic determinants: immunogenicity of epitopes of foot-and-mouth disease virus A fusogenic peptide expressed on the surface of Salmonella enterica elicits CTL responses to a dengue virus epitope Enhanced immunity to Plasmodium falciparum circumsporozoite protein (PfCSP) by using Salmonella enterica serovar Thypi expressing PfCSP and a PfCSP-encoding DNA vaccine in a heterologous primeboost strategy Development of an optimized expression system for the screening of antibody libraries displayed on the Escherichia coli surface Structural tolerance of bacterial autotransporters for folded passenger protein domains Display and release of the Plasmodium falciparum circumsporozoite protein using the autotransporter MisL of Salmonella enterica Versatility of a vector for expressing foreigner polypeptides at the surface of Gram-negative bacteria Transport and anchoring of β-lactamase to the external surface of Escherichia coli Peptide display on bacterial flagella: principles and applications The normally periplasmic enzyme β-lactamase is specifically and efficiently translocated through the Escherichia coli outer membrane when it is fused to the cell-surface enzyme pullulanase Pseudomonas aeruginosa outer membrane protein OprF as an expression vector for foreign epitopes: the effects of positioning and length on the antigenicity of the epitope A new membrane-bound OprI lipoprotein expression vector. keywords: antibodies; antibody; bacteria; bond; chaperone; coli; cytoplasm; disulfide; disulfide bond; dsba; dsbc; escherichia; escherichia coli; expression; folding; formation; fusion; isomerase; periplasm; production; proteins; refolding; thioredoxin cache: cord-317675-s1ac5vcx.txt plain text: cord-317675-s1ac5vcx.txt item: #408 of 541 id: cord-318551-c1qr27lg author: Boguszewska‐Chachulska, Anna M. title: Rna Viruses Redirect Host Factors to Better Amplify Their Genome date: 2005-12-29 words: 10689 flesch: 33 summary: The incoming genome of many (þ) strand RNA viruses ( Fig. 1 ) serves as mRNA for virus protein synthesis including the RdRp, and is then replicated yielding the complementary (À) RNA strand. key: cord-318551-c1qr27lg authors: Boguszewska‐Chachulska, Anna M.; Haenni, Anne‐Lise title: Rna Viruses Redirect Host Factors to Better Amplify Their Genome date: 2005-12-29 journal: Adv Virus Res DOI: 10.1016/s0065-3527(05)65002-6 sha: doc_id: 318551 cord_uid: c1qr27lg This chapter provides an updated view of the host factors that are, at present, believed to participate in replication/transcription of RNA viruses. keywords: binding; cell; et al; factors; genome; host; polymerase; protein; replication; rna; rna synthesis; strand; synthesis; transcription; translation; viral; virus; viruses cache: cord-318551-c1qr27lg.txt plain text: cord-318551-c1qr27lg.txt item: #409 of 541 id: cord-318749-k91oku7h author: Dong, Hui-Jun title: Selective regulation in ribosome biogenesis and protein production for efficient viral translation date: 2020-10-29 words: 7270 flesch: 22 summary: IRES) Host targeted antiviral (HTA): functional inhibitor compounds of scaffold protein RACK1 inhibit herpes simplex virus proliferation Arabidopsis receptor of activated C kinase1 phosphorylation by WITH NO LYSINE8 KINASE Viral ribonucleoprotein complex formation and nucleolar-cytoplasmic relocalization of nucleolin in poliovirus-infected cells RNA-binding properties of influenza A virus matrix protein M1 Ribosomal protein RPL26 is the principal target of UFMylation Cloning of mouse genomic ribosomal protein L6 gene and analysis of its promoter The association of ribosomal protein L18 (RPL18) with infectious bursal disease virus viral protein VP3 enhances viral replication UFMylation of RPL26 links translocation-associated quality control to endoplasmic reticulum protein homeostasis Interferon production and inhibition of host synthesis in cells infected with vesicular stomatitis virus Impact of RNA polymerase I inhibitor CX-5461 on viral kinase-dependent and -independent cytomegalovirus replication New mRNAs are preferentially translated during vesicular stomatitis virus infection The structure and function of the eukaryotic ribosome Hepatitis C virus 3'X region interacts with human ribosomal proteins Specialized ribosomes: a new frontier in gene regulation and organismal biology RNA regulons in Hox 5' Ribosomal protein L4 (RPL4) ) and ribosomal protein L18 were identified as interacting partners of VP3 protein and as being involved in the regulation of IBDV replication. keywords: antiviral; biogenesis; cells; et al; host; infection; ires; mrna; protein; replication; ribosomal; ribosome; rna; rps; synthesis; translation; virus; viruses cache: cord-318749-k91oku7h.txt plain text: cord-318749-k91oku7h.txt item: #410 of 541 id: cord-318853-mxyxwkhx author: Sallie, Richard title: Replicative homeostasis II: Influence of polymerase fidelity on RNA virus quasispecies biology: Implications for immune recognition, viral autoimmunity and other "virus receptor" diseases date: 2005-08-22 words: 10548 flesch: 17 summary: Of necessity, some receptor affinity studies have used cloned viral protein ligands, an artificial situation that cannot approach the phenotypic complexity of RNA viral protein quasispecies. Viral receptor disease is a unifying hypothesis that may also explain some diseases with well-established, but multi-factorial and apparently unrelated aetiologies – like coronary artery and other vascular diseases – in addition to diseases like schizophrenia that are poorly understood and lack plausible, coherent, pathogenic explanations. keywords: cell; disease; envelope; fidelity; hcv; hepatitis; infection; leptin; patients; pol; proteins; quasispecies; receptor; replication; responses; rna; rna pol; sequence; type; variant; virus; viruses cache: cord-318853-mxyxwkhx.txt plain text: cord-318853-mxyxwkhx.txt item: #411 of 541 id: cord-319291-6l688krc author: Hung, Chun-Min title: Alignment using genetic programming with causal trees for identification of protein functions date: 2006-09-01 words: 8947 flesch: 47 summary: Nonlinear Anal Theory Methods Appl DOI: 10.1016/j.na.2005.09.048 sha: doc_id: 319291 cord_uid: 6l688krc A hybrid evolutionary model is used to propose a hierarchical homology of protein sequences to identify protein functions systematically. Because some novel proteins might align without meaningful conserved domains, maximizing the score of sequence alignment is not the best criterion for predicting protein functions. keywords: causal; feature; function; genetic; model; moment; node; programming; protein; sequence; tree cache: cord-319291-6l688krc.txt plain text: cord-319291-6l688krc.txt item: #412 of 541 id: cord-319517-denczc6t author: Salipalli, Sandeep title: Recent advances in live cell imaging of hepatoma cells date: 2014-07-08 words: 9219 flesch: 41 summary: An enhanced monomeric blue fluorescent protein with the high chemical stability of the chromophore Evolutionary optimization of fluorescent proteins for intracellular FRET Fluorescent proteins from nonbioluminescent Anthozoa species A monomeric red fluorescent protein Dynamic motion of paxillin on actin filaments in living endothelial cells A guide to choosing fluorescent proteins Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein Bright monomeric red fluorescent protein with an extended fluorescence lifetime Green fluorescent protein as a marker for gene expression Aequorea green fluorescent protein: expression of the gene and fluorescence characteristics of the recombinant protein Two-photon fluorescence absorption and emission spectra of dyes relevant for cell imaging In vitro activity of fluorescent dyes against asexual blood stages of Plasmodium falciparum Antibodies for fluorescent molecular rotors ReAsH/FlAsH labeling and image analysis of tetracysteine sensor proteins in cells Specific covalent labeling of recombinant protein molecules inside live cells Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin New biarsenical ligands and tetracysteine motifs for protein labeling in vitro and in vivo: synthesis and biological applications Fluorogen-activating single-chain antibodies for imaging cell surface proteins Moreover, ELuc was tested in cell lines such as NIH/3T3 using various promoters, and it was shown that the luciferase primarily localizes in nucleus, cytosol and in peroxisomes. keywords: cell; droplets; efficiency; emission; expression; fluorescent; fluorescent protein; gene; gfp; green; imaging; lines; lipid; methods; protein; red; study; transfection; transfer; vectors cache: cord-319517-denczc6t.txt plain text: cord-319517-denczc6t.txt item: #413 of 541 id: cord-319563-9lwr6k8p author: Aitekenov, Sultan title: Review: Detection and quantification of proteins in human urine date: 2020-10-14 words: 10113 flesch: 31 summary: meta-analysis Proteinuria in adults: a diagnostic approach Proteinuria: potential causes and approach to evaluation Classification of renal proteinuria: a simple algorithm Pathophysiology of proteinuria Proteinuria in children infected with the human immunodeficiency virus Proteinuria in Children: Evaluation and Differential Diagnosis Understanding the Mechanisms of Proteinuria: Therapeutic Implications Chronic Kidney Disease Blood and urine biomarkers in chronic kidney disease: An update Prevalence of chronic kidney disease and decreased kidney function in the adult US population: Third national health and nutrition examination survey Prevalence of chronic kidney disease in population-based studies: Systematic review Prevalence of kidney damage in Chinese elderly: a large-scale population-based study Chapter 3: Morbidity and Mortality in Patients With CKD Global, regional, and national age-sex specific all-cause and cause-specific mortality for 240 causes of death, 1990-2013: a systematic analysis for the Global Burden of Disease Study Urine proteomics in clinical applications: technologies, principal considerations and clinical implementation Discovery and validation of new protein biomarkers for urothelial cancer: a prospective analysis Virus Bioresistor (VBR) for Detection of Bladder Cancer Marker DJ-1 in Urine at 10 pM in One Minute Update on urine as a biomarker in cancer: a necessary review of an old story Urinary Proteomic Biomarkers in Coronary Artery Disease Urinary Proteomics in Diabetes and CKD The Potential of Albuminuria as a Biomarker of Diabetic Complications An immunoassay cassette with a handheld reader for HIV urine testing in point-of-care diagnostics Analysis of viruses present in urine from patients with interstitial cystitis Development of Universal and Lineage-Specific Primer Sets for Rapid Detection of the Zika Virus (ZIKV) in Blood and Urine Samples Using One-Step Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Quantitative detection of hepatitis C virus RNA in urine of patients with chronic hepatitis C using a novel real-time PCR assay Detection and Phylogenetic Analysis of Human Papilloma Virus in Urine from a Sample of Iraqi Women with Vaginal Discharge Find the right sample: A study on the versatility of saliva and urine samples for the diagnosis of emerging viruses Urinalysis: A Review of Methods and Procedures Fundamentals of Urine and Body Fluid Analysis Long-term urine biobanking: Storage stability of clinical chemical parameters under moderate freezing conditions without use of preservatives Free light chains nephelometric assay: human urine stability in different storage conditions Effect of common storage temperatures and container types on urine protein : creatinine ratios in urine samples of proteinuric dogs Comparison of various methods for the determination of total protein in urine Protein Measurement with the Folin Phenol Reagent A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding Measurement of protein using bicinchoninic acid Urinary protein as measured with a pyrogallol red-molybdate complex, manually and in a Hitachi 726 automated analyzer Assessment of proteinuria Semiquantitative, fully automated urine test strip analysis The emergence of low-cost compact mass spectrometry detectors for chromatographic analysis Human Urine Proteomics: Analytical Techniques and Clinical Applications in Renal Diseases Urine in Clinical Proteomics Automation of nanoflow liquid chromatography-tandem mass spectrometry for proteome analysis by using a strong cation exchange trap column An enzyme immunoassay for determining albumin in human urine samples using an ultra-microanalytical system Electrophoresis: The march of pennies, the march of dimes Recent developments in capillary and microchip electroseparations of peptides High-Sensitivity Electrophoretic Method for the Detection of Bence Jones Protein and for the Study of Proteinuria in Unconcentrated Urines A novel approach for a non competitive capillary electrophoresis immunoassay with laser-induced fluorescence detection for the determination of human serum albumin Urine protein quantification in stacking gel by SDS-PAGE Gel-Eluted Liquid Fraction Entrapment Electrophoresis: An Electrophoretic Method for Broad Molecular Weight Range Proteome Separation Preconcentration techniques in capillary electrophoresis Electrophoretic determination of albumin in urine using on-line concentration techniques Determination of peptides and proteins in human urine with capillary electrophoresis-mass spectrometry, a suitable tool for the establishment of new diagnostic markers Mapping and Identification of the Urine Proteome of Prostate Cancer Patients by 2D PAGE/MS Cellulose Acetate Membrane Electrophoresis Based Urinary Proteomics for the Identification of Characteristic Proteins: CAME-Based Urinary Proteomics Fast gas chromatography-mass spectrometry: A review of the last decade High-performance liquid chromatography combined with electron ionization mass spectrometry: A review of current trends and advances in modern bio-analytical methods: Chromatography and sample preparation Highly sensitive reversed-phase high-performance liquid chromatography assay for the detection of Tamm-Horsfall protein in human urine Detection of urine protein by a paper-based analytical device enhanced with ion concentration polarization effect, Microfluid Nanofluid Proteomics approach and techniques in identification of reliable biomarkers for diseases Interpretation of Mass Spectra Electrospray Ionisation Mass Spectrometry: keywords: albumin; analysis; biomarkers; chromatography; detection; determination; diseases; fluorescence; human; immunoassay; kidney; mass; methods; patients; protein; proteinuria; review; spectrometry; spectroscopy; technique; urinary; urine cache: cord-319563-9lwr6k8p.txt plain text: cord-319563-9lwr6k8p.txt item: #414 of 541 id: cord-319609-y0gdjn64 author: Van Duyne, Rachel title: The identification of unique serum proteins of HIV-1 latently infected long-term non-progressor patients date: 2010-07-06 words: 8561 flesch: 42 summary: The utilization of proteomic techniques to globally identify differentially expressed serum proteins in response to HIV-1 infection is a significant undertaking that is complicated due to the innate protein profile of human serum. These findings also indicate a difference in composition of serum proteins present in HIV-1 infected individuals undergoing HAART treatment versus those that are naturally non-progressing. keywords: abundance; cell; figure; gst; haart; infected; infection; ink4a; low; ltnp; p16; patient; presence; proteins; samples; serum; treatment cache: cord-319609-y0gdjn64.txt plain text: cord-319609-y0gdjn64.txt item: #415 of 541 id: cord-319614-4qi59pbz author: Benej, Martin title: Quantitative Proteomics Reveal Peroxiredoxin Perturbation Upon Persistent Lymphocytic Choriomeningitis Virus Infection in Human Cells date: 2019-10-25 words: 8920 flesch: 38 summary: A highly suitable tool to study virus-host cell interactions is proteomics, since viral infection fundamentally affects host cell proteins. Using a luciferase reporter containing HRE, we detected a modest, but significant increase in HIF-1 transactivation in infected HeLa cells in comparison to control cells ( Figure 7A) . keywords: akt; analysis; cells; choriomeningitis; et al; figure; gel; hela; host; infection; lcmv; levels; min; persistent; protein; ros; signaling; virus cache: cord-319614-4qi59pbz.txt plain text: cord-319614-4qi59pbz.txt item: #416 of 541 id: cord-319658-u0wjgw50 author: Guven-Maiorov, Emine title: Structural host-microbiota interaction networks date: 2017-10-12 words: 4672 flesch: 36 summary: Most proteins of bacterial and eukaryotic pathogens are not accessible to bind to host proteins; but some of their proteins either bind to host surface receptors [11] or enter the host cell and interact with host cytoplasmic proteins. Systems biology approaches that integrate the HMIs with host endogenous protein interaction networks reveal the systematic trends in virulence strategies of pathogens. keywords: hmis; host; human; immune; interactions; interface; microbiota; networks; pathways; protein; species cache: cord-319658-u0wjgw50.txt plain text: cord-319658-u0wjgw50.txt item: #417 of 541 id: cord-319722-udqu5jub author: Ng, Eddy W. Y. title: Advances in MALDI Mass Spectrometry in Clinical Diagnostic Applications date: 2013-04-07 words: 12534 flesch: 39 summary: Since then, MALDI MS technologies have been evolving, and successfully used in genome, proteome, metabolome, and clinical diagnostic research. Real applications of MALDI MS technologies in clinical diagnostics should be forthcoming. keywords: analysis; biomarkers; cancer; desorption; detection; discovery; ionization; laser; maldi; mass; matrix; peptides; profiling; proteins; quantification; seldi; serum; spectrometry; time; tof; tof mass; tof ms cache: cord-319722-udqu5jub.txt plain text: cord-319722-udqu5jub.txt item: #418 of 541 id: cord-319754-5isw53wl author: Balgoma, David title: Lipidomics Issues on Human Positive ssRNA Virus Infection: An Update date: 2020-08-31 words: 12122 flesch: 37 summary: This energetic burden has been demonstrated to be afforded by the cooperation of three fusion peptides in influenza virus membrane fusion [23] , whereas two adjacent trimers of the fusion protein are required in West Nile virus [24] . This process implies viral envelope and host cell membrane fusion, for which an energetically cost-effective barrier must be overcome. keywords: cell; cell membrane; cholesterol; entry; host; host cell; infection; lipid; membrane; membrane fusion; metabolism; pathway; protein; replication; role; sars; study; virus; virus entry; virus infection; virus replication; viruses cache: cord-319754-5isw53wl.txt plain text: cord-319754-5isw53wl.txt item: #419 of 541 id: cord-319780-rfj9t99r author: Alexander, S.P.H. title: A rational roadmap for SARS‐CoV‐2/COVID‐19 pharmacotherapeutic research and development. IUPHAR Review 29 date: 2020-05-01 words: 15233 flesch: 30 summary: A truncated version of human recombinant ACE2, lacking the transmembrane domain, mitigated against SARS-CoV infection of cells (Li et al., 2003) and has been used in animal models to reduce symptoms of severe acute lung failure , diabetic nephropathy (Oudit et al., 2010) and cardiac hypertrophy and fibrosis . It has been used to treat influenza A infection through targeting the M2 ion channel (Pinto et al., 1992; Wang et al., 1993; Holsinger et al., 1994) , although it is no longer recommended in the UK or US because of drug resistance (for review, see Li et al., 2015) . keywords: ace2; activity; acute; angiotensin; binding; cells; converting; coronavirus; cov-2; covid-19; domain; drug; entry; enzyme; et al; host; human; infection; inhibitors; interferon; membrane; mers; protease; protein; receptor; replication; review; rna; sars; sars coronavirus; spike; structure; syndrome; target; tmprss2 cache: cord-319780-rfj9t99r.txt plain text: cord-319780-rfj9t99r.txt item: #420 of 541 id: cord-319809-33i6lzjd author: Drew, Elliot D. title: Identification of a druggable binding pocket in the spike protein reveals a key site for existing drugs potentially capable of combating Covid-19 infectivity date: 2020-07-01 words: 4579 flesch: 50 summary: Thus, the following combined score, ComboPC, was created to rank the compounds applying equal weight to the estimated docking scores from each docking method and to the agreement between the superpositions from each of the methods, as measured by avRMSD: Where LedockPC is the percentile rank of the docking score of the pose as docked by Ledock, vinaPC is the Coronavirus envelope protein: current knowledge Molecular epidemiology, evolution and phylogeny of SARS coronavirus A comparative analysis of factors influencing two outbreaks of middle eastern respiratory syndrome (MERS) in Saudi Arabia and South Korea Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan Protein structure and sequence re-analysis of 2019-nCoV genome does not indicate snakes as its intermediate host or the unique similarity between its spike protein insertions and HIV-1 I-TASSER server: new development for protein structure and function predictions Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission SWISS-MODEL: homology modelling of protein structures and complexes Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation 2StrucCompare: a webserver for visualizing small but noteworthy differences between protein tertiary structures through interrogation of the secondary structure content Combining global and local measures for structure-based druggability predictions AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise Enriching screening libraries with bioactive fragment space LigPlot+: multiple ligand-protein interaction diagrams for drug discovery Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2 MTiOpenScreen: a web server for structure-based virtual screening ChEMBL: a largescale bioactivity database for drug discovery DrugBank 5. 0: a major update to the DrugBank database for 2018 DrugCentral: online drug compendium SuperDRUG2: a one stop resource for approved/ marketed drugs Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power ChemMine tools: an online service for analyzing and clustering small molecules ClassyFire: automated chemical classification with a comprehensive, computable taxonomy We thank Prof. B.A. Wallace for her discussions throughout the preparation of this manuscript. In related spike proteins like that from human SARS-CoV (PDB code: 6ACK), when this domain is in the up position it interacts with ACE2 facilitating entry to the cell [16] . keywords: chain; docking; pocket; poses; position; protein; residues; spike; structure cache: cord-319809-33i6lzjd.txt plain text: cord-319809-33i6lzjd.txt item: #421 of 541 id: cord-319884-d8n0aokl author: Natesan, Mohan title: Protein Microarrays and Biomarkers of Infectious Disease date: 2010-12-16 words: 7097 flesch: 31 summary: Drug Des Protein-protein interactions and selection: Array-based techniques for screening disease-associated biomarkers in predictive/early diagnosis Defining the humoral immune response to infectious agents using high-density protein microarrays Design of high-density antibody microarrays for disease proteomics: Key technological issues Extensive antibody cross-reactivity among infectious gram-negative bacteria revealed by proteome microarray analysis Analysis of the human immune response to vacccina by use of novel protein microarray suggests that antibodies recognize less than 10% of the total viral proteome Applications of protein microarrays for biomarker discovery Protein microarrays: High-throughput tools for proteomics Advances and perspectives in aptamer arrays Affibody molecules in protein capture microarrays: Evaluation of multidomain ligands and different detection formats Use of a single-chain antibody library for ovarian cancer biomarker discovery Reversephase protein microarrays: Application to biomarker discovery and translational medicine Development of reverse phase protein microarrays for clinical applications and patient-tailored therapy Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front Analysis of signaling pathways in 90 cancer cell lines by protein lysate array Reverse-phase protein lysate microarrays for cell signaling analysis Multiplex approaches in protein microarray technology Printing proteins as microarrays for high-throughput function determination Self-assembling protein microarrays Global analysis of protein activities using proteome chips Proteome-wide analysis of the serological response to vaccinia and smallpox Antibody profiling by proteome microarray reveals the immunogenicity of the attenuated smallpox vaccine modified vaccinia virus ankara is comparable to that of Dryvax A Burkholderia pseudomallei protein microarray reveals serodiagnostic and cross-reactive antigens Protein microarray for profiling antibody responses to Yersinia pestis live vaccine Serologic survey of the sentinel animals for plague surveillance and screening for complementary diagnostic markers to F1 antigen by protein microarray Antibody profiling in plague patients by protein microarray From protein microarrays to diagnostic antigen discovery: A study of the pathogen Francisella tularensis Immunodominant Francisella tularensis antigens identified using proteome microarray Candidate antigens for Q fever serodiagnosis revealed by immunoscreening of a Coxiella burnetii protein microarray Large scale immune profiling of infected humans and goats reveals differential recognition of Brucella melitensis antigens A genome-wide proteome array reveals a limited set of immunogens in natural infections of humans and white-footed mice with Borrelia burgdorferi Genome-wide study of Pseudomonas aeruginosa outer membrane protein immunogenicity using self-assembling protein microarrays Bacterial protein microarrays for identification of new potential diagnostic markers for Neisseria meningitidis infections Analysis of phagosomal proteomes: From latex-bead to bacterial phagosomes Anthrax infection inhibits the AKT signaling involved in the E-cadherin-mediated adhesion of lung epithelial cells Capturing host-pathogen interactions by protein microarrays: Identification of novel streptococcal proteins binding to human fibronectin, fibrinogen, and C4BP Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method) Distinct formats of protein microarrays have been developed for different applications, including abundance-based and function-based methods. keywords: analysis; antibodies; antibody; antigens; binding; detection; human; infection; interactions; methods; microarrays; protein; proteome; responses; study; use; vaccinia; virus cache: cord-319884-d8n0aokl.txt plain text: cord-319884-d8n0aokl.txt item: #422 of 541 id: cord-320015-lbr2q4qh author: Chinchar, V. Gregory title: The Molecular Biology of Frog Virus 3 and other Iridoviruses Infecting Cold-Blooded Vertebrates date: 2011-10-20 words: 9150 flesch: 36 summary: However, because the absence of a full-sized vIF-2α gene in FV3 does not adversely affect viral protein synthesis, other viral proteins may also play roles in maintaining viral protein synthesis in infected cells. As progressively larger amounts of viral proteins bind the membrane scaffold, crescent-shaped structures that resemble icosahedral vertices are formed. keywords: 18k; cells; dna; expression; frog; fv3; gene; host; infection; iridovirus; mutants; protein; ranavirus; replication; synthesis; vif-2α; virion; virus; viruses cache: cord-320015-lbr2q4qh.txt plain text: cord-320015-lbr2q4qh.txt item: #423 of 541 id: cord-320083-0k15w624 author: Leitão, Jorge H. title: Microbial Virulence Factors date: 2020-07-27 words: 2822 flesch: 32 summary: Central attention is given to the various mechanism used to manipulate gene expression, including histone modification, control of host DNA methylation patterns, sabotage of host long non-coding RNAs, interfering with the host RNA transcription and translation, as well as with host protein stability [13] . Bacterial small non-coding regulatory RNAs (sRNAs) have emerged over the last decade as key regulators of post-transcriptional regulators of gene expression, being involved in a wide range of cellular processes, including bacterial virulence [19] . keywords: authors; bacteria; factors; host; pathogens; protein; virulence cache: cord-320083-0k15w624.txt plain text: cord-320083-0k15w624.txt item: #424 of 541 id: cord-320092-0qnvydux author: Ehsani, Sepehr title: COVID-19 and iron dysregulation: distant sequence similarity between hepcidin and the novel coronavirus spike glycoprotein date: 2020-10-16 words: 7552 flesch: 37 summary: Hypoferremia predicts hospitalization and oxygen demand in COVID-19 patients HAMP promoter hypomethylation and increased hepcidin levels as biomarkers for Kawasaki disease Human coronaviruses OC43 and HKU1 bind to 9-O-acetylated sialic acids via a conserved receptor-binding site in spike protein domain a The solution structure of human hepcidin, a peptide hormone with antimicrobial activity that is involved in iron uptake and hereditary hemochromatosis COVID-19 and Kawasaki disease: novel virus and novel case Hepcidin revisited, disulfide connectivity, dynamics, and structure Mechanisms of virus membrane fusion proteins Chondrostean sturgeon hepcidin: an evolutionary link between teleost and tetrapod hepcidins Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus LEAP-1, a novel highly disulfide-bonded human peptide, exhibits antimicrobial activity A dynamic COVID-19 immune signature includes associations with poor prognosis Intracellular iron deficiency in pulmonary arterial smooth muscle cells induces pulmonary arterial hypertension in mice Bass hepcidin synthesis, solution structure, antimicrobial activities and synergism, and in vivo hepatic response to bacterial infections Post-translational processing of hepcidin in human hepatocytes is mediated by the prohormone convertase furin Hepatobiliary pathology Structure, function, and evolution of coronavirus spike proteins Rethinking living fossils Palmitoylation: policing protein stability and traffic Characterization and functional analysis of liver-expressed antimicrobial peptide-2 (LEAP-2) from golden pompano Trachinotus ovatus (Linnaeus 1758) Protein sequence: A unique but restricted sequence similarity exists between mature hepcidin and the cysteine-rich cytoplasmic tail of coronavirus spike proteins. keywords: coronavirus; coronavirus spike; covid-19; disease; domain; ferroportin; hepcidin; human; iron; levels; patients; protein; sars; sequence; similarity; spike; structure cache: cord-320092-0qnvydux.txt plain text: cord-320092-0qnvydux.txt item: #425 of 541 id: cord-320713-b37c8aye author: Roberts, Lisa O. title: Chapter 9 Viral Strategies to Subvert the Mammalian Translation Machinery date: 2009-10-27 words: 20235 flesch: 41 summary: A study to understand the components of the eIF4F complex that are required for translation of viral mRNAs has recently demonstrated that influenza virus translation has no requirement for eIF4E, as viral mRNAs are translated in cells depleted of eIF4E and in cells treated with rapamycin. 48 Members of several different families of RNA viruses are able to bypass the canonical, cap-dependent, translation initiation process by employing this strategy of internal initiation of protein synthesis. keywords: binding; cells; cellular; cleavage; complex; eif4e; expression; host; host translation; human; infected; infection; ires; kinase; mechanisms; mrnas; pabp; phosphorylation; pkr; protein; protein synthesis; ribosomal; ribosome; rna; sequence; site; translation; translation initiation; virus; viruses cache: cord-320713-b37c8aye.txt plain text: cord-320713-b37c8aye.txt item: #426 of 541 id: cord-320790-ley91488 author: Fogg, M. J. title: Application of the use of high‐throughput technologies to the determination of protein structures of bacterial and viral pathogens date: 2006-10-04 words: 7069 flesch: 42 summary: key: cord-320790-ley91488 authors: Fogg, M. J.; Bahar, M.; Alzari, P.; Bertini, I.; Betton, J.‐M.; Burmeister, W. P.; Cambillau, C.; Coll, M.; Canard, B.; Carrondo, M.; Daenke, S.; Dym, O.; Geerlof, A.; Egloff, M.‐P.; Haouz, A.; Enguita, F. J.; Jones, T. A.; Ma, Qingjun; Manicka, S. N.; Owens, R.J.; Migliardi, M.; Nordlund, P.; Peleg, Y.; Schneider, G.; Schnell, R.; Stuart, D. I.; Unge, T.; Tarbouriech, N.; Wilkinson, A. J.; Wilmanns, M.; Wilson, K. S.; Zimhony, O.; Grimes, J. M. title: Application of the use of high‐throughput technologies to the determination of protein structures of bacterial and viral pathogens date: 2006-10-04 journal: Acta Crystallogr D Biol Crystallogr DOI: 10.1107/s0907444906030915 sha: doc_id: 320790 cord_uid: ley91488 The Structural Proteomics In Europe (SPINE) programme is aimed at the development and implementation of high‐throughput technologies for the efficient structure determination of proteins of biomedical importance, such as those of bacterial and viral pathogens linked to human health. NMR target proteins were checked for correct folding using 1 H-15 N heteronuclear single-quantum correlation (HSQC) spectroscopy and metal-binding properties checked by atomic absorption, using extended X-ray absorption fine structure (EXAFS) spectroscopy, UV-Vis spectroscopy and (where appropriate) electron paramagnetic resonance (EPR) spectroscopy. keywords: coli; domain; et al; expression; human; mtb; number; oxford; proteins; spine; structure; targets cache: cord-320790-ley91488.txt plain text: cord-320790-ley91488.txt item: #427 of 541 id: cord-321013-8pkrg0mx author: McBride, Ruth title: The Coronavirus Nucleocapsid Is a Multifunctional Protein date: 2014-08-07 words: 10773 flesch: 40 summary: IBV N protein contains a functional nuclear export signal (NES) to traffic N protein to the cytoplasm [68, 71] , and an 8 amino acid NoRS motif at its NTD and is necessary and sufficient for nucleolar retention [68] . It has been proposed that the flexible, positively charged finger-like β-hairpin extension in the NTD of both IBV and SARS-CoV N protein is able to grasp RNA by neutralizing its phosphate groups, while the base moieties can make contact with exposed aromatic residues from the hydrophobic palm [16, 21] . keywords: assembly; binding; cell; coronavirus; cov; cov n; ctd; domain; interaction; localization; mhv; n protein; nucleocapsid; protein; residues; rna; sars; structure cache: cord-321013-8pkrg0mx.txt plain text: cord-321013-8pkrg0mx.txt item: #428 of 541 id: cord-321275-7haq0e38 author: Renzi, Fabiana title: Large-scale purification and crystallization of the endoribonuclease XendoU: troubleshooting with His-tagged proteins date: 2006-02-28 words: 1971 flesch: 50 summary: XendoU is conserved among higher eukaryotes and has no homology to any known cellular ribonuclease, although it shows significant homology to proteins tentatively annotated as serine proteases. In order to obtain large amounts of protein for crystallization screening, XendoU was overexpressed in bacteria keywords: crystals; protein; xendou cache: cord-321275-7haq0e38.txt plain text: cord-321275-7haq0e38.txt item: #429 of 541 id: cord-321386-u1imic5l author: Li, Chun title: Protein Sequence Comparison and DNA-binding Protein Identification with Generalized PseAAC and Graphical Representation date: 2018-02-17 words: 5524 flesch: 56 summary: The results illustrated the better performance of our method. Identification of DNA-binding proteins using support vector machines and evolutionary profiles DNA-prot: identification of DNA binding proteins from protein sequence information using random forest iDNA-prot: identification of DNA binding proteins using random forest with grey model enDNA-Prot: identification of DNA-binding proteins by applying ensemble learning gDNA-Prot: predict DNA-binding proteins by employing support vector machine and a novel numerical characterization of Protein sequence Numerical characterization of protein sequences based on the generalized Chou's pseudo amino acid composition Light-directed synthesis of peptide nucleic acids (PNAs) chips Protein structure prediction from sequence variation Principles that govern the folding of protein chains Prediction of protein cellular attributes using pseudoamino acid composition Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes Pseudo amino acid composition and its applications in bioinformatics, proteomics and system biology iNuc-STNC: a sequence-based predictor for identification of nucleosome positioning in genomes by extending the concept of SAAC and Chou's PseAAC PseKNC-General: a cross-platform package for generating various modes of pseudo nucleotide compositions Identify recombination spots with pseudo dinucleotide composition Sequence-based identification of recombination spots using pseudo nucleic acid representation and recursive feature extraction by linear kernel SVM Protein sequence comparison based on physicochemical properties and the position-feature energy matrix A Novel protein characterization based on pseudo amino acids composition and star-like graph topological indices Chaos game representation of protein sequences based on the detailed HP model and their multifractal and correlation analyses A computational approach to simplifying the protein folding problem Modeling study on the validity of a possibly simplified representation of proteins 2-D graphical representation of protein sequences and its application to coronavirus phylogeny Clustering of the protein design alphabets by using hierarchical self-organizing map A novel descriptor of protein sequences and its application BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences Amino acid difference formula to help explain protein Correlation analysis of some physical chemistry properties among genetic codons and amino acids Similarity analysis of protein sequences based on the normalized relative entropy On 3-D graphical representation of DNA primary sequences and their numerical characterization Analysis of similarity/dissimilarity of DNA sequences based on novel 2-D graphical representation Milestones in graphical bioinformatics Graphical representation of proteins Representation of proteins as walks in 20-D space Phylogenetic analysis of DNA sequences based on k-word and rough set theory On the characterization of DNA primary sequences by triplet of nucleic acid bases DV-Curve: A novel intuitive tool for visualizing and analyzing DNA sequences A Novel method for similarity analysis and protein sub-cellular localization prediction The Zagreb indices 30 years after On vertex-degree-based molecular structure descriptors Graphs with fixed number of pendent vertices and minimal Zeroth-order general Randic index New invariant of DNA sequences Genetic drift of human coronavirus OC43 spike gene during adaptive evolution WHO MERS-CoV global summary and risk assessment Assessing the accuracy of prediction algorithms for classification: an overview iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition Using deformation energy to analyze nucleosome positioning in genomes iRNA-PseU: identifying RNA pseudouridine sites Recognition of protein coding genes in the yeast genome at better than 95% accuracy based on the Z curve Using a Euclid distance discriminant method to find protein coding genes in the yeast genome The authors' greatest gratitude goes to the anonymous referees for their insightful suggestions and generous support. This study is undertaken to develop an efficient computational approach for timely encoding protein sequences and extracting the hidden information. keywords: acids; amino; dataset; dna; group; matrix; method; model; protein; sequence; vector cache: cord-321386-u1imic5l.txt plain text: cord-321386-u1imic5l.txt item: #430 of 541 id: cord-321441-t1v0pu0w author: Yang, Yiming title: Polycistronic Genome Segment Evolution and Gain and Loss of FAST Protein Function during Fusogenic Orthoreovirus Speciation date: 2020-06-29 words: 8668 flesch: 34 summary: The reovirus fusion-associated small transmembrane (FAST) proteins: Virus-encoded cellular fusogens Unusual topological arrangement of structural motifs in the baboon reovirus fusion-associated small transmembrane protein Myristoylation, a protruding loop, and structural plasticity are essential features of a nonenveloped virus fusion peptide motif Palmitoylation, membrane-proximal basic residues, and transmembrane glycine residues in the reovirus p10 protein are essential for syncytium formation Structural and functional properties of an unusual internal fusion peptide in a nonenveloped virus membrane fusion protein Cell-cell membrane fusion induced by p15 fusion-associated small transmembrane (FAST) protein requires a novel fusion peptide motif containing a myristoylated polyproline type II helix Reptilian reovirus utilizes a small type III protein with an external myristylated amino terminus to mediate cell-cell fusion Reovirus FAST protein transmembrane domains function in a modular, primary sequence-independent manner to mediate cell-cell membrane fusion Helix-destabilizing, beta-branched, and polar residues in the baboon reovirus p15 transmembrane domain influence the modularity of FAST proteins A novel tribasic Golgi export signal directs cargo protein interaction with activated Rab11 and AP-1-dependent Golgi-plasma membrane trafficking Golgi complex-plasma membrane trafficking directed by an autonomous, tribasic Golgi export signal Reovirus FAST Proteins Drive Pore Formation and Syncytiogenesis Using a Novel Helix-Loop-Helix Fusion-Inducing Lipid Packing Sensor Multifaceted sequence-dependent and -independent roles for reovirus FAST protein cytoplasmic tails in fusion pore formation and syncytiogenesis Efficient reovirus-and measles virus-mediated pore expansion during syncytium formation is dependent on annexin A1 and intracellular calcium Reovirus infection of young Muscovy ducks (Cairina moschata) Genomic characteristics of a novel reovirus from Muscovy duckling in China Isolation and genomic characterization of a classical Muscovy duck reovirus isolated in Zhejiang Muscovy duck reovirus sigmaC protein is atypically encoded by the smallest genome segment Features of a spatially constrained cystine loop in the p10 FAST protein ectodomain define a new class of viral fusion peptides A compact, multifunctional fusion module directs cholesterol-dependent homomultimerization and syncytiogenic efficiency of reovirus p10 FAST proteins PixFRET, an ImageJ plug-in for FRET calculation that can accommodate variations in spectral bleed-throughs The rapid generation of mutation data matrices from protein sequences Molecular Evolutionary Genetics Analysis across Computing Platforms Crystal structure of reovirus attachment protein sigma1 in complex with sialylated oligosaccharides Viral mutation rates Mechanisms and consequences of positive-strand RNA virus recombination A duck reovirus variant with a unique deletion in the sigma C gene exhibiting high pathogenicity in Pekin ducklings The 5'-terminal sequence of potato leafroll virus RNA: Evidence of recombination between virus and host RNA Why do RNA viruses recombine? Lineage diversification, homo-and heterologous reassortment and recombination shape the evolution of chicken orthoreoviruses A Bat-Derived Putative Cross-Family Recombinant Coronavirus with a Reovirus Gene Evolutionary aspects of recombination in RNA viruses Increased viral pathogenicity after insertion of a 28S ribosomal RNA sequence into the haemagglutinin gene of an influenza virus Ubiquitin in a togavirus The p10 FAST protein fusion peptide functions as a cystine noose to induce cholesterol-dependent liposome fusion without liposome tubulation Mechanistic insights into avian reovirus p17-modulated suppression of cell cycle CDK-cyclin complexes and enhancement of p53 and cyclin H interaction The second open reading frame of the avian reovirus S1 gene encodes a transcription-dependent and CRM1-independent nucleocytoplasmic shuttling protein Isolation of a Novel Fusogenic Orthoreovirus from Eucampsipoda africana Bat Flies in South Africa Rotavirus Species B Encodes a Functional Fusion-Associated Small Transmembrane (FAST) FAST proteins are a unique family of viral membrane fusion proteins that are structurally and evolutionarily unrelated to the fusion proteins that are responsible for enveloped virus entry into cells. keywords: arv; cell; events; fast; fiber; figure; fusion; fusogenic; genome; membrane; orf; orthoreovirus; p10; proteins; recombination; segments; sequence; species cache: cord-321441-t1v0pu0w.txt plain text: cord-321441-t1v0pu0w.txt item: #431 of 541 id: cord-321762-7kiahjyy author: Nandy, Ashesh title: Chapter 5 The GRANCH Techniques for Analysis of DNA, RNA and Protein Sequences date: 2015-12-31 words: 9799 flesch: 43 summary: Developments in the graphical representation and numerical characterization of DNA sequences raised the possibilities of using similar analysis of protein sequences, albeit with difficulty arising from the fact that now we have to contend with 20 amino acids making up a protein chain whereas DNA sequences were made up of only four nucleotides. Paper presented at the Indo-US Workshop on Mathematical Chemistry Indexing scheme and similarity measures for macromolecular sequences On 3-D representation of DNA primary sequences Novel analysis of DNA and Protein sequences through Graphical Representation and Numerical Characterization techniques Novel Techniques of Graphical Representation and Analysis of DNA Sequences -A Review Visualization and analysis of DNA sequences using DNA walks Mathematical descriptors of DNA sequences: development and applications New Approaches to Drug-DNA Interactions Based on Graphical Representation and Numerical Characterization of DNA Sequences Graphical representation and mathematical characterization of protein sequences and applications to viral proteins DNA Sequence Visualization Charcaterizations of DNA Primary Sequences Molecular Descriptors for Chemoinformatics, Methods and Principles in Medicinal Chemistry Genome analysis: A new approach for visualisation of sequence organisation in genomes Mathematicalc haracterisationo f chaos, game representation: New algorithms for nucleotide sequence analysis Chaos game representation of similarities and differences between genomic sequences H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences Random walk and gap plots of DNA sequences Graphical analysis of DNA sequence structure: III. keywords: analysis; bases; descriptors; dna; dna sequences; et al; gene; graphical; method; numerical; protein; protein sequences; representation; sequences cache: cord-321762-7kiahjyy.txt plain text: cord-321762-7kiahjyy.txt item: #432 of 541 id: cord-322231-jltk42dt author: Huy, Nguyen-Xuan title: Immunogenicity of an S1D epitope from porcine epidemic diarrhea virus and cholera toxin B subunit fusion protein transiently expressed in infiltrated Nicotiana benthamiana leaves date: 2016-08-23 words: 6962 flesch: 51 summary: Blood serum was collected at 3 days after the final booster and tested for antibody-binding activity with purified S1D antigen by Western blot analysis and subsequently used to detect expression of S1D protein in plants. The N-glycosylated structures of S1D protein produced in plants were determined using a deglycosylation enzyme. keywords: anti; buffer; ctb; expression; fig; fusion; gene; leaves; levels; mice; p19; protein; s1d cache: cord-322231-jltk42dt.txt plain text: cord-322231-jltk42dt.txt item: #433 of 541 id: cord-322926-xlwsj3v2 author: Shanmugaraj, Balamurugan title: Plant Molecular Farming: A Viable Platform for Recombinant Biopharmaceutical Production date: 2020-07-04 words: 4670 flesch: 15 summary: Considering the low costs and greater scalability of plant production systems, the commercialization of non-pharmaceutical proteins is straightforward and faster due to lower regulatory challenges. In this review, we consider the importance of a plant- based production system for recombinant protein production, and its potential to produce biopharmaceuticals is discussed. keywords: antibodies; expression; human; monoclonal; plant; production; protein; system; tobacco; transgenic; transient; vaccines; virus cache: cord-322926-xlwsj3v2.txt plain text: cord-322926-xlwsj3v2.txt item: #434 of 541 id: cord-322955-7dw32xby author: Kathwate, Gunderao H title: In Silico design and characterization of multi-epitopes vaccine for SARS-CoV2 from its spike proteins date: 2020-06-12 words: 5732 flesch: 41 summary: nature I-TASSER: a unified platform for automated protein structure and function prediction In silico analysis of epitope-based vaccine candidates against hepatitis B virus polymerase protein Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization GalaxyWEB server for protein structure prediction and refinement. In conclusion, predicted vaccine is a good antigen, probable no allergen and has potential to induce cellular and humoral immunity. keywords: cell; cov2; covid-19; development; epitopes; prediction; protein; response; sars; score; sequence; server; structure; tools; vaccine; web cache: cord-322955-7dw32xby.txt plain text: cord-322955-7dw32xby.txt item: #435 of 541 id: cord-323072-4rsgeag7 author: Han, Xueqing title: The expression of SARS–CoV M gene in P. Pastoris and the diagnostic utility of the expression product date: 2004-12-01 words: 3744 flesch: 46 summary: Here, we report the expression of recombinant M protein in P. Pastoris and its antigenicity. Methanol was added every 24 h to a final concentration of 0.5% to induce the expression of recombinant M protein, and the incubation was continued for further 3-4 days. keywords: coronavirus; cov; expression; gene; protein; recombinant; sars cache: cord-323072-4rsgeag7.txt plain text: cord-323072-4rsgeag7.txt item: #436 of 541 id: cord-323331-80d01l6f author: Li, Jie title: Golgi Structure and Function in Health, Stress, and Diseases date: 2019-01-01 words: 13524 flesch: 33 summary: Interestingly, αSNAP depletion induces apoptosis independent of the cleavage of Golgi proteins such as GRASP65, golgin-160, and p115 but rather by dysregulation of ER-Golgi vesicle cycling and possibly through ER stress (Naydenov et al. 2012) . The Golgi matrix protein giantin is required for normal cilia function in zebrafish Role of phosphatidylinositol 4-phosphate (PI4P) and its binding protein GOLPH3 in hepatitis C virus secretion Selective export of human GPI-anchored proteins from the endoplasmic reticulum Membrane targeting of p115 phosphorylation mutants and their effects on Golgi integrity and secretory traffic Characterization of PSKH1, a novel human protein serine kinase with centrosomal, golgi, and nuclear localization Mutants of the protein serine kinase PSKH1 disassemble the Golgi apparatus Involvement of Golgin-160 in cell surface transport of renal ROMK channel: co-expression of Golgin-160 increases ROMK currents Rab and Arl GTPase family members cooperate in the localization of the golgin GCC185 The GOLPH3 pathway regulates Golgi shape and function and is activated by DNA damage Fragmentation and dispersal of Golgi proteins and redistribution of glycoproteins and glycolipids processed through the Golgi apparatus after infection with herpes simplex virus 1 The AAA-ATPase Cdc48/p97 regulates spindle disassembly at the end of mitosis Making the Auroras glow: regulation of Aurora A and B kinase function by interacting proteins Aurrand-Lions M (2017) Genetic, structural, and chemical insights into the dual function of GRASP55 in germ cell Golgi remodeling and JAM-C polarized localization during spermatogenesis JNK2 controls fragmentation of the Golgi complex and the G2/M transition through phosphorylation of GRASP65 Thyroid hormone, T3-dependent phosphorylation and translocation of Trip230 from the Golgi complex to the nucleus Caspase cleavage of the Golgi stacking factor GRASP65 is required for Fas/CD95-mediated apoptosis ERK8 is a negative regulator of O-GalNAc glycosylation and cell migration P21-activated protein kinase is overexpressed in hepatocellular carcinoma and enhances cancer metastasis involving c-Jun NH2-terminal kinase activation and paxillin phosphorylation A caspase cleavage fragment of p115 induces fragmentation of the Golgi apparatus and apoptosis ZFPL1, a novel ring finger protein required for cis-Golgi integrity and efficient ER-to-Golgi transport Adhesion of Golgi cisternae by proteinaceous interactions: intercisternal bridges as putative adhesive structures The Golgi mitotic checkpoint is controlled by BARS-dependent fission of the Golgi ribbon into separate stacks in G2 Rab1A over-expression prevents Golgi apparatus fragmentation and partially corrects motor deficits in an alpha-synuclein based rat model of Parkinson's disease Identification and characterization of two novel (neuro)endocrine long coiled-coil proteins HACE1 (HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1) GRASP65 and GRASP55 sequentially promote the transport of C-terminal valine-bearing cargos to and through the Golgi complex DVC1 (C1orf124) recruits the p97 protein segregase to sites of DNA damage Rab18 and Rab43 have key roles in ER-Golgi trafficking The endosomal pathway and the Golgi complex are involved in the infectious bursal disease virus life cycle Pentameric assembly of potassium channel tetramerization domain-containing protein 5 New insights into membrane trafficking and protein sorting The trans-Golgi network golgin, GCC185, is required for endosome-to-Golgi transport and maintenance of Golgi structure The coiled-coil membrane protein golgin-84 is a novel rab effector required for Golgi ribbon formation Coordination of golgin tethering and SNARE assembly: GM130 binds syntaxin 5 in a p115-regulated manner GOLPH3 bridges phosphatidylinositol-4-phosphate and actomyosin to stretch and shape the Golgi to promote budding Phosphorylation of the vesicletethering protein p115 by a casein kinase II-like enzyme is required for Golgi reassembly from isolated mitotic fragments A general amphipathic alpha-helical motif for sensing membrane curvature Asymmetric tethering of flat and curved lipid membranes by a golgin Autophagy-based unconventional secretory pathway for extracellular delivery of IL-1beta The role of GRASP55 in Golgi fragmentation and entry of cells into mitosis Asymmetric CLASP-dependent nucleation of noncentrosomal microtubules at the trans-Golgi network How accelerated Golgi trafficking may drive Alzheimer's disease (comment on Human autoantibodies to a novel Golgi protein golgin-67: high similarity with golgin-95/gm 130 autoantigen DNA damage triggers Golgi dispersal via DNA-PK and GOLPH3 Signalling to and from the secretory pathway GRASP55 keywords: apoptosis; apparatus; binding; cell; complex; cycle; et al; formation; fragmentation; function; gm130; golgi; golph3; grasp65; interaction; kinase; membrane; mitotic; p115; p97; phosphorylation; protein; ribbon; role; stacking; structure; terminal; tethering; trafficking; trans; transport; vesicle; virus; wang cache: cord-323331-80d01l6f.txt plain text: cord-323331-80d01l6f.txt item: #437 of 541 id: cord-323358-05bk91lm author: Bhaskar, Sathyamoorthy title: Engineering protein nanocages as carriers for biomedical applications date: 2017-04-07 words: 9556 flesch: 35 summary: 65 Application of protein nanocages as vaccine/immune modulators Protein nanocages have shown promising potential as a display platform for pathogenic epitopes to elicit the production of neutralizing antibodies. 1, 3 Examples of naturederived nanocarriers include protein nanocages such as viruses, ferritin and many others that are formed by the self-assembly of protein subunits, resulting in a cage-like structure. keywords: applications; assembly; cell; delivery; drug; ferritin; interior; ligands; molecules; nanocages; nanoparticles; protein; protein nanocages; self; structure; subunits; surface; targeting; virus; viruses cache: cord-323358-05bk91lm.txt plain text: cord-323358-05bk91lm.txt item: #438 of 541 id: cord-323768-r7jbm1et author: Lagarda-Diaz, Irlanda title: Legume Lectins: Proteins with Diverse Applications date: 2017-06-12 words: 6815 flesch: 35 summary: Throughout the history of lectin research, legume seeds have been screened for lectin activity. Among plant lectins, those of legumes have been the most widely considered [2] . keywords: activity; agglutinin; antimicrobial; binding; carbohydrate; cell; complex; effect; insecticidal; interactions; lectins; legume; phaseolus; plant; proteins; seeds; specificity; structures; vulgaris; wall cache: cord-323768-r7jbm1et.txt plain text: cord-323768-r7jbm1et.txt item: #439 of 541 id: cord-324325-rmlrhyf2 author: Chan, Wai S title: Coronaviral hypothetical and structural proteins were found in the intestinal surface enterocytes and pneumocytes of severe acute respiratory syndrome (SARS) date: 2005-05-13 words: 3741 flesch: 37 summary: This set of antibodies will be useful in tissue diagnosis of SARS and in future studies of the in vitro models of SARS. Severe Acute Respiratory Syndrome (SARS) last accessed A major outbreak of severe acute respiratory syndrome in Hong Kong A cluster of cases of severe acute respiratory syndrome in Hong Kong Digestive system manifestations in patients with severe acute respiratory syndrome Enteric involvement of severe acute respiratory syndrome-associated coronavirus infection Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome Identification of a novel coronavirus in patients with severe acute respiratory syndrome Koch's postulates fulfilled for SARS virus The genome sequence of the SARS-associated coronavirus Characterization of a novel coronavirus associated with severe acute respiratory syndrome A novel severe acute respiratory syndrome coronavirus protein, U274, is transported to the cell surface and undergoes endocytosis Characterization of a unique group-specific protein (U122) of the severe acute respiratory syndrome coronavirus Pulmonary pathological features in coronavirus associated severe acute respiratory syndrome (SARS) SARS-associated viral hepatitis caused by a novel coronavirus: report of three cases Persistent infection of SARS coronavirus in colonic cells in vitro Tissue and cellular tropism of the coronavirus associated with severe acute respiratory syndrome: an in situ hybridization study of fatal cases Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Pneumocytes (combined, a-i, arrows) and enterocytes (b-i, arrows) infected with the viral genome (iii, arrows) were positive for SARS 3a protein (ii, arrows). keywords: antibodies; cells; coronavirus; cov; proteins; sars; signals; syndrome cache: cord-324325-rmlrhyf2.txt plain text: cord-324325-rmlrhyf2.txt item: #440 of 541 id: cord-324640-2zhaknbi author: Munday, Diane C. title: Quantitative Proteomic Analysis of A549 Cells Infected with Human Respiratory Syncytial Virus date: 2010-07-20 words: 12374 flesch: 31 summary: The relative level of host cell proteins can have a direct effect on HRSV disease progression where secondary bacterial infections are observed. These included mitochondrial proteins, cell cycle regulatory proteins, ND10s, components of the nuclear pore complex, and nucleocytoplasmic trafficking proteins. keywords: a549; abundance; analysis; cells; complex; cytoplasmic; data; fig; fraction; host; hrsv; infection; mock; nuclear; nucleus; pml; pore; proteins; response; rna; study; virus cache: cord-324640-2zhaknbi.txt plain text: cord-324640-2zhaknbi.txt item: #441 of 541 id: cord-324667-wmhdw1qs author: Nishtala, Krishnatej title: Tear biomarkers for keratoconus date: 2016-08-04 words: 4085 flesch: 30 summary: Tear proteins have been reported to be altered in patients with keratoconus with and without contact lens wear when compared to controls [36] . One of the major challenges in tear proteomics is the wide dynamic range of tear proteins. keywords: analysis; biomarkers; changes; disease; eye; fluid; keratoconus; levels; patients; proteins; tear cache: cord-324667-wmhdw1qs.txt plain text: cord-324667-wmhdw1qs.txt item: #442 of 541 id: cord-325043-vqjhiv7p author: Gorbalenya, Alexander E. title: An NTP-binding motif is the most conserved sequence in a highly diverged monophyletic group of proteins involved in positive strand RNA viral replication date: 1989 words: 6807 flesch: 42 summary: In fact, in recent studies, protein sequences were searched for the A consensus alone as the B consensus in its loosest form is obviously too degenerate to be unequivocally recognized, except in a family of diverged proteins (see below). Protein sequences were extracted from the current literature (for references see Table 1 ). keywords: consensus; et al; families; family; motif; ntp; proteins; residues; rna; sequence; viruses cache: cord-325043-vqjhiv7p.txt plain text: cord-325043-vqjhiv7p.txt item: #443 of 541 id: cord-325230-3kg4oe4g author: Agol, Vadim I. title: Viral security proteins: counteracting host defences date: 2010-11-09 words: 8721 flesch: 30 summary: At the same time, however, there is a certain division of labour between viral proteins. The reasons for this variability are poorly understood, although receptor compatibility and effects on viral protein and RNA synthesis that are caused by differences in the availability of host factors are surely important contributors. keywords: cardiovirus; disease; host; interferon; leader; picornavirus; poliovirus; proteins; replication; rna; security; security proteins; translation; virus; viruses cache: cord-325230-3kg4oe4g.txt plain text: cord-325230-3kg4oe4g.txt item: #444 of 541 id: cord-325282-20l9xcmg author: Helal, Mohamed A. title: Molecular basis of the potential interaction of SARS-CoV-2 spike protein to CD147 in COVID-19 associated-lymphopenia date: 2020-09-16 words: 6760 flesch: 43 summary: Also, CD147 protein made polar contacts to the SARS-CoV protein using the same residues, namely, Gly100, His102, and Lys191. Interestingly, CD147 receptor is expressed on red blood cells (RBCs), providing a route for malaria entry (Zhang et al., 2018) . keywords: binding; cd147; cells; complex; cov-2; docking; energy; et al; interaction; protein; receptor; residues; sars; simulation; spike; surface cache: cord-325282-20l9xcmg.txt plain text: cord-325282-20l9xcmg.txt item: #445 of 541 id: cord-325559-di8lljoi author: Cappello, Francesco title: Does SARS-CoV-2 Trigger Stress-Induced Autoimmunity by Molecular Mimicry? A Hypothesis date: 2020-06-29 words: 5212 flesch: 36 summary: By resorting to previously known information on genome sequences and protein structures and functions as well, bioinformaticians have been successfully assisting virologists by structurally characterizing proteins of the novel virus, determining the evolutionary trajectories, identifying interactions with host proteins, and providing other important biological insights. Alphavirus Sequence alignment of structural polyproteins belonging to arthritogenic alphaviruses revealed conserved regions which share homology with human proteins implicated in rheumatoid arthritis. keywords: cells; coronavirus; cov-2; covid-19; disease; human; immune; mimicry; patients; proteins; sars; virus cache: cord-325559-di8lljoi.txt plain text: cord-325559-di8lljoi.txt item: #446 of 541 id: cord-325825-0lyt8gfq author: Griffiths, Samantha J. title: A Systematic Analysis of Host Factors Reveals a Med23-Interferon-λ Regulatory Axis against Herpes Simplex Virus Type 1 Replication date: 2013-08-08 words: 12575 flesch: 40 summary: These data suggest HSV-1 proteins preferentially target highly connected central human proteins in the cellular interaction network, similar to other viruses [23] . A direct comparison of HSV-1 protein interaction partners and the siRNA screen HFs found 215 genes in common. keywords: cells; complex; data; expression; figure; gene; herpes; hfs; host; hsv-1; human; ifn; infection; interaction; interferon; med23; media; plates; protein; replication; screen; sirna; transfection; type; virus cache: cord-325825-0lyt8gfq.txt plain text: cord-325825-0lyt8gfq.txt item: #447 of 541 id: cord-325943-3hvy7b7c author: Bouwman, Kim M. title: Guinea Fowl Coronavirus Diversity Has Phenotypic Consequences for Glycan and Tissue Binding date: 2019-05-01 words: 4828 flesch: 43 summary: Overall, we demonstrate that diversity in GfCoV S1 proteins results in differences in glycan and tissue binding properties. Concentrationdependent binding of GfCoV S1 proteins to Gal␤1,4GlcNAc␤1,3Gal␤1,4GlcNAc in ELISA. keywords: binding; fig; fowl; gfcov; gfcov/2014; glycan; guinea; proteins; receptor; spike; tissues cache: cord-325943-3hvy7b7c.txt plain text: cord-325943-3hvy7b7c.txt item: #448 of 541 id: cord-326015-ky4y2xjt author: Füllekrug, Joachim title: Protein sorting in the Golgi complex date: 1998-08-14 words: 3945 flesch: 44 summary: ERGIC-53 carries a cytosolic endoplasmic reticulum determinant interacting with COP II A hypothesis on the tra¤c of MG160, a medial Golgi sialoglycoprotein, from the trans-Golgi network to the Golgi cisternae Warren, Evidence for recycling of the resident medial/trans Golgi enzyme, N-acetylglucosaminyltransferase I, in ldlD cells Localization of a yeast early Golgi mannosyltransferase, Och 1p, involves retrograde transport Rapid redistribution of Golgi proteins into the ER in cells treated with brefeldin A: evidence for membrane cycling from Golgi to ER Retention of membrane proteins by the endoplasmic reticulum Do other Golgi resident proteins display similar signals? keywords: apparatus; enzymes; golgi; membrane; pathway; proteins; residents; transport cache: cord-326015-ky4y2xjt.txt plain text: cord-326015-ky4y2xjt.txt item: #449 of 541 id: cord-327000-oyg3oyx1 author: Li, Shasha title: Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response date: 2020-05-11 words: 11139 flesch: 41 summary: These cap structures enhance the initiation of translation of viral proteins, protect viral mRNAs against cellular 5 -3 -exoribonuclease and limit the recognition of viral RNA by host innate system [120, 121] . Although several studies have been performed to understand the pathogenicity of PEDV, there remains limited information about the interaction between viral proteins and host cell factors during viral infection. keywords: activity; coronavirus; cov; covs; diarrhea; epidemic; expression; host; ifn; nsp1; pedv; porcine; production; protein; replication; response; rna; sars; signaling; type; virus cache: cord-327000-oyg3oyx1.txt plain text: cord-327000-oyg3oyx1.txt item: #450 of 541 id: cord-327199-ggomuomb author: Moerdyk-Schauwecker, Megan title: Cellular Proteins Associated with the Interior and Exterior of Vesicular Stomatitis Virus Virions date: 2014-08-08 words: 6429 flesch: 35 summary: mature and extracellular enveloped virions Protein composition of the vaccinia virus mature virion Identification of proteins associated with murine gammaherpesvirus 68 virions Proteomic analysis of pathogenic and attenuated alcelaphine herpesvirus 1 Proteins of purified Epstein-Barr virus Identification of proteins associated with murine cytomegalovirus virions Comprehensive characterization of extracellular herpes simplex virus type 1 virions Identification of proteins in human cytomegalovirus (HCMV) particles: the HCMV proteome Virion proteins of Kaposi's sarcomaassociated herpesvirus Proteomic characterization of pseudorabies virus extracellular virions Cellular proteins in influenza virus particles Proteomics analysis unravels the functional repertoire of coronavirus nonstructural protein 3 Proteomic analysis of purified coronavirus infectious bronchitis virus particles Proteomic and biochemical analysis of purified human immunodeficiency virus type 1 produced from infected monocyte-derived macrophages Proteomic analysis of human immunodeficiency virus using liquid chromatography/tandem mass spectrometry effectively distinguishes specific incorporated host proteins Identification of host proteins associated with retroviral vector particles by proteomic analysis of highly purified vector preparations Distinct host cell proteins incorporated by SIV replicating in CD4+ T cells from natural disease resistant versus non-natural disease susceptible hosts Protein analysis of purified respiratory syncytial virus particles reveals an important role for heat shock protein 90 in virus particle assembly Proteomic analysis of purified Newcastle disease virus particles Proteomics of the Autographa californica nucleopolyhedrovirus budded virions Correlation between structure, protein composition, morphogenesis and cytopathology of Glossina pallidipes salivary gland hypertrophy virus Profiling of cellular proteins in porcine reproductive and respiratory syndrome virus virions by proteomics analysis Analysis of virion associated host proteins in vesicular stomatitis virus using a proteomics approach A single amino acid change in the L-polymerase protein of vesicular stomatitis virus completely abolishes viral mRNA cap methylation Recombinant vesicular stomatitis viruses from DNA The lipidomes of vesicular stomatitis virus, semliki forest virus, and the host plasma membrane analyzed by quantitative shotgun mass spectrometry Specific interactions of vesicular stomatitis virus L and NS proteins with heterologous genome ribonucleoprotein template lead to mRNA synthesis in vitro Systematic characterization of nuclear proteome during apoptosis: a quantitative proteomic study by differential extraction and stable isotope labeling Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search Code developments to improve the efficiency of automated MS/MS spectra interpretation Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases Future prospects for the analysis of complex biological systems using micro-column liquid chromatography-electrospray tandem mass spectrometry Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists Biophysical studies of vesicular stomatitis virus Structural domains of vesicular stomatitis virus. Here we aimed to determine the localization of host proteins within the VSV virions by analyzing: i) whole VSV virions; and ii) whole VSV virions treated with Proteinase K to remove all proteins outside the viral envelope. keywords: analysis; budding; cell; host; human; prok; proteins; rnp; stomatitis; type; virions; virus; viruses; vsv cache: cord-327199-ggomuomb.txt plain text: cord-327199-ggomuomb.txt item: #451 of 541 id: cord-327744-5k8np850 author: Munteanu, Cristian Robert title: Multi-target QPDR classification model for human breast and colon cancer-related proteins using star graph topological indices date: 2009-03-21 words: 4742 flesch: 43 summary: The cancer probabilities represent the fractions of proteins HBC/HCC-related from the entire Sjö blom's proteins (cancer proteins) and have values of 0.639 (HBC) and 0.361 (HCC). In order to illustrate the performance of the approach when applied to a single set of cancer related proteins (e.g. either breast or colon), we obtained two equations, one for HBC and other for HCC. keywords: cancer; classification; hbc; hcc; model; non; protein; star; tis cache: cord-327744-5k8np850.txt plain text: cord-327744-5k8np850.txt item: #452 of 541 id: cord-327883-s9nbr5y8 author: None title: Section Virology date: 1990-03-31 words: 10597 flesch: 45 summary: Inst. of Virology, Univ., D-6300 Giessen A highly purified nucleoprotein (NP) preparation from influenza virus infected cells yielded in addition to the commonly known 56 kd protein a 42 kd component which could not be detected in virus particles. The biological activity of the clone was confirmed by a variety of criteria: induction of characteristic CPE in susceptible cells infected with cell-free supernatant from cultures transfected with pHSRV; indirect immunofluorescence; radioimmunoprecipitation of viral proteins and electron microscopy. keywords: antibodies; antibody; antigen; binding; cells; dna; ebv; expression; gene; hcmv; hepatitis; hsv; human; infection; patients; positive; protein; region; results; sequences; sera; specific; virus; viruses cache: cord-327883-s9nbr5y8.txt plain text: cord-327883-s9nbr5y8.txt item: #453 of 541 id: cord-327934-hjimlb6i author: Acar, Delphine D. title: Identification of peptide domains involved in the subcellular localization of the feline coronavirus 3b protein date: 2019-10-01 words: 6793 flesch: 38 summary: How proteins enter the nucleus To be or not to be in the nucleolus Nucleolar targeting: the hub of the matter Characterization and prediction of protein nucleolar localization sequences Viruses as modulators of mitochondrial functions Viral proteins targeting mitochondria: controlling cell death Mitochondrial localization of viral proteins as a means to subvert host defense Mitochondrial dynamics and viral infections: a close nexus Mitochondria and viruses Viral product trafficking to mitochondria, mechanisms and roles in pathogenesis Importing mitochondrial proteins: machineries and mechanisms Refining the definition of plant mitochondrial presequences through analysis of sorting signals, N-terminal modifications, and cleavage motifs Mitochondrial targeting sequences may form amphiphilic helices Domain structure of mitochondrial and chloroplast targeting peptides A chemically synthesized pre-sequence of an imported mitochondrial protein can form an amphiphilic helix and perturb natural and artificial phospholipid bilayers Amphiphilicity is essential for mitochondrial presequence function Mitochondrial presequences Nmr solution structure of the mitochondrial f1beta presequence from Nicotiana plumbaginifolia Tom20 recognizes mitochondrial presequences through dynamic equilibrium among multiple bound states Tom20 and Tom22 share the common signal recognition pathway in mitochondrial protein import Experimental feline enteric coronavirus infection reveals an aberrant infection pattern and shedding of mutants with impaired infectivity in enterocyte cultures Prediction of protein antigenic determinants from amino acid sequences Mutations of 3C and spike protein genes correlate with the occurrence of feline infectious peritonitis Genetics and pathogenesis of feline infectious peritonitis virus Some of these viral proteins mimic or hijack mitochondrial proteins to their advantage, or alter the dynamics or intracellular localization of mitochondria (reviewed in [46] keywords: cells; coronavirus; egfp; expression; fcov; feline; localization; mitochondria; nuclear; nucleolar; protein; residues cache: cord-327934-hjimlb6i.txt plain text: cord-327934-hjimlb6i.txt item: #454 of 541 id: cord-328003-yovp8squ author: Duan, Liangwei title: The SARS-CoV-2 Spike Glycoprotein Biosynthesis, Structure, Function, and Antigenicity: Implications for the Design of Spike-Based Vaccine Immunogens date: 2020-10-07 words: 7368 flesch: 23 summary: The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity The D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. Accordingly, there has been mounting interest in exploring the potential of immunogenic glycan moieties as vaccine candidates against multiple viruses, including SARS-CoV-2 (75, 76) . keywords: ace2; antibodies; antibody; coronavirus; cov-2; fusion; glycoprotein; human; protein; rbd; receptor; sars; spike; vaccine cache: cord-328003-yovp8squ.txt plain text: cord-328003-yovp8squ.txt item: #455 of 541 id: cord-328046-5us4se5o author: Xu, H. Y. title: Further Identification and Characterization of Novel Intermediate and Mature Cleavage Products Released from the ORF 1b Region of the Avian Coronavirus Infectious Bronchitis Virus 1a/1b Polyprotein date: 2001-09-30 words: 5783 flesch: 42 summary: Colocalization of viral proteins with the organelle markers is represented by the yellow region within each cell in the merged images (C, F, I, L, and O). Replication and morphogenesis of avian coronavirus in Vero cells and their inhibition by monensin Impaired integrinmediated adhesion and signaling in fibroblasts expressing a dominant-negative mutant PTP1B Subcellular distribution of normal and mutant vitamin D receptors in living cells Four proteins processed from the replicase gene polyprotein of mouse hepatitis virus colocalize in the cell periphery and adjacent to sites of virion assembly Completion of the sequence of the genome of the coronavirus avian infectious bronchitis virus Comparison of the replication of positive-stranded RNA viruses of plants and animals The putative helicase of the coronavirus mouse hepatitis virus is processed from the replicase gene polyprotein and localizes in complexes that are active in viral RNA synthesis Molecular chaperones Eukaryotic transient-expression system based on recombinant vaccinia virus that synthesizes bacteriophage T7 RNA polymerase Protein folding in the cell Identification of an ATPase activity associated with a 71-kilodalton polypeptide encoded in gene 1 of the human coronavirus 229E Identification and subcellular localization of a 41 kDa, polyprotein 1ab processing product in human coronavirus 229E-infected cells Cleavage of structural proteins during the assembly of the head of bacteriophage T4 Characterization of the two overlapping papain-like proteinase domains encoded in gene 1 of the coronavirus infectious bronchitis virus and determination of the C-terminal cleavage site of an 87 kDa protein Identification of a novel cleavage activity of the first papain-like proteinase domain encoded by ORF 1a of the coronavirus avian infectious bronchitis virus and characterization of the cleavage products The missing link in coronavirus assembly: Retention of the avian coronavirus infectious bronchitis virus envelope protein in the pre-Golgi compartments and physical interaction between the envelope and membrane proteins Induction of caspase-dependent apoptosis in cultured cells by the avian coronavirus infectious bronchitis virus Characterisation and mutational analysis of an ORF 1a-encoding proteinase domain responsible for proteolytic processing of the infectious bronchitis virus 1a/1b polyprotein A 100-kilodalton polypeptide encoded by open reading frame (ORF) 1b of the coronavirus infectious bronchitis virus is processed by ORF 1a products Identification, expression, and processing of an 87-kDa polypeptide encoded by ORF 1a of the coronavirus infectious bronchitis virus Proteolytic processing of the coronavirus infectious bronchitis virus 1a polyprotein: Identification of a 10 kDa polypeptide and determination of its cleavage sites Proteolytic mapping of the coronavirus infectious bronchitis virus 1b polyprotein: evidence for the presence of four cleavage sites of the 3C-like proteinase and identification of two novel cleavage products Identification of a 24 kDa polypeptide processed from the coronavirus infectious bronchitis virus 1a polyprotein by the 3C-like proteinase and determination of its cleavage sites Further characterization of the coronavirus infectious bronchitis virus 3C-like proteinase and determination of a new cleavage site Processing of the coronavirus MHV-JHM polymerase polyprotein: identification of precursors and proteolytic products spanning 400 kilodaltons of ORF1a The human coronavirus 229E superfamily 1 helicase has RNA and DNA duplexunwinding activities with 5Ј-3Ј polarity Biochemical characterization of the equine arteritis virus helicase suggests a close functional relationship between arterivirus and coronavirus helicases Colocalization and membrane association of murine hepatitis virus gene 1 products and de novo-synthesized viral RNA in infected cells Mouse hepatitis virus replicase proteins associate with two distinct populations of intracellular membranes Characterization of endoplasmic reticulum by colocalization of B-p and dicarbocyanine dyes Localization of mouse hepatitis virus nonstructural proteins and RNA synthesis indicates a role for late endosomes in viral replication Integral membrane proteins of the nuclear envelope are dispersed throughout the endoplasmic reticulum during mitosis Processing of the human coronavirus keywords: cells; cleavage; fig; ibv; kda; kda protein; products; protein cache: cord-328046-5us4se5o.txt plain text: cord-328046-5us4se5o.txt item: #456 of 541 id: cord-328483-sj8i9ss2 author: Jaegle, Mike title: Protein‐Templated Fragment Ligations—From Molecular Recognition to Drug Discovery date: 2017-05-31 words: 9602 flesch: 41 summary: M oreover, the definition creates ac lear distinction between templated fragment ligations and other catalytic transformations exerted by proteins similar to the turn-over of enzyme substrates. [13] [14] and irreversible reactions,also denominated as target-guided synthesis (TGS), [15] are treated together,a sb oth reaction categories deliver examples of templated fragment ligations and in many cases it is difficult to categorize one reaction unambiguously. keywords: assays; binding; chemical; detection; discovery; drug; enzyme; figure; formation; fragment; inhibitor; ligand; ligation; ligation products; ligation reactions; methods; nmr; products; protein; reactions; site; target; templated cache: cord-328483-sj8i9ss2.txt plain text: cord-328483-sj8i9ss2.txt item: #457 of 541 id: cord-329149-1giy1fow author: Martinez-Martin, Nadia title: Technologies for Proteome-Wide Discovery of Extracellular Host-Pathogen Interactions date: 2017-02-22 words: 11184 flesch: 20 summary: Interestingly, this study highlighted a small set of extracellular host proteins recurrently targeted by several of the viral and bacterial pathogens analyzed, including cell surface receptors such as VEGFR2/KDR and collagen, possibly indicating previously unrecognized roles in the immune response against pathogens. In addition, interactions between cell surface proteins are often characterized by fast dissociation rates and therefore weak binding affinities, and in consequence well-established PPI methods such as yeast-two-hybrid or affinity purification-mass spectrometry (AP/MS) largely fail to detect these interactions. keywords: approach; binding; cell; detection; entry; extracellular; genes; host; human; identification; infection; interactions; membrane; microarrays; molecules; novel; pathogen; protein; receptor; screens; studies; study; surface; virus cache: cord-329149-1giy1fow.txt plain text: cord-329149-1giy1fow.txt item: #458 of 541 id: cord-329403-jzrlywfe author: Teo, Su Hui Catherine title: A NS1-binding monoclonal antibody interacts with two residues that are highly conserved in seasonal as well as newly emerged influenza A virus date: 2019-03-06 words: 4473 flesch: 47 summary: Rabbit anti-Myc antibody was used as primary antibody to detect the presence of NS1 protein and goat anti-rabbit HRP-conjugated antibody (Pierce) was used as secondary antibody, followed by the Recombinant viruses were generated with pHW2000 reverse genetic system as described previously (Hoffmann et al. 2000) . Besides testing the binding of mAb 19H9 to NS1 protein overexpressed in 293T cells, recombinant viruses with various NS1 mutations (rgPR8-NS1-P85A, rgPR8-NS1-Y89A and rgPR8-NS1-Y89F) were generated so that binding of mAb 19H9 to NS1 expressed in infected cells can be assessed. keywords: 19h9; cells; influenza; mab; ns1; p85β; protein; virus cache: cord-329403-jzrlywfe.txt plain text: cord-329403-jzrlywfe.txt item: #459 of 541 id: cord-329448-kxxy60x9 author: Kumari, Sudha title: Endocytosis unplugged: multiple ways to enter the cell date: 2010-02-02 words: 11551 flesch: 27 summary: It is likely that there are many different biochemical and physical principles behind the formation of vesicles in cell membrane. Characterization and epitope-mapping of a novel flotillin-1 monoclonal antibody probe Molecular mechanisms of clathrinindependent endocytosis Evolutionary analysis and molecular dissection of caveola biogenesis CXCL12-induced partitioning of flotillin-1 with lipid rafts plays a role in CXCR4 function Endocytosis of flotillin-1 and flotillin-2 is regulated by Fyn kinase CD82 endocytosis and cholesterol-dependent reorganization of tetraspanin webs and lipid rafts Cholesterol depletion activates rapid internalization of submicron-sized acetylcholine receptor domains at the cell membrane Pathways of clathrin-independent endocytosis Clathrin-independent endocytosis: from nonexisting to an extreme degree of complexity Magnetosomes are cell membrane invaginations organized by the actin-like protein MamK Reconstructing the evolution of the endocytic system: insights from genomics and molecular cell biology Protein and lipid requirements for endocytosis A novel fluorescence-activated cell sorter-based screen for yeast endocytosis mutants identifies a yeast homologue of mammalian eps15 Regulators of yeast endocytosis identified by systematic quantitative analysis Endocytosis in the plant-pathogenic fungus Ustilago maydis Kinesin from the plant pathogenic fungus Ustilago maydis is involved in vacuole formation and cytoplasmic migration Aspergillus nidulans ArfB plays a role in endocytosis and polarized growth Role for Arf3p in development of polarity, but not endocytosis, in Saccharomyces cerevisiae Endocytosis, endosome trafficking, and the regulation of Drosophila development Macromolecular uptake in Drosophila pericardial cells requires rudhira function Phagocytosis of Candida albicans by RNAi-treated Drosophila S2 cells Genome-wide analysis identifies a general requirement for polarity proteins in endocytic traffic Receptor-mediated endocytosis in plants is energetically possible Uptake of a fluorescent marker in plant cells is sensitive to brefeldin A and wortmannin Molecular dissection of endosomal compartments in plants Actin-dependent fluid-phase endocytosis in inner cortex cells of maize root apices Sucrose-inducible endocytosis as a mechanism for nutrient uptake in heterotrophic plant cells Distinct endocytic pathways identified in tobacco pollen tubes using charged nanogold Clathrin-mediated constitutive endocytosis of PIN auxin efflux carriers in Arabidopsis Phylogeny of endocytic components yields insight into the process of nonendosymbiotic organelle evolution keywords: actin; cargo; caveolae; caveolin; cell; clathrin; coat; dynamin; endocytic; endocytosis; formation; independent; internalization; macropinocytosis; membrane; pathway; process; proteins; receptor; surface; uptake; vesicle cache: cord-329448-kxxy60x9.txt plain text: cord-329448-kxxy60x9.txt item: #460 of 541 id: cord-329493-ueqlhgn0 author: Stadler, Konrad title: SARS — beginning to understand a new virus date: 2003 words: 5153 flesch: 43 summary: Coronavirus as a possible cause of severe acute respiratory syndrome Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in Hong Kong Clinical presentations and outcome of severe acute respiratory syndrome in children Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study Acute respiratory syndrome in China Summary of probable SARS cases with onset of illness from 1 Identification of a novel coronavirus in patients with severe acute respiratory syndrome A Nnvel coronavirus associated with severe acute respiratory syndrome Aetiology: Koch's postulates fulfilled for SARS virus Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome Transmission dynamics of the etiological agent of SARS in Hong Kong: impact of public health interventions Transmission dynamics and control of severe acute respiratory syndrome Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China SARS in China: tracking the roots of a killer Severe acute respiratory syndrome (SARS) in Singapore Virus Taxonomy The genome sequence of the SARSassociated coronavirus References 17 and 18 are the first reports of the complete genome sequences of two SARS-CoV isolates (TOR2 and Urbani strains, respectively) The complete genome sequence of severe acute respiratory syndrome coronavirus strain HKU-39849 (HK-39) Mechanisms and enzymes involved in SARS coronavirus genome expression The complete genome sequence of a SARS-CoV isolate (FRA) and experimental data on its key RNA elements and protein functions are described. Their efficacy still needs to be shown, but our laboratory (and possibly others) are in the process of testing vaccines on the basis of inactivated SARS virus in pre-clinical models. keywords: coronavirus; cov; domain; genome; group; protein; rna; sars; sequence; spike; syndrome; virus cache: cord-329493-ueqlhgn0.txt plain text: cord-329493-ueqlhgn0.txt item: #461 of 541 id: cord-329625-hx2rsi91 author: You, Jae-Hwan title: A model for the dynamic nuclear/nucleolar/cytoplasmic trafficking of the porcine reproductive and respiratory syndrome virus (PRRSV) nucleocapsid protein based on live cell imaging date: 2008-08-15 words: 5647 flesch: 30 summary: The localisation of porcine reproductive and respiratory syndrome virus nucleocapsid protein to the nucleolus of infected cells and identification of a potential nucleolar localization signal sequence Peptide domains involved in the localization of the porcine reproductive and respiratory syndrome virus nucleocapsid protein to the nucleolus Intracellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein: absence of nucleolar accumulation during infection and after expression as a recombinant protein in Vero cells Disruption of the nucleolus mediates stabilization of p53 in response to DNA damage and other stresses Intranuclear ataxin1 inclusions contain both fast-and slow-exchanging components Potential subversion of autophagosomal pathway by picornaviruses Crossing the nuclear envelope: hierarchical regulation of nucleocytoplasmic transport Nuclear localization of non-structural protein 1 and nucleocapsid protein of equine arteritis virus Model of the trafficking of PRRSV N protein within the cell where the width of arrows denotes the relative movement of N protein and shading is relative concentration of the protein. This property is common with related viruses including the equine arterivirus (EAV) N protein (Tijms et al., 2002) and the coronavirus N proteins Wurm et al., 2001) with the possible exception of the severe acute respiratory syndrome coronavirus (SARS-CoV) N protein (Li et al., 2005; Rowland et al., 2005; Timani et al., 2005; You et al., 2005; You et al., 2007) . keywords: cells; cytoplasm; egfp; n protein; nucleolus; nucleus; protein; prrsv; trafficking cache: cord-329625-hx2rsi91.txt plain text: cord-329625-hx2rsi91.txt item: #462 of 541 id: cord-329840-f3dsu36p author: Hati, Sanchita title: Impact of Thiol-Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin Converting Enzyme 2 Receptor date: 2020-05-11 words: 2502 flesch: 41 summary: In particular, the interaction of viral spike proteins with ACE2 is a critical step in the viral replication cycle. [3] [4] The role of oxidative stress on the binding of viral proteins on the host cell surface receptors is a relatively underexplored area of biomedical research. keywords: ace2; binding; cov; cov-2; disulfide; protein; sars cache: cord-329840-f3dsu36p.txt plain text: cord-329840-f3dsu36p.txt item: #463 of 541 id: cord-329844-w969lczb author: Robson, B. title: Bioinformatics studies on a function of the SARS-CoV-2 spike glycoprotein as the binding of host sialic acid glycans date: 2020-06-08 words: 15937 flesch: 45 summary: Also, more generally, in preparative work, comparison of the spike protein sequence of the spike protein with sialic acid glycan binding proteins and other sugar binding proteins, or domains of them. A likely relevant observation was that the first set of amino acid residues (the set containing aspartate) and binding sialic acids tended to occur in a subsequence that adopted a local loop conformation, while the second set (that containing glutamate) were frequently associated with α-helices and particularly their termini. keywords: acid; acid glycan; acid residues; amino; amino acid; binding; cov-2; glycan; influenza; method; prediction; present; proteins; residues; sars; score; sequence; sialic; sites; spike; sugar; tryptophan; virus cache: cord-329844-w969lczb.txt plain text: cord-329844-w969lczb.txt item: #464 of 541 id: cord-330337-d41imvo7 author: Basu, Souradip title: Impact of clade specific mutations on structural fidelity of SARS-CoV-2 proteins date: 2020-10-20 words: 6430 flesch: 42 summary: Our final scoring revealed that ORF8 protein mutation L84S was the most disruptive of the mutations under study. In our analyses we have been able to clearly show that mutations caused significant changes in protein structures where highest RMSD value was observed for S protein (5.67), while maximum number of mismatches were observed in case of N protein (24 out of 419). keywords: analysis; binding; cell; cov-2; epitopes; et al; mutant; mutations; protein; sars; score; structures; type cache: cord-330337-d41imvo7.txt plain text: cord-330337-d41imvo7.txt item: #465 of 541 id: cord-330475-mameyzih author: Shi, Da title: Molecular Characterizations of Subcellular Localization Signals in the Nucleocapsid Protein of Porcine Epidemic Diarrhea Virus date: 2014-03-13 words: 5590 flesch: 37 summary: Furthermore, by utilizing fusion proteins with green fluorescent protein (GFP), deletion mutations or site-directed mutagenesis of PEDV N protein, coupled with live cell imaging and confocal microscopy, it was revealed that, a region spanning amino acids (aa), 71–90 in region 1 of the N protein was sufficient for nucleolar localization and R87 and R89 were critical for its function. To identify whether there were subcellular localization signals in PEDV N protein, we first conducted a bioinformatics analysis on the protein using existing motif prediction algorithms. keywords: acgfp; amino; cells; cytoplasm; localization; nes; nols; nuclear; nucleolar; nucleolus; pedv; protein; signals cache: cord-330475-mameyzih.txt plain text: cord-330475-mameyzih.txt item: #466 of 541 id: cord-330668-7aw17jf8 author: Chen, Cheng-Chang title: ORF8a of SARS-CoV forms an ion channel: Experiments and molecular dynamics simulations date: 2011-02-28 words: 4813 flesch: 53 summary: The role played by lipids unsaturation upon the membrane interaction of the Heliobacter pylori HP(2-20) antimicrobial peptide analogue HPA3 Identification of an ion channel activity of the Vpu transmembrane domain and its involvement in the regulation of virus release from HIV-1-infected cells The Vpu protein of human immunodeficiency virus type 1 forms cation-selective ion channels Cation-selective ion channels formed by p7 of hepatitis C virus are blocked by hexamethylene amiloride Activation-dependent subconductance levels in the drk1 K channel suggest a subunit basis for ion permeation and gating Accurate bond and angle parameter for X-ray proteinstructure refinement Molecular dynamics simulations of the ErbB-2 transmembrane domain within an explicite membrane environment: comparison with vacuum simulations Mapping the energy surface of transmembrane helixhelix interactions Experimentally based orientational refinement of membrane protein models: a structure for the influenza A M2 H + channel The structure of the HIV-1 Vpu ion channel: modelling and simulation studies Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations Side-chain contributions to membrane protein structure and stability Solving the membrane protein folding problem Bundles consisting of extended transmembrane segments of Vpu from HIV-1: computer simulations and conductance measurements Viral channel forming proteins (VCPs) participate in several viral functions. keywords: bundle; channel; fig; helix; ion; lipid; membrane; models; pore; protein; residues; structure cache: cord-330668-7aw17jf8.txt plain text: cord-330668-7aw17jf8.txt item: #467 of 541 id: cord-330715-olypwdoq author: Sun, Zeyu title: Mass Spectrometry Analysis of Newly Emerging Coronavirus HCoV-19 Spike Protein and Human ACE2 Reveals Camouflaging Glycans and Unique Post-Translational Modifications date: 2020-08-30 words: 5580 flesch: 45 summary: HCoV-19 S protein was expressed in Sf9 insect cells using the Bac-to-Bac system (Life Technologies Inc.) and harvested from the cell culture medium; this was followed by a purification procedure using a Ni-NTA column and Superdex 200 gel filtration column (GE Healthcare, UK) in tandem. Using an occupancy greater than 50% as a criterion to identify sites dominantly decorated with PTMs, we found that 78R, 224E, 654E, and 661E in HCoV-19 S protein and 57E, 68K, and 329E in hACE2 were highly methylated. keywords: binding; coronavirus; fig; glycan; glycosylation; hace2; hcov-19; mass; protein; sars; sites; spike cache: cord-330715-olypwdoq.txt plain text: cord-330715-olypwdoq.txt item: #468 of 541 id: cord-330852-n7j0c4ne author: Fischer, Wolfgang B. title: Mechanism of Function of Viral Channel Proteins and Implications for Drug Development date: 2012-02-23 words: 23723 flesch: 45 summary: An increasing number of proteins are identified as channel proteins, but the precise role in the viral life cycle is yet unknown for the majority of them. The question emerges why the virus needs three channels while all other channel expressing viruses known to date proteins only need one type of channel protein. keywords: activity; amantadine; amino; assembly; channel; channel activity; channel protein; data; domain; drug; et al; function; helix; host; influenza; ion; ion channel; lipid; mechanism; membrane; membrane protein; nmr; peptide; pore; protein; proton; residues; state; structure; studies; tmd; tmds; virus; virus protein; vpu; vpu protein cache: cord-330852-n7j0c4ne.txt plain text: cord-330852-n7j0c4ne.txt item: #469 of 541 id: cord-332317-wrztpeb8 author: Zhang, Xin title: Identification of the interaction between vimentin and nucleocapsid protein of transmissible gastroenteritis virus date: 2015-03-16 words: 3986 flesch: 42 summary: To confirm the interaction between N protein of TGEV and cellular vimentin, immunoprecipitation assay was utilized to identify whether TGEV N protein interacted with cellular vimentin in TGEVinfected ST cells. The present study thus provides protein-related information about interaction of TGEV N protein with host cell that should be useful for understanding host cell response to coronavirus pathogenesis infection and the underlying mechanism of coronavirus replication. keywords: cells; coronavirus; infection; protein; replication; tgev; vimentin; virus cache: cord-332317-wrztpeb8.txt plain text: cord-332317-wrztpeb8.txt item: #470 of 541 id: cord-332344-upsn0zb4 author: Jeswin, Joseph title: Proteomic analysis by iTRAQ in red claw crayfish, Cherax quadricarinatus, hematopoietic tissue cells post white spot syndrome virus infection date: 2016-02-01 words: 5898 flesch: 36 summary: Similarly, in our study the up-regulation of CK1 might be indicative of its interaction with WSSV proteins. WSSV envelope proteins like VP28 and VP19 were previously reported to be threonine phosphorylated keywords: cells; crayfish; expression; host; hpi; hpt; infection; kinase; min; pathway; protein; replication; role; shrimp; virus; wssv cache: cord-332344-upsn0zb4.txt plain text: cord-332344-upsn0zb4.txt item: #471 of 541 id: cord-332784-xkc89uaz author: Mishra, Shashank Shekhar title: Computational investigation of potential inhibitors of novel coronavirus 2019 through structure-based virtual screening, molecular dynamics and density functional theory studies date: 2020-07-15 words: 4254 flesch: 43 summary: The selected five potential hit molecules in the binding site of protease protein, interacting with amino acid residues Phe140, Gly143, Thr26, Thr190, Glu166, Pro168, Met165 and Leu141 with a docking score of À7.524 and À6.711 kcal/mol. The active site of COVID-19 main protease protein was located in region 3 site and the receptor grid files were generated using Grid Generation panel of Glide module. keywords: binding; covid-19; docking; drug; hit; interactions; molecules; protein; site; structure cache: cord-332784-xkc89uaz.txt plain text: cord-332784-xkc89uaz.txt item: #472 of 541 id: cord-332811-kjgah8ts author: Lee, Do Hyun title: Immunoprophylactic effect of chicken egg yolk antibody (IgY) against a recombinant S1 domain of the porcine epidemic diarrhea virus spike protein in piglets date: 2015-06-23 words: 5958 flesch: 40 summary: The sections were then counterstained with DAPI and examined using a fluorescence microscope at 2009 magnification The coronavirus spike protein is a class I virus fusion protein: structural and functional characterization of the fusion core complex Identification of the epitope region capable of inducing neutralizing antibodies against the porcine epidemic diarrhea virus Molecular characterization and phylogenetic analysis of membrane protein genes of porcine epidemic diarrhea virus isolates in China Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States Experimental infection of pigs with a new porcine enteric coronavirus, CV 777 Sequence of the spike protein of the porcine epidemic diarrhoea virus Detection of antibodies against porcine epidemic diarrhea virus in serum and colostrum by indirect ELISA Propagation of the virus of porcine epidemic diarrhea in cell culture Spike glycoprotein cleavage recognition site analysis of infectious bronchitis virus Multiplex real-time RT-PCR for the simultaneous detection and quantification of transmissible gastroenteritis virus and porcine epidemic diarrhea virus Isolation of porcine epidemic diarrhea virus (PEDV) in Korea Immunoprophylactic effect of chicken egg yolk immunoglobulin (IgY) against porcine epidemic diarrhea virus (PEDV) in piglets A method of egg yolk fractionation. Characterization of fractions Mutations within the nuclear localization signal of the porcine reproductive and respiratory syndrome virus nucleocapsid protein attenuate virus replication Heterogeneity in spike protein genes of porcine epidemic diarrhea viruses isolated in Korea The N-terminal region of the porcine epidemic diarrhea virus spike protein is important for the receptor binding Outbreak-related porcine epidemic diarrhea virus strains similar to US strains, South Korea Reemergence of porcine epidemic diarrhea virus on Jeju Island Full-genome sequence analysis of a variant strain of porcine epidemic diarrhea virus in South Korea Cytokine production in immortalized porcine alveolar macrophages infected with porcine reproductive and respiratory syndrome virus New variants of porcine epidemic diarrhea virus, China US-like strain of porcine epidemic diarrhea virus outbreaks in Taiwan Chicken egg yolk antibodies as therapeutics in enteric infectious disease: a review Deadly pig virus slips through US borders Contribution of the porcine aminopeptidase N (CD13) receptor density to porcine epidemic diarrhea virus infection Immunogenicity and protective efficacy of recombinant S1 domain of the porcine epidemic diarrhea virus spike protein Letter to the editor A new coronavirus-like particle associated with diarrhea in swine Porcine epidemic diarrhoea virus as a cause of persistent diarrhoea in a herd of breeding and finishing pigs Chinese-like strain of porcine epidemic diarrhea virus Porcine reproductive and respiratory syndrome virus nucleocapsid protein modulates interferon-b production by inhibiting IRF3 activation in immortalized porcine alveolar macrophages Human telomerase reverse transcriptase-immortalized porcine monomyeloid cell lines for the production of porcine reproductive and respiratory syndrome virus Diseases of swine Molecular cloning: a laboratory manual Emergence of Porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences Proteolytic cleavage of peplomeric glycoprotein E2 of MHV yields two 90K subunits and activates cell fusion Spike protein region (aa 636789) of porcine epidemic diarrhea virus is essential for induction of neutralizing antibodies An outbreak of swine diarrhea of a new-type associated with coronavirus-like particles in Japan Acknowledgments This research was supported by Technology Development Program for Bio-Industry, Ministry for Agriculture, Food and Rural Affairs, Republic of Korea (311007-05-1-HD120). keywords: cells; cfc; chicken; diarrhea; epidemic; group; igy; pedv; piglets; porcine; protein; rs1; virus cache: cord-332811-kjgah8ts.txt plain text: cord-332811-kjgah8ts.txt item: #473 of 541 id: cord-332948-h297ukuu author: Olotu, Fisayo A. title: Leaving no stone unturned: Allosteric targeting of SARS-CoV-2 Spike protein at putative druggable sites disrupts human angiotensin-converting enzyme interactions at the receptor binding domain. date: 2020-10-16 words: 5186 flesch: 42 summary: Assessment of Binding Site Prediction Methods and a Protocol for Validation of Predicted Binding Sites Identifying and characterizing binding sites and assessing druggability Fpocket: An open source platform for ligand pocket detection PrankWeb: a web server for ligand binding site prediction and visualization New method for fast and accurate binding-site identification and analysis Therapeutic target-site variability in α 1-antitrypsin characterized at high J o u r n a l P r e The N protein makes up the nucleocapsid and other viral genome-related processes 21 while the M protein is the most abundant of the four, playing major roles in maintaining viral structural integrity as well as coordinating other structural proteins. keywords: allosteric; binding; coronavirus; cov; entry; hace2; host; human; protein; rbd; sars; sites cache: cord-332948-h297ukuu.txt plain text: cord-332948-h297ukuu.txt item: #474 of 541 id: cord-333089-ufyzqgqk author: Aguilar-Pineda, Jorge Alberto title: Structural and functional analysis of female sex hormones against SARS-Cov2 cell entry date: 2020-07-29 words: 6978 flesch: 45 summary: Our findings that estrogens interfere with S protein and ACE2 interactions in silico that is associated with reduced S protein uptake in an in vitro model of SARS-CoV-2 infectivity in cultured human endothelial cells are consistent with prior studies demonstrating that estrogens have antiviral properties against HIV, Ebola and hepatitis viruses 33 . We then examined the ability of estrogen molecules to interfere with S protein uptake into pulmonary epithelial cells using an in vivo model of SARS-CoV2 infectivity. keywords: 17β; ace2; cells; cov-2; diol; entry; equol; estrogen; figure; glycan; interactions; molecules; protein; rbd; receptor; residues; sars cache: cord-333089-ufyzqgqk.txt plain text: cord-333089-ufyzqgqk.txt item: #475 of 541 id: cord-333262-xvfl7ycj author: Robson, B. title: COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles’ heel conserved region to minimize probability of escape mutations and drug resistance date: 2020-04-11 words: 21686 flesch: 45 summary: Not least, protein binding sites are often partially disordered before binding, and in any case there may be several binding modes. Several three dimensional structures are known for ACE2 complexed with SARS spike protein e.g. protein data bank (PDB) entry (6ACG) and of variants of the latter (e.g. TMPRSS2 protein data bank entry 2OQ5). keywords: ace2; acid; amino; binding; compounds; coronavirus; cov-2; data; dehydrogenase; design; e.g.; emodin; entry; human; krsfiedllfnkv; like; molecules; motif; paper; peptides; pharmacophore; present; protein; residues; sars; sequence; site; spike; studies; type; vaccine; virus cache: cord-333262-xvfl7ycj.txt plain text: cord-333262-xvfl7ycj.txt item: #476 of 541 id: cord-333309-21czobqy author: Byun, Hyewon title: ERAD and how viruses exploit it date: 2014-07-03 words: 11777 flesch: 33 summary: The cytosolic domain of MHC-I is required for US11mediated ERAD targeting (Story et al., 1999; Barel et al., 2003) , and deletion of the C-terminal valine of MHC-I reduced interaction with Derlin-1 (Cho et al., 2013a) . Cho et al. speculated that US11 recognizes MHC-I through its cytosolic domain and transfers it to Derlin-1, which then interacts with the p97 ATPase for membrane dislocation (Cho et al., 2013a ; Figure 2B ). keywords: atpase; cd4; cell; complex; components; cytosolic; degradation; endoplasmic; erad; et al; figure; ligase; membrane; mhc; p97; protein; rem; replication; reticulum; retrotranslocation; substrates; transmembrane; ubiquitin; virus; yeast cache: cord-333309-21czobqy.txt plain text: cord-333309-21czobqy.txt item: #477 of 541 id: cord-333757-h12aozg2 author: Modis, Yorgo title: Class II Fusion Proteins date: 2013-07-10 words: 6796 flesch: 44 summary: The structures show that, despite the absence of similarities in the protein folds of the two classes, fusion proteins from both classes use the same physical principles and general topology to drive membrane fusion. Although class II fusion proteins are genetically and structurally unrelated to class I fusion proteins, they use the same physical principles and topology as other fusion proteins to drive membrane fusion. keywords: class; class ii; domain; fusion; fusion proteins; ii fusion; loop; membrane; membrane fusion; protein; virus cache: cord-333757-h12aozg2.txt plain text: cord-333757-h12aozg2.txt item: #478 of 541 id: cord-333966-st6gyozv author: Taherkhani, Reza title: Design and production of a multiepitope construct derived from hepatitis E virus capsid protein date: 2015-03-17 words: 5209 flesch: 47 summary: At a concentration of 1  10 5 cells/well, PBMCs of each sample in RPMI 1640 and 10% FCS were added to the four wells of 96-well plates, and stimulated with truncated ORF2 protein (10 mg/ml), high density multiepitope protein (10 mg/ml), and PHA (5 mg/ml) separately at 37˚C. The unstimulated PBMCs of each sample were used to evaluate spontaneous production of cytokines. The cell proliferative responses in HEV-recovered group following stimulation with high density multiepitope protein and truncated ORF2 protein were found higher than control group (P < 0.001); and these responses were observed higher with high density multiepitope protein than truncated ORF2 protein in HEV-recovered group (P ¼ 0.013) keywords: cells; density; epitopes; et al; hepatitis; hev; multiepitope; orf2; protein; vaccine; virus cache: cord-333966-st6gyozv.txt plain text: cord-333966-st6gyozv.txt item: #479 of 541 id: cord-334220-sqvfr31q author: Messina, Francesco title: Looking for pathways related to COVID-19 phenotypes: Confirmation of pathogenic mechanisms by SARS-CoV-2 - Host interactome date: 2020-11-03 words: 4228 flesch: 28 summary: We provide a network analysis on protein–protein interactions (PPI) between viral and host proteins to better identify host biological responses, induced by both whole proteome of SARS-CoV-2 and specific viral proteins. The ubiquitin proteasome system deletes viral proteins to control the infection, but the virus can use them for its propagation (34) . keywords: cov-2; covid-19; host; human; infection; interactions; interactome; pathways; patients; proteins; sars cache: cord-334220-sqvfr31q.txt plain text: cord-334220-sqvfr31q.txt item: #480 of 541 id: cord-334511-lx9608vy author: Emwas, Abdul-Hamid title: NMR as a “Gold Standard” Method in Drug Design and Discovery date: 2020-10-09 words: 29290 flesch: 43 summary: Furthermore, the slow time scale of NMR relaxation allows the user to manipulate the external conditions (i.e., length and power of pulse) to increase the resolution of targets and potential drugs [155] in NMR drug design experiments. However, this slow timescale also sets the lower limit at which NMR drug design experiments can be performed [155] , meaning that any external manipulations cannot decrease experimental time below a certain threshold. keywords: approach; binding; chemical; data; design; diffusion; discovery; drug; drug design; drug discovery; example; experiments; fragment; interactions; ligand; methods; molecules; nmr; nmr experiments; nmr spectra; nmr spectroscopy; noe; nuclear; nuclei; protein; pulse; relaxation; resonance; screening; signal; spectra; spin; state; std; std nmr; structure; studies; target; techniques; time; use cache: cord-334511-lx9608vy.txt plain text: cord-334511-lx9608vy.txt item: #481 of 541 id: cord-334592-54dofkxh author: Levine, Beth title: Autophagy in immunity and inflammation date: 2011-01-20 words: 10295 flesch: 21 summary: Autophagy proteins function in adaptive immunity, including in the development and homeostasis of the immune system and in antigen presentation (Table 1 and Fig. 3) . Autophagy proteins function in both the activation and inactivation of innate immune signalling 4 . keywords: atg16l1; autophagosome; autophagy; cells; disease; function; immune; immunity; infection; inflammation; inflammatory; intracellular; membrane; pathway; presentation; proteins; role; signalling; viral; virus cache: cord-334592-54dofkxh.txt plain text: cord-334592-54dofkxh.txt item: #482 of 541 id: cord-335310-61wibso4 author: Chen, Hui-Wen title: Synthetic virus-like particles prepared via protein corona formation enable effective vaccination in an avian model of coronavirus infection date: 2016-08-15 words: 5491 flesch: 35 summary: The result demonstrates the feasibility of studying the evolution of nanoparticle protein corona formation using nanoparticle tracking analysis, which reveals changes in light scattering and size simultaneously. structural characterization of the spike protein From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses The group-specific murine coronavirus genes are not essential, but their deletion, by reverse genetics, is attenuating in the natural host Live, attenuated coronavirus vaccines through the directed deletion of group-specific genes provide protection against feline infectious peritonitis A truncated receptorbinding domain of MERS-CoV spike protein potently inhibits MERS-CoV infection and induces strong neutralizing antibody responses: implication for developing therapeutics and vaccines Purified coronavirus spike protein nanoparticles induce coronavirus neutralizing antibodies in mice A type-specific blocking ELISA for the detection of infectious bronchitis virus antibody A simple method of estimating fifty per cent endpoints A Laboratory Manual for the Isolation and Identification of Avian Pathogens Identification of Taiwan and China-like recombinant avian infectious bronchitis viruses in Taiwan Quantitative profiling of the protein coronas that form around nanoparticles Comparison of the expression of cytokine genes in the bursal tissues of the chickens following challenge with infectious bursal disease viruses of varying virulence Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) keywords: analysis; antigen; corona; coronavirus; fig; free; ibv; nanoparticles; pbs; protein; spike; svlps; vaccine; virus cache: cord-335310-61wibso4.txt plain text: cord-335310-61wibso4.txt item: #483 of 541 id: cord-335915-2apj4qy9 author: Melillo, Alessandro title: Applications of Serum Protein Electrophoresis in Exotic Pet Medicine date: 2013-01-22 words: 5437 flesch: 39 summary: Applications of protein electrophoresis in avian diagnostics Plasma protein electrophoresis of the Atlantic Loggerhead Sea Turtle Caretta caretta Biochemical and hematologic values for 18 clinically healthy radiated tortoises (Geochelone radiata) on St Catherines Island Immune status of free-ranging green turtles with fibropapillomatosis from Hawaii Comparative haematology and blood chemistry of endangered lizards (Gallotia species) in the Canary Islands Electrophoretic proteinogram reference interval from Argentina Northeastern captive caimans (crocodylia: Alligatoridae) Clinical biochemistry of domestic animals Acute phase proteins in dogs and cats: current knowledge and future perspectives Serum concentration of acute phase proteins in dogs with leishmaniasis New testing options for the diagnosis of Encephalitozoon cuniculi in rabbits Identification and characterization of three Encephalitozoon cuniculi strains Altered immune responsiveness associated with Encephalitozoon cuniculi infection in Rabbits Acute and long term humoral immunity following active immunization of rabbits with inactivated spores of various Encephalitozoon species Encephalitozoon cuniculi in pet rabbits L'electrophorese des proteins seriques en pathologie du furet (Mustela putorius furo) In ferrets, dehydration progresses very quickly in case of insufficient intake or increased losses, so hyperproteinemia is a frequently encountered clinical sign (for example in diarrhea, intestinal obstruction, acute gastritis, or renal failure) but in the case of noninfectious diseases, proteins raise in their entirety for hemoconcentration, so the pattern will result basically normal; in the case of inflammatory diseases, globulins increase, altering the electrophoretic curve. keywords: albumin; electrophoresis; fraction; globulins; peak; plasma; protein; response; serum; species cache: cord-335915-2apj4qy9.txt plain text: cord-335915-2apj4qy9.txt item: #484 of 541 id: cord-336119-8g37xsys author: Nimgampalle, Mallikarjuna title: Screening of Chloroquine, Hydroxychloroquine and its derivatives for their binding affinity to multiple SARS-CoV-2 protein drug targets date: 2020-06-24 words: 5466 flesch: 41 summary: These results point to the fact that the Chloroquine Chloroquine sulfate_ChEBI_50178 À3.9 (À4.0) À4.5 À5.5 (À5.2) À5.9 (À5.1) À5.0 (À5.1) À6.0 (À5.9) À5.1 (À4.9) 4. Chloroquine pyrolidylin_ZINC1666887 À7.0 (À8.0) À5.0 À6 (À5.8) À6.6 (À5.8) À5.5 (6.0) À6.3 (À6.7) À5.7 (À3.7) 5. Chloroquine mustard_ZINC5751278 À5.4 (À6.9) À4.2 À5.8 (À5.2) À5.5 (À5.5) À5.1 (À5.5) À5.5 (À5.6) À5.1 (À3.9) Chemically synthesized chloroquine derivatives 6. CQN2A ( derivatives can bind to Spike glycoprotein, which can potentially lead to disruption of Spike protein interaction with the ACE-2 on host cell surface. Furthermore, Chloroquine derivatives have been tested on Pneumocystis pneumonia (PcP) for their therapeutic activity to repurposing antimalarial drugs for Pneumonia (Gomes et al., 2018; Yeo et al., 2020) . keywords: binding; chloroquine; derivatives; docking; drug; hydroxychloroquine; potential; proteins; results; sars; site cache: cord-336119-8g37xsys.txt plain text: cord-336119-8g37xsys.txt item: #485 of 541 id: cord-336364-2ust3qoq author: Artigas, Laura title: In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm date: 2020-10-02 words: 5863 flesch: 41 summary: Starting from different drug targets the effect of the drugs converges on human proteins with a known role in SARS-CoV-2 infection cycle. The 'Coronavirus-host interaction set' is composed of human proteins with a relevant role in SARS-CoV-2 infection and a set of human coronaviruses host interactome retrieved through manual curation of scientific publications (S1 Table) . keywords: ard; combination; cov-2; drug; effect; infection; melatonin; network; pirfenidone; proteins; sars; set cache: cord-336364-2ust3qoq.txt plain text: cord-336364-2ust3qoq.txt item: #486 of 541 id: cord-336542-6asieplk author: Tanco, Sebastián title: Structure–Function Analysis of the Short Splicing Variant Carboxypeptidase Encoded by Drosophila melanogaster silver date: 2010-08-20 words: 7668 flesch: 49 summary: This model contained protein residues Lys29-Val419 (numbering according Fig. 1b) for chain A, Ile28-Glu420 for chain B, Glu30-Val419 for chain C, and Thr27-Glu420 for chain D plus a zinc ion, an N-acetylglucosamine sugar moiety attached to Asn133, and a GEMSA molecule for each protomer. In contrast, DmCPD1Bs is not inhibited by protein inhibitors from potato, leech, tick, or mammal, even at micromolar concentrations. keywords: activity; carboxypeptidase; cleavage; dmcpd1bs; domain; drosophila; enzyme; fig; funnelins; human; protein; repeat; residues; sequence; structure; surface; svr; terminal; type cache: cord-336542-6asieplk.txt plain text: cord-336542-6asieplk.txt item: #487 of 541 id: cord-337032-s4g4g80w author: Gupta, Manoj Kumar title: In-silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel date: 2020-04-15 words: 3974 flesch: 40 summary: SARS-CoV2 is an enveloped virus and E proteins present in them are reported to form ion channels, which is mainly associated with pathogenesis. While M and S protein constitutes the major portion of the viral envelope, E proteins are reported to oligomerize and form ion channels (Venkatagopalan et al., 2015) . keywords: cov2; cov2 e; et al; ion; protein; sars; structure cache: cord-337032-s4g4g80w.txt plain text: cord-337032-s4g4g80w.txt item: #488 of 541 id: cord-337067-j8ebslif author: Mades, Andreas title: Role of Human Sec63 in Modulating the Steady-State Levels of Multi-Spanning Membrane Proteins date: 2012-11-15 words: 8753 flesch: 43 summary: This prompted us to examine whether or not Sec63 may play a more general role in the production of ER proteins. It also did not affect the glycosylation pattern of VSV.G. Since these data are in seemingly conflict with the results obtained for the HBV envelope proteins, we next assessed the behavior of multispanning membrane proteins synthesized in the presence of upregulated Sec63. keywords: bip; cells; complex; control; dna; envelope; fig; function; hbv.s; human; levels; membrane; protein; sec63; signal; state; translocation; translocon cache: cord-337067-j8ebslif.txt plain text: cord-337067-j8ebslif.txt item: #489 of 541 id: cord-337158-0iw2kcaf author: Tiernan, Hannah title: ATR-FTIR spectroscopy and spectroscopic imaging for the analysis of biopharmaceuticals date: 2020-06-22 words: 7405 flesch: 27 summary: Recent Advances and Applications to Biological Systems Recent Applications of ATR FTIR Spectroscopy and Imaging to Proteins The New Drugs of 2019 Affinity Profiling of Monoclonal Antibody and Antibody-Drug-Conjugate Preparations by Coupled Liquid Chromatography-Surface Plasmon Resonance Biosensing The Role of UHPLC in Pharmaceutical Development Real Time Monitoring of Bioreactor mAb IgG3 Cell Culture Process Dynamics via Fourier Transform Infrared Spectroscopy: Implications for Enabling Cell Culture Process Analytical Technology The Therapeutic Monoclonal Antibody Market Advances and Challenges in Enveloped Virus-Like Particle (VLP)-Based Vaccines Generation and Characterization of Murine Monoclonal Antibodies Against Immunoreactive Trypsinogen for Newborn Screening of Cystic Fibrosis Potent Binding of 2019 Novel Coronavirus Spike Protein By a SARS Coronavirus-Specific Human Monoclonal Antibody Cell-Penetrating Peptides Selectively Cross the Blood-Brain Barrier Throughout the review comparisons will be made between FTIR spectroscopy and alternative analytical techniques, and areas will be identified where FTIR spectroscopy could perhaps offer a better alternative in future studies. keywords: analysis; antibodies; antibody; atr; biopharmaceuticals; changes; ftir; ftir spectroscopy; imaging; infrared; line; monoclonal; processing; production; protein; spectroscopy; structure cache: cord-337158-0iw2kcaf.txt plain text: cord-337158-0iw2kcaf.txt item: #490 of 541 id: cord-337825-ujq9mxk7 author: Chen, Bin title: Overview of lethal human coronaviruses date: 2020-06-10 words: 13457 flesch: 43 summary: lung injury Retrospective comparison of convalescent plasma with continuing high-dose methylprednisolone treatment in SARS patients Aberrant pathogenic GM-CSF+ T cells and inflammatory CD14 +CD16+ monocytes in severe pulmonary syndrome patients of a new coronavirus Characterization of novel monoclonal antibodies against MERScoronavirus spike protein Discovery of hydrocarbon-stapled short α-helical peptides as promising Middle East respiratory syndrome coronavirus (MERS-CoV) fusion inhibitors A systematic review of therapeutic agents for the treatment of the Middle East respiratory syndrome coronavirus (MERS-CoV) Identification of a broad-spectrum antiviral small molecule against severe acute respiratory syndrome coronavirus and Ebola, Hendra, and Nipah viruses by using a novel high-throughput screening assay Current treatment options and the role of peptides as potential therapeutic components for Middle East respiratory syndrome (MERS): a review Cell therapy in acute respiratory distress syndrome Challenges and responses in human vaccine development Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine Expression of B subunit of E. coli heat-labile enterotoxin in the progenies of transgenic tobacco bred by crossing nuclear-and chloroplast-transgenic lines Immunogenicity of an adenoviral-based Middle East respiratory syndrome coronavirus vaccine in BALB/c mice One-Health: a safe, efficient, dual-use vaccine for humans and animals against Middle East respiratory syndrome coronavirus and rabies virus Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation DNA vaccine of SARS-Cov S gene induces antibody response in mice ChAdOx1 and MVA based vaccine candidates against MERS-CoV elicit neutralising antibodies and cellular immune responses in mice An orthopoxvirus-based vaccine reduces virus excretion after MERS-CoV infection in dromedary camels Searching for an ideal vaccine candidate among different MERS coronavirus receptor-binding fragments-the importance of immunofocusing in subunit vaccine design Adenosine deaminase acts as a natural antagonist for dipeptidyl peptidase 4-mediated entry of the Middle East respiratory syndrome coronavirus Inhibition of Middle East respiratory syndrome coronavirus infection by anti-CD26 monoclonal antibody An emerging role of dipeptidyl peptidase 4 (DPP4) beyond glucose control: potential implications in cardiovascular disease Structural modeling of 2019-novel coronavirus (nCoV) spike protein reveals a proteolytically-sensitive activation loop as a distinguishing feature compared to SARS-CoV and related SARS-like coronaviruses Comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against MERS-CoV Disulfiram can inhibit MERS and SARS coronaviruspapain-like proteases via different modes De novo design of α-helical lipopeptides targeting viral fusion proteins: a promising strategy for relatively broad-spectrum antiviral drug discovery Structure-based discovery of Middle East respiratory syndrome coronavirus fusion inhibitor New vaccine technologies to combat outbreak situations Safety and immunogenicity of an anti-Middle East respiratory syndrome coronavirus DNA vaccine: a phase 1, open-label, single-arm, dose-escalation trial A DNA vaccine induces SARS coronavirus neutralization and protective immunity in mice A SARS DNA vaccine induces neutralizing antibody and cellular immune responses in healthy adults in a Phase I clinical trial Potent binding of 2019 novelcoronavirus spike protein by a SARS coronavirus-specific human monoclonalantibody Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association Potent cross-reactive neutralization of SARS coronavirus isolates by human monoclonal antibodies Exceptionally potent neutralizationof Middle East respiratory syndrome coronavirus by human monoclonalantibodies Interaction between heptad repeat 1 and 2 regions inspike protein of SARS-associated coronavirus: implications for virus fusogenic mechanism and identification of fusion inhibitors Fusion mechanism of 2019-nCoV andfusion inhibitors targeting HR1 domain in spike protein The authors gratefully acknowledge the financial support from the National Natural Science Foundation of China (Grant No. 31870836), and the 1.3.5 Project for Disciplines Excellence, West China Hospital, Sichuan University (ZYYC20005 to W.C.). Epidemiology, genetic recombination, and pathogenesis of coronaviruses Origins and evolution of the global RNA virome Classify viruses-the gain is worth the pain Detection of a group 2 coronavirus in dogs with canine infectious respiratory disease Human coronaviruses: what do they cause? Epidemiology and cause of severe acute respiratory syndrome (SARS) in Guangdong, People's Republic of China Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia Ecology, evolution and classification of bat coronaviruses in the aftermath of SARS A pneumonia outbreak associated with a new coronavirus of probable bat origin Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV On the origin and continuing evolution of SARS-CoV-2 Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China Mutations, recombination and insertion in the evolution of 2019-nCoV SARS and MERS: recent insights into emerging coronaviruses Global epidemiology of bat coronaviruses From SARS to MERS, thrusting coronaviruses into the spotlight Challenges presented by MERS corona virus, and SARS corona virus to global health Middle East respiratory syndrome coronavirus: another zoonotic betacoronavirus causing SARS-like disease MERS-CoV as an emerging respiratory illness: a review of prevention methods The Middle East respiratory syndrome (MERS) keywords: ace2; acute; antibodies; binding; cells; coronavirus; cov; cov-2; domain; east; gene; host; human; infection; mers; middle; novel; patients; protein; receptor; s protein; sars; spike; syndrome; syndrome coronavirus; type; vaccine; viruses cache: cord-337825-ujq9mxk7.txt plain text: cord-337825-ujq9mxk7.txt item: #491 of 541 id: cord-338468-c0jv3i1t author: Kanduc, Darja title: From Anti-SARS-CoV-2 Immune Responses to COVID-19 via Molecular Mimicry date: 2020-07-16 words: 4156 flesch: 32 summary: Immunoreactive epitopes present in SARS-CoV-2 were mostly composed of peptide sequences present in human proteins that—when altered, mutated, deficient or, however, improperly functioning—may associate with a wide range of disorders, from respiratory distress to multiple organ failure. Actually, the mere sharing of peptide sequences between pathogens and human proteins might be of little significance whether it remained sterile of cross-reactive autoimmune reactions. keywords: cov-2; cross; epitopes; gene; hexapeptides; immune; mutations; proteins; receptor; sars; sharing; syndrome; table cache: cord-338468-c0jv3i1t.txt plain text: cord-338468-c0jv3i1t.txt item: #492 of 541 id: cord-338485-4zqeq1se author: Aiking, Harry title: The next protein transition() date: 2018-07-27 words: 6837 flesch: 40 summary: Thus, food consumption does not have impacts on human health, exclusively, but huge overall impacts on ecology, economy and society. Livestock in food security Food, livestock production, energy, climate change, and health Meals in science and practice: Interdisciplinary research and business applications The acceptability of the New Nordic Diet by participants in a controlled six-month dietary intervention A circular economy in The Netherlands by 2050-Government-wide programme for a circular economy Guidelines for the new nordic diet Quantitative assessment of political Fragility indices and food prices as indicators of food riots in countries Consumer-orientated development of hybrid beef burger and sausage analogues Environmental impacts of food consumption by dogs and cats Food waste within food supply chains: Quantification and potential for change to 2050 Soil erosion threatens food production Climate change 2014: Impacts, adaptation, and vulnerability. keywords: aiking; animal; boer; change; consumption; diet; food; health; impacts; meat; production; products; protein; transition cache: cord-338485-4zqeq1se.txt plain text: cord-338485-4zqeq1se.txt item: #493 of 541 id: cord-338980-pygykil7 author: Rahaman, Jordon title: Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses date: 2016-11-09 words: 5807 flesch: 45 summary: (C) NSP14, based on PDB id 5C8T A computationally optimized broadly reactive antigen (COBRA) based H5N1 VLP vaccine elicits broadly reactive antibodies in mice and ferrets Computationally optimized antigens to overcome influenza viral diversity Rapid evolution of virus sequences in intrinsically disordered protein regions Molecular pathology of emerging coronavirus infections MRBAYES: Bayesian inference of phylogenetic trees ETE 3: Reconstruction, analysis, and visualization of phylogenomic data Virus taxonomy: classification and nomenclature of viruses: Ninth Report of the International Committee on Taxonomy of Viruses The rapid generation of mutation data matrices from protein sequences MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform Minimization of genetic distances by the consensus, ancestral, and center-of-tree (COT) sequences for HIV-1 variants within an infected individual and the design of reagents to test immune reactivity Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerase-containing protein of all nidoviruses Bayesian model of protein primary sequence for secondary structure prediction Bat-to-human: spike features determining 'host jump' of coronaviruses SARS-CoV, MERS-CoV, and beyond Structural basis and functional analysis of the SARS coronavirus nsp14-nsp10 complex Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior An evaluation of phylogenetic methods for reconstructing transmitted HIV variants using longitudinal clonal HIV sequence data The PSIPRED protein structure prediction server Metagenomics and future perspectives in virus discovery Rapid evolutionary dynamics of structural disorder as a potential driving force for biological divergence in flaviviruses Marked variability in the extent of protein disorder within and between viral families Cross host transmission in the emergence of MERS coronavirus MrBayes 3: Bayesian phylogenetic inference under mixed models Exploring the viral world through metagenomics The evolution of protein structures and structural Ensembles under functional constraint The challenge of protein structure determination-lessons from structural genomics Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human Epidemiology, genetic recombination, and pathogenesis of coronaviruses Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans The DISOPRED server for the prediction of protein disorder Genetic relatedness of the novel human group C betacoronavirus to Tylonycteris bat coronavirus HKU4 and Pipistrellus bat coronavirus HKU5 World Health Organization. Protein sequences were identified by individual BLAST searches with MERS-CoV (Taxonomy ID: 1335626) proteins ORF1ab (YP_009047202.1; polyprotein), S protein (YP_009047204.1), M protein (YP_009047210.1), E protein (YP_009047209.1), and N protein (YP_009047211.1) against coronaviruses. keywords: coronaviruses; cov; disorder; et al; mers; protein; regions; sequence; sites; structure cache: cord-338980-pygykil7.txt plain text: cord-338980-pygykil7.txt item: #494 of 541 id: cord-339091-3xk2w0d2 author: Flower, Darren R title: Computer aided selection of candidate vaccine antigens date: 2010-11-03 words: 10671 flesch: 37 summary: However, rather than look at nucleic acid sequences, or at protein sequences directly, a new approach, based upon alignment-free techniques, has been developed which shows significant potential; we examine this next. In attempting to overcome the limitations imposed by alignment-dependent sequence similarity methods, we have implemented a novel alignment-independent method for antigen identification based on auto cross covariance (ACC) transformation of protein sequences into uniform equal-length vectors. keywords: antigens; approach; binding; cell; database; epitopes; host; identification; immunogenicity; location; methods; mhc; peptides; prediction; properties; protein; sequence; similarity; system; vaccines cache: cord-339091-3xk2w0d2.txt plain text: cord-339091-3xk2w0d2.txt item: #495 of 541 id: cord-339333-7tpnbr8q author: CHEN, YUXIAN title: Comparative serum proteome expression of the steroid-induced femoral head osteonecrosis in adults date: 2014-11-12 words: 3633 flesch: 44 summary: Serum protein samples prepared as described above were diluted 1:25 in Laemmli buffer and resolved by 10% SDS-PAGE (Invitrogen Life Technologies, Carlsbad, CA, USA). The differential expression of serum proteins from patients with SONFH and healthy volunteers was analyzed by the proteomics method. keywords: analysis; head; itih4; patients; protein; samples; serum; sonfh; study cache: cord-339333-7tpnbr8q.txt plain text: cord-339333-7tpnbr8q.txt item: #496 of 541 id: cord-339558-li65qvq9 author: Rana, Rashmi title: A comprehensive overview of proteomics approach for COVID 19: new perspectives in target therapy strategies date: 2020-11-02 words: 5943 flesch: 35 summary: They also developed a computer algorithm that uses multiple classifiers to predict samples from SARS patients and used to predict 206 sera from Chinese fever patients. This protein marker is observed to be elevated in SARS patients as compared to healthy individuals (Yi 2004) . keywords: analysis; coronavirus; cov-2; covid-19; et al; human; mass; patients; protein; proteomics; sars; spectrometry; study cache: cord-339558-li65qvq9.txt plain text: cord-339558-li65qvq9.txt item: #497 of 541 id: cord-340387-ohkjheat author: Wynne, James W. title: Purification and Characterisation of Immunoglobulins from the Australian Black Flying Fox (Pteropus alecto) Using Anti-Fab Affinity Chromatography Reveals the Low Abundance of IgA date: 2013-01-07 words: 7022 flesch: 47 summary: Antiserum generated against P. alecto IgG H showed reactivity to IgG H of the fruit bats P. conspicillatus and, to a lesser extent, Rosettus megaphylus (Fig. 7B, lanes 2 and 3 respectively) . P. alecto bats were captured in southern Queensland, Australia as described previously [35] and transported live by air to the CSIRO Australian Animal Health Laboratory (AAHL). keywords: affinity; alecto; bats; fab; fig; human; iga; igg; igm; immunoglobulin; mucosal; p. alecto; protein; sds; serum cache: cord-340387-ohkjheat.txt plain text: cord-340387-ohkjheat.txt item: #498 of 541 id: cord-340746-icuzy3vp author: Liang, Yunfei title: Comprehensive Antibody Epitope Mapping of the Nucleocapsid Protein of Severe Acute Respiratory Syndrome (SARS) Coronavirus: Insight into the Humoral Immunity of SARS date: 2005-08-01 words: 8439 flesch: 38 summary: This result demonstrates that N protein is one of the immunoreactive coronavirus structural proteins that elicit the specific humoral immune responses in animals. The slides were stained with 0.25 g/L Evans blue in PBS and analyzed with a Leica Eclipse epifluorescence microscope. preparation of n-protein-specific antisera For vaccination, four 6-week-old female BALB/c mice were immunized intradermally with 100 g of purified recombinant N protein in complete Freund's adjuvant emulsion (Sigma) for the first injection on day 0. keywords: acids; amino; antibody; antigenic; cov; cov n; denaturation; epitopes; mabs; n protein; patients; sars; sera; specific; yeast cache: cord-340746-icuzy3vp.txt plain text: cord-340746-icuzy3vp.txt item: #499 of 541 id: cord-341129-eo0vjcmk author: Kielian, Margaret title: Virus membrane-fusion proteins: more than one way to make a hairpin date: 2006 words: 6993 flesch: 35 summary: Membrane fusion Intracellular and viral membrane fusion: a uniting mechanism The many mechanisms of viral membrane fusion proteins How viruses enter animal cells Viral entry On the entry of Semliki Forest virus into BHK-21 cells SFV infection in CHO cells: cell-type specific restrictions to productive virus entry at the cell surface Changes in the conformation of influenza virus hemagglutinin at the pH optimum of virus-mediated membrane fusion Structures and mechanisms in flavivirus fusion HIV-1 entry cofactor: functional cDNA cloning of a seven-transmembrane, G protein-coupled receptor Mechanisms of viral membrane fusion and its inhibition Paramyxovirus fusion: a hypothesis for changes Retroviral entry mediated by receptor priming and low pH triggering of an envelope glycoprotein Sequential roles of receptor binding and low pH in forming prehairpin and hairpin conformations of a retroviral envelope glycoprotein Endosomal proteolysis of the Ebola virus glycoprotein is necessary for infection A spring-loaded mechanism for the conformational change of influenza hemagglutinin Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin Mechanism of membrane fusion by viral envelope proteins Conformational changes in the hemagglutinin of influenza virus which accompany heat-induced fusion of virus with liposomes Influenza hemagglutinin is spring-loaded by a metastable native conformation Structure of the hemagglutinin precursor cleavage site, a determinant of influenza pathogenicity and the origin of the labile conformation Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 Å resolution First structure of a viral membrane-fusion protein First structure of the 'post-fusion' conformation of a viral membrane-fusion protein Evidence that the transition of HIV-1 gp41 into a six-helix bundle, not the bundle configuration, induces membrane fusion First demonstration that class I fusion is driven by hairpin formation Membrane fusion machines of paramyxoviruses: capture of intermediates of fusion Membrane structure and fusion-triggering conformational change of the fusion domain from influenza hemagglutinin Membrane fusion mediated by the influenza virus hemagglutinin requires the concerted action of at least three hemagglutinin trimers Synchronized activation and refolding of influenza hemagglutinin in multimeric fusion machines Influenza hemagglutinins outside of the contact zone are necessary for fusion pore expansion The entry of entry inhibitors: a fusion of science and medicine A synthetic peptide from HIV-1 gp41 is a potent inhibitor of virus-mediated cell-cell fusion Potent suppression of HIV-1 replication in humans by T-20, a peptide inhibitor of gp41-mediated virus entry Targeting a binding pocket within the trimer-of-hairpins: small-molecule inhibition of viral fusion Molecular mechanism underlying the action of a novel fusion inhibitor of influenza A virus Structurebased identification of an inducer of the low-pH conformational change in the influenza virus hemagglutinin: irreversible inhibition of infectivity The fusion glycoprotein shell of Semliki Forest virus: an icosahedral assembly primed for fusogenic activation at endosomal pH Prefusion structure of alphavirus E1 protein, showing unexpected similarity to flavivirus E protein, leading to concept of 'class II' membrane-fusion proteins Membrane fusion process of Semliki Forest virus II: cleavage-dependent reorganization of the spike protein complex controls virus entry Furin processing and proteolytic activation of Semliki Forest virus Proteolytic activation of tick-borne encephalitis virus by furin Cell-associated West Nile flavivirus is covered with E+pre-M protein heterodimers which are destroyed and reorganized by proteolytic cleavage during virus release Budding of alphaviruses A structural perspective of the flavivirus life cycle Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki forest virus Placement of the structural proteins in sindbis virus Structures of immature flavivirus particles First description of mature flavivirus surface organization, showing the striking herringbone arrangement of fusion protein homodimers Visualization of membrane protein domains by cryo-electron microscopy of dengue virus Structure of West Nile virus Crystal structure of the Semliki Forest virus envelope protein E1 in its monomeric conformation: identification of determinants for icosahedral particle formation The envelope glycoprotein from tickborne encephalitis virus at 2 Å resolution A ligand-binding pocket in the dengue virus envelope glycoprotein Variable surface epitopes in the crystal structure of dengue virus type 3 envelope glycoprotein Conformational changes of the flavivirus E glycoprotein Membrane fusion process of Semliki Forest virus I: low pH-induced rearrangement in spike protein quaternary structure precedes virus penetration into cells Membrane fusion of Semliki Forest virus involves homotrimers of the fusion protein References 56 and 57 comprise the first reports of homotrimer formation for a class II fusion protein Oligomeric rearrangement of tickborne encephatitis virus envelope proteins induced by an acidic pH Formation and characterization of the trimeric form of the fusion protein of Semliki Forest virus Role of metastability and acidic pH in membrane fusion by tick-borne encephalitis virus Mechanisms of mutations inhibiting fusion and infection by Semliki Forest virus Mutational evidence for an internal fusion peptide in flavivirus envelope protein E The heterodimeric association between the membrane proteins of Semliki Forest virus changes its sensitivity to low pH during virus maturation Membrane and protein interactions of a soluble form of the Semliki Forest virus fusion protein First demonstration that class II ectodomain can form homotrimer when treated at low pH in presence of target membrane Membrane interactions of the tick-borne encephalitis virus fusion protein E at low pH Purification and crystallization reveal two types of interactions of the fusion protein homotrimer of Semliki Forest virus Characterization of a membraneassociated trimeric low-pH-induced form of the class II viral fusion protein E from tick-borne encephalitis virus and its crystallization Conformational change and protein-protein interactions of the fusion protein of Semliki Forest virus Structure of the dengue virus envelope protein after membrane fusion References 68, 69 and 70 are the first reports of low-pH-induced homotrimer structure of class II fusion proteins Multistep regulation of membrane insertion of the fusion peptide of Semliki Forest virus T20 blocks the interaction of the C-terminal segment of the fusion protein with the groove of the central coiled coil (FIG. 4) , and blocks virus fusion and infection. keywords: class; class ii; fusion; fusion proteins; membrane; membrane fusion; proteins; structure; virus; viruses cache: cord-341129-eo0vjcmk.txt plain text: cord-341129-eo0vjcmk.txt item: #500 of 541 id: cord-341324-f9g9gitn author: Rojas, José M. title: Viral pathogen-induced mechanisms to antagonize mammalian interferon (IFN) signaling pathway date: 2020-10-21 words: 10861 flesch: 35 summary: The measles virus V protein binding site to STAT2 overlaps with that of IRF9 STAT2 is a primary target for measles virus V protein-mediated alpha/ beta interferon signaling inhibition The interferon signaling antagonist function of yellow fever virus NS5 protein is activated by type I interferon Dengue virus co-opts UBR4 to degrade STAT2 and antagonize type I interferon signaling Nonstructural protein 11 of porcine reproductive and respiratory syndrome virus induces STAT2 degradation to inhibit interferon signaling The V protein of simian virus 5 inhibits interferon signalling by targeting STAT1 for proteasome-mediated degradation Association of mumps virus V protein with RACK1 results in dissociation of STAT-1 from the alpha interferon receptor complex The human papillomavirus type 16 E7 protein binds human interferon regulatory factor-9 via a novel PEST domain required for transformation Expression of hepatitis C virus proteins interferes with the antiviral action of interferon independently of PKR-mediated control of protein synthesis Herpes simplex virus 1 gene products occlude the interferon signaling pathway at multiple sites Human cytomegalovirus inhibits IFN-alpha-stimulated antiviral and immunoregulatory responses by blocking multiple levels of IFN-alpha signal transduction The polyoma virus T antigen interferes with interferon-inducible gene expression Foot-and-mouth disease virus leader protease cleaves G3BP1 and G3BP2 and inhibits stress granule formation Stress granule formation induced by measles virus is protein kinase PKR dependent and impaired by RNA adenosine deaminase ADAR1 G3BP1, G3BP2 and CAPRIN1 are required for translation of interferon stimulated mRNAs and are targeted by a dengue virus non-coding RNA Inhibitory activity for the interferoninduced protein kinase is associated with the reovirus serotype 1 sigma 3 protein Site-directed mutagenic analysis of reovirus sigma 3 protein binding to dsRNA Rift Valley fever virus NSs protein functions and the similarity to other bunyavirus NSs proteins RNA-specific adenosine deaminase ADAR1 suppresses measles virus-induced apoptosis and activation of protein kinase PKR Double-stranded RNA deaminase ADAR1 increases host susceptibility to virus infection ADAR1 interacts with PKR during human immunodeficiency virus infection of lymphocytes and contributes to viral replication Silencing the alarms: Innate immune antagonism by rotavirus NSP1 and VP3 Homologous 2',5'-phosphodiesterases from disparate RNA viruses antagonize antiviral innate immunity Rotavirus open cores catalyze 5′-capping and methylation of exogenous RNA: evidence that VP3 is a methyltransferase 2′-O methylation of the viral mRNA cap evades host restriction by IFIT family members Attenuation and restoration of severe acute respiratory syndrome coronavirus mutant lacking 2'-o-methyltransferase activity Biochemical and structural insights into the mechanisms of SARS coronavirus RNA ribose 2'-O-methylation by nsp16/nsp10 protein complex Middle East Respiratory Syndrome Coronavirus Nonstructural Protein 16 Is Necessary for Interferon Resistance and Viral Pathogenesis The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus Interferon induction of IFITM proteins promotes infection by human coronavirus OC43 HIV-1 mutates to evade IFITM1 restriction In vivo evasion of MxA by avian influenza viruses requires human signature in the viral nucleoprotein Irreversible inactivation of ISG15 by a viral leader protease enables alternative infection detection strategies Consecutive inhibition of ISG15 expression and ISGylation by cytomegalovirus regulators The abundant tegument protein pUL25 of human cytomegalovirus prevents proteasomal degradation of pUL26 and supports its suppression of ISGylation Transmembrane protein pUL50 of human cytomegalovirus inhibits ISGylation by downregulating UBE1L ISG15, a ubiquitin-like interferon-stimulated gene, promotes hepatitis C virus production in vitro: implications for chronic infection and response to treatment For instance, Ebola virus VP35 protein, Middle East respiratory syndrome Viral interference with accessory cellular components involved in PRR activation. keywords: activation; activity; binding; cell; degradation; human; ifn; induction; interferon; mechanism; phosphorylation; protease; protein; receptor; recognition; response; rig; rna; signaling; type; viral; virus; viruses cache: cord-341324-f9g9gitn.txt plain text: cord-341324-f9g9gitn.txt item: #501 of 541 id: cord-341378-pw60qx7c author: Armstrong, John title: Sequence and topology of a model intracellular membrane protein, E1 glycoprotein, from a coronavirus date: 1984 words: 1583 flesch: 47 summary: First, in contrast to the majority of membrane proteins, El is known to lack a cleaved 'signal peptide' 9 : the N-terminal region of the sequence contains no good candidate for a cleava3e site 34 • Second, the N-terminal region bears 0-linked sugars 5 ' 36 , which, uniquely among viral proteins so far studied, are the only known post-translational modification to El. Each of the compartments of this transport pathway carries out particular metabolic functions(5–8), and therefore presumably contains a distinct complement of membrane proteins. keywords: cell; membrane; protein; sequence cache: cord-341378-pw60qx7c.txt plain text: cord-341378-pw60qx7c.txt item: #502 of 541 id: cord-341564-fvuwick5 author: Qi, Zhao-Hui title: Novel Method of 3-Dimensional Graphical Representation for Proteins and Its Application date: 2018-06-12 words: 2660 flesch: 50 summary: Novel spectral representation of RNA secondary structure without loss of information Milestones in graphical bioinformatics Four-component spectral representation of DNA sequences Graphical and numerical representations of DNA sequences: statistical aspects of similarity 2D-dynamic representation of DNA sequences Spectral-dynamic representation of DNA sequences 3D-dynamic representation of DNA sequences A group of 3D graphical representation of DNA sequences based on dual nucleotides WITHDRAWN: 2-D graphical representation of proteins based on physico-chemical properties of amino acids ADLD: a novel graphical representation of protein sequences and its application Protein map: an alignment-free sequence comparison method based on various properties of amino acids An efficient numerical method for protein sequences similarity analysis based on a new two-dimensional graphical representation Graphical representation of proteins as four-color maps and their numerical characterization A protein mapping method based on physicochemical properties and dimension reduction The graphical representation of protein sequences based on the physicochemical properties and its applications F-Curve, a graphical representation of protein sequences for similarity analysis based on physicochemical properties of amino acids Analysis of similarity/dissimilarity of protein sequences The genetic code and error transmission In this article, we propose a 3-dimensional graphical representation of protein sequences based on 10 physicochemical properties of 20 amino acids and the BLOSUM62 matrix. keywords: amino; method; protein; representation; sequences; similarity cache: cord-341564-fvuwick5.txt plain text: cord-341564-fvuwick5.txt item: #503 of 541 id: cord-341701-zropd3mo author: Adhikari, Subash title: A high-stringency blueprint of the human proteome date: 2020-10-16 words: 10143 flesch: 20 summary: Provides definitive MS data on 166,174 proteotypic peptides that facilitate the design of multiple, independent assays to quantify most human proteins, numerous splice-variants, non-synonymous mutations Identification and validation of human missing proteins and peptides in public proteome databases: data mining strategy Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry A human protein atlas for normal and cancer tissues based on antibody proteomics Spatial proteomics: a powerful discovery tool for cell biology Getting to know the neighborhood: using proximity-dependent biotinylation to characterize protein complexes and map organelles Antibodypedia, a portal for sharing antibody and antigen validation data Towards a knowledge-based human protein atlas A genome-wide transcriptomic analysis of protein-coding genes in human blood cells An atlas of the protein-coding genes in the human, pig, and mouse brain A subcellular map of the human proteome A pathology atlas of the human cancer transcriptome An atlas of human metabolism First of many encyclopedic HPA atlases that map the spatio-temporal expression human proteome based on integrated multi-omics data involving quantitative transcriptomics and Finally, the book of life and instructions for navigating it Metrics for the human proteome project 2013-2014 and strategies for finding missing proteins Standard guidelines for the chromosome-centric human proteome project A first step toward completion of a genome-wide characterization of the human proteome 2019 annual HPP metrics publication (NeXtProt 2019-01-11) reporting progress in credibly identifying and characterising the human proteome Details current high-stringency MS guidelines criteria used by the HPP for PE1 status (evidence for protein existence), where only protein entries with two or more neXtProt uniquely-mapping, non-nested peptides with length 9 amino acids or greater are deemed to have sufficient evidence Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics The neXtProt peptide uniqueness checker: a tool for the proteomics community Looking for missing proteins in the proteome of human spermatozoa: an update On the proper use of mass accuracy in proteomics Precision proteomics: the case for high resolution and high mass accuracy Human proteome project mass spectrometry data interpretation guidelines 2.1 The FAIR guiding principles for scientific data management and stewardship A draft map of the human proteome Mass-spectrometry-based draft of the human proteome Analyzing the first drafts of the human proteome Flexible and fast mapping of peptides to a proteome with ProteoMapper The chromosome-centric human proteome project for cataloging proteins encoded in the genome Advances in the chromosome-centric human proteome project: looking to the future Launching the C-HPP neXt-CP50 pilot project for functional characterization of identified proteins with no known function Human liver proteome project: plan, progress, and perspectives A cell-type-resolved liver proteome Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma Integrated multiomics example (proteome, phosphoproteome, transcriptome, and whole-exome sequencing) analyses leading to clinical outcomes, performed on 103 lung adenocarcinomas, revealing many cancer-associated features (e.g., tumourassociated variants, patient clinical outcome correlation with EGFR or TP53 mutational status, proteomic stratification of lung cancer subtypes and potential drug targets Proteome-wide profiling of activated transcription factors with a concatenated tandem array of transcription factor response elements A region-resolved mucosa proteome of the human stomach Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens The immunopeptidomic landscape of ovarian carcinomas Precision profiling of the cardiovascular post-translationally modified proteome: where there is a will, there is a way In vivo phosphoproteome analysis reveals kinome reprogramming in hepatocellular carcinoma Protein s-nitrosylation controls glycogen synthase kinase 3β function independent of its phosphorylation state Generation and verification of a compendium of highly specific SRM assays that enable quantification of >95% of all annotated human proteins. keywords: analysis; assays; atlas; biology; cancer; cell; chr; community; data; detection; disease; entries; fig; genome; hpp; human; identification; infection; mass; nextprot; pe1; protein; proteome; proteomics; sars; spectrometry; stringency cache: cord-341701-zropd3mo.txt plain text: cord-341701-zropd3mo.txt item: #504 of 541 id: cord-342118-fsmuqktd author: Dyakov, Ilya N. title: FN3 protein fragment containing two type III fibronectin domains from B. longum GT15 binds to human tumor necrosis factor alpha in vitro date: 2020-08-06 words: 2460 flesch: 46 summary: The use of anti-inflammatory drugs in the treatment 611 of people with severe coronavirus disease 2019 (COVID-19): The Perspectives of 612 clinical immunologists from China Specific interaction of FN3 protein with cytokines. key: cord-342118-fsmuqktd authors: Dyakov, Ilya N.; Mavletova, Dilara A.; Chernyshova, Irina N.; Snegireva, Nadezda A.; Gavrilova, Marina V.; Bushkova, Kristina K.; Dyachkova, Marina S.; Alekseeva, Maria G.; Danilenko, Valery N. title: FN3 protein fragment containing two type III fibronectin domains from B. longum GT15 binds to human tumor necrosis factor alpha in vitro date: 2020-08-06 journal: Anaerobe DOI: 10.1016/j.anaerobe.2020.102247 sha: doc_id: 342118 cord_uid: fsmuqktd Most species of the genus Bifidobacterium contain the gene cluster PFNA, which is presumably involved in the species-specific communication between bacteria and their hosts. keywords: antibodies; cytokines; fn3; protein; specific cache: cord-342118-fsmuqktd.txt plain text: cord-342118-fsmuqktd.txt item: #505 of 541 id: cord-342189-ya05m58o author: Banerjee, Abhik K. title: SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses date: 2020-10-08 words: 11499 flesch: 45 summary: Because viral membrane proteins also require trafficking to the ER, viral disruption of SRP might negatively impact viral propagation, unless viral proteins are trafficked in an SRP-independent manner ( Figure S7E ) or if NSP8/9 selectively impacts host (but not viral) proteins. Understanding the interactions between viral proteins and components of human cells is essential for elucidating their pathogenic mechanisms and for development of effective therapeutics. keywords: binding; cells; cov-2; et al; expression; figure; gene; gfp; host; human; ifn; infection; membrane; mrna; nsp1; protein; ribosome; rna; sars; splicing; srp; translation cache: cord-342189-ya05m58o.txt plain text: cord-342189-ya05m58o.txt item: #506 of 541 id: cord-342634-4ouhdjsr author: Semrad, Katharina title: Proteins with RNA Chaperone Activity: A World of Diverse Proteins with a Common Task—Impediment of RNA Misfolding date: 2010-12-26 words: 7147 flesch: 46 summary: RNA chaperones and the RNA folding problem A DEAD-Box protein functions as an ATP-dependent RNA chaperone in group I intron splicing Escherichia coli proteins, including ribosomal protein S12, facilitate in vitro splicing of phage T4 introns by acting as RNA chaperones Escherichia coli protein StpA stimulates self-splicing by promoting RNA assembly in vitro RNA chaperone activity and RNA-binding properties of the E. coli protein StpA Spectroscopic observation of RNA chaperone activities of Hfq in post-transcriptional regulation by a small non-coding RNA Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator Geometric nomenclature and classification of RNA base pairs RNA tertiary interactions in the large ribosomal subunit: the A-minor motif Two interconvertible forms of tryptophanyl sRNA in E. coli Native and renatured transfer ribonucleic acid A ribosomal function is necessary for efficient splicing of the T4 phage thymidylate synthase intron in vivo Alternative secondary structures in the 5 exon affect both forward and reverse self-splicing of the Tetrahymena intervening sequence RNA A tyrosyl-tRNA synthetase recognizes a conserved tRNA-like structural motif in the group I intron catalytic core Domain structure and RNA annealing activity of the Escherichia coli regulatory protein StpA RNA annealing activities in HeLa nuclei HIV-1 nucleocapsid protein as a nucleic acid chaperone: spectroscopic study of its helix-destabilizing properties, structural binding specificity, and annealing activity Coupling RNA annealing and strand displacement: a FRET-based microplate reader assay for RNA chaperone activity Dissecting RNA chaperone activity An RNA chaperone activity of non-specific RNA binding proteins in hammerhead ribozyme catalysis RNA chaperone activity of large ribosomal subunit proteins from Escherichia coli RNA chaperone activity of protein components of human Ro RNPs Assaying RNA chaperone activity in vivo in bacteria using a ribozyme folding trap Escherichia coli CspA-family RNA chaperones are transcription antiterminators Transcription antitermination by translation initiation factor IF1 Assay of transcription antitermination by proteins of the CspA family RNA chaperones, RNA annealers and RNA helicases Protein enhancement of hammerhead ribozyme catalysis Identification and characterization of the RNA chaperone activity of hepatitis delta antigen peptides The hepatitis C virus Core protein is a potent nucleic acid chaperone that directs dimerization of the viral (+) strand RNA in vitro RNA chaperoning and intrinsic disorder in the core proteins of Flaviviridae Role of RNA chaperones in virus replication Coronavirus nucleocapsid protein is an RNA chaperone Coronavirus nucleocapsid protein facilitates template switching and is required for efficient transcription Assaying RNA chaperone activity in vivo using a novel RNA folding trap Assays for the RNA chaperone activity of proteins RNA chaperone StpA loosens interactions of the tertiary structure in the td group I intron in vivo The role of structural disorder in the function of RNA and protein chaperones How common are extraribosomal functions of ribosomal proteins? Recently, it was demonstrated that E. coli ribosomal proteins L15, L16, L18, and L19, that showed RNA chaperone activity in vitro, further possess protein chaperone activity comparable to other protein chaperones such as Hsp90 [43] . keywords: activity; annealing; assay; chaperone; chaperone activity; folding; group; intron; proteins; ribosomal; rna; splicing; structure; vivo cache: cord-342634-4ouhdjsr.txt plain text: cord-342634-4ouhdjsr.txt item: #507 of 541 id: cord-342639-vf9n2vf9 author: Chang, Chung-ke title: Transient Oligomerization of the SARS-CoV N Protein – Implication for Virus Ribonucleoprotein Packaging date: 2013-05-23 words: 5393 flesch: 36 summary: The data is consistent with the helical oligomer packing model of N protein observed in crystal. These results qualitatively suggest that the CTD of SARS-CoV N protein is capable of transient self-association through the oligomer interface identified in the crystal structure. keywords: coronavirus; cov; ctd; disulfide; n protein; nucleocapsid; oligomerization; protein; rna; sars; structure cache: cord-342639-vf9n2vf9.txt plain text: cord-342639-vf9n2vf9.txt item: #508 of 541 id: cord-342756-rgm9ffpk author: Senger, Mario Roberto title: COVID-19: molecular targets, drug repurposing and new avenues for drug discovery date: 2020-10-02 words: 16157 flesch: 39 summary: Structure-based virtual screening and molecular dynamics simulation of SARS-CoV-2 Guanine-N7 methyltransferase (nsp14) for identifying antiviral inhibitors against COVID-19 Virtual screening, ADME/T, and binding free energy analysis of anti-viral, anti-protease, and anti-infectious compounds against NSP10/ NSP16 methyltransferase and main protease of SARS CoV-2 Targeting SARS-COV-2 non-structural protein 16: a virtual drug repurposing study Ready, set, fuse! (148) Other targets -Apart from SARS-CoVs infection, some relevant molecular targets of other viral diseases and host metabolism have also been investigated in COVID-19 drug discovery, such as viral neuraminidases and the DPP4 cell receptor. keywords: ace2; activity; cells; coronavirus; cov-2; covid-19; disease; drug; fig; host; human; infection; inhibitors; lopinavir; mers; new; patent; patients; potential; protease; protein; remdesivir; replication; repurposing; ritonavir; rna; sars; structure; studies; syndrome; target; treatment; trials cache: cord-342756-rgm9ffpk.txt plain text: cord-342756-rgm9ffpk.txt item: #509 of 541 id: cord-343791-0vykwml5 author: Hainline, Kelly M. title: Progress towards the clinical translation of bio-inspired peptide and protein assemblies date: 2017-11-08 words: 7324 flesch: 38 summary: [11] Since then, fibrillar peptide amphiphile materials have been explored in a broad range of medical applications ranging between wound healing, [97] bone healing, [98] the delivery of proteins, [99] nervous tissue repair, [100] and others. The immunogenic features of peptide assemblies are advantageous for the development of synthetic vaccines and other engineered immunotherapies, a topic which has been recently reviewed by our group and others, [1, 2, 5, 82, 83] but it is also important to note for other assemblies containing high densities of protein or peptide ligands/epitopes that such multivalent displays may induce unwanted immune responses. keywords: applications; cell; delivery; design; development; hpv; materials; peptide; platforms; protein; range; self; use; vaccine; virus; vlps cache: cord-343791-0vykwml5.txt plain text: cord-343791-0vykwml5.txt item: #510 of 541 id: cord-345088-krb1eidw author: Shen, S title: A single amino acid mutation in the spike protein of coronavirus infectious bronchitis virus hampers its maturation and incorporation into virions at the nonpermissive temperature date: 2004-09-01 words: 6978 flesch: 47 summary: Although S protein is dispensable for the formation of virus-like-particles (VLPs), its incorporation into virion is critical to the assembly of infectious virus particles. A portion of S protein might be transported to the plasma membrane and responsible for the cell-to-cell membrane fusion, resulting in the formation of typical syncycia and spread of virus infection to neighboring cells. keywords: cells; mutant; protein; s protein; temperature; virus cache: cord-345088-krb1eidw.txt plain text: cord-345088-krb1eidw.txt item: #511 of 541 id: cord-345712-gmzue6lj author: Palazzo, Luca title: ADP‐ribosylation: new facets of an ancient modification date: 2017-04-26 words: 6656 flesch: 37 summary: Eight of them are uncharacterized DraG homologues and three are macrodomain proteins representing three different classes within the macrodomain superfamily ( Table 1) . and counting Structures and mechanisms of enzymes employed in the synthesis and degradation of PARP-dependent protein ADP-ribosylation Functional aspects of protein mono-ADP-ribosylation PARP16 is a tail-anchored endoplasmic reticulum protein required for the PERKand IRE1a-mediated unfolded protein response Tankyrase-1 polymerization of poly(ADP-ribose) is required for spindle structure and function Poly(ADP-ribose) regulates stress responses and microRNA activity in the cytoplasm PARP-1 inhibition increases mitochondrial metabolism through SIRT1 activation PARP-2 regulates SIRT1 expression and whole-body energy expenditure PARP-1 mechanisms for coupling DNA damage detection to poly(ADP-ribose) synthesis Expanding functions of intracellular resident mono-ADPribosylation in cell physiology ATM controls proper mitotic spindle structure Poly(ADP-ribosyl)ation in regulation of chromatin structure and the DNA damage response Biology of poly(ADP-ribose) polymerases: the factotums of cell maintenance The family of toxin-related ecto-ADPribosyltransferases in humans and the mouse NAD-induced T cell death: ADP-ribosylation of cell surface proteins by ART2 activates the cytolytic P2X7 purinoceptor Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins NAD⁺ in aging, metabolism, and neurodegeneration The human sirtuin family: evolutionary divergences and functions Sirtuins in mammals: insights into their biological function The substrate specificity of sirtuins Identification of a class of protein ADP-ribosylating sirtuins in microbial pathogens Glycation and glycoxidation of histones by ADP-ribose New readers and interpretations of poly(ADP-ribosyl) ation The macro domain is an ADP-ribose binding module Macrodomain-containing proteins: regulating new intracellular functions of mono(ADP-ribosyl)ation Macrodomains: structure, function, evolution, and catalytic activities Identification of macrodomain proteins as novel O-acetyl-ADPribose deacetylases The SARS-unique domain (SUD) of SARS coronavirus contains two macrodomains that bind G-quadruplexes Differential activities of cellular and viral macro domain proteins in binding of ADP-ribose metabolites Visualization of poly(ADPribose) bound to PARG reveals inherent balance between exo-and endo-glycohydrolase activities Deficiency of terminal ADP-ribose protein glycohydrolase TARG1/C6orf130 in neurodegenerative disease ATM induces MacroD2 nuclear export upon DNA damage Structural basis of severe acute respiratory syndrome coronavirus ADP-ribose-1″-phosphate dephosphorylation by a conserved domain of nsP3 Poly(ADP-ribose)-binding zinc finger motifs in DNA repair/checkpoint proteins Recognition of the iso-ADP-ribose moiety in poly(ADP-ribose) by WWE domains suggests a general mechanism for poly(ADPribosyl)ation-dependent ubiquitination The oligonucleotide/oligosaccharide-binding fold motif is a poly(ADP-ribose)-binding domain that mediates DNA damage response Poly(ADP-ribose) binds to specific domains in DNA damage checkpoint proteins The recognition and removal of cellular poly(ADP-ribose) signals Regulation of nitrogenase by reversible mono-ADPribosylation Mechanism of ADP-ribosylation removal revealed by the structure and ligand complexes of the dimanganese mono-ADP-ribosylhydrolase DraG A family of macrodomain proteins reverses cellular mono-ADPribosylation Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases Preferential perinuclear localization of poly(ADP-ribose) glycohydrolase Human poly(ADP-ribose) glycohydrolase is expressed in alternative splice variants yielding isoforms that localize to different cell compartments ADPribosylhydrolase 3 (ARH3), not poly(ADP-ribose) glycohydrolase (PARG) isoforms, is responsible for degradation of mitochondrial matrix-associated poly (ADP-ribose) Orphan macrodomain protein (human C6orf130) is an O-acyl-ADP-ribose deacylase: solution structure and catalytic properties A highly specific phosphatase that acts on ADP-ribose 1″-phosphate, a metabolite of tRNA splicing in Saccharomyces cerevisiae ADP-ribosylation, a mechanism regulating nitrogenase activity Enhanced sensitivity to cholera toxin in ADP-ribosylarginine hydrolase-deficient mice The structure of human ADP-ribosylhydrolase 3 (ARH3) provides insights into the reversibility of protein ADP-ribosylation Identification and characterization of a mammalian 39-kDa poly(ADPribose) glycohydrolase Sequence and structural links between distant ADP-ribosyltransferase families ARTC1-mediated ADPribosylation of GRP78/BiP: a new player in endoplasmic-reticulum stress responses Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites Proteome-wide identification of the endogenous ADPribosylome of mammalian cells and tissue Structure and function of the ARH family of ADP-ribosyl-acceptor hydrolases The 39-kDa poly(ADP-ribose) glycohydrolase ARH3 ribose, a product of the Sir2 family of acetyl-histone deacetylases Hydrolysis of O-acetyl-ADP-ribose isomers by ADPribosylhydrolase 3 Structures and mechanisms of Nudix hydrolases The Nudix hydrolase superfamily ADP-ribose-derived nuclear ATP synthesis by NUDIX5 is required for chromatin remodeling Nucleotide pyrophosphatases/ phosphodiesterases on the move Processing of protein ADP-ribosylation by Nudix hydrolases Nudix hydrolases degrade protein-conjugated ADP-ribose Leung AK & Ahel I (2016) keywords: activity; adp; adpr; damage; dna; enzymes; fig; macrodomain; mono; parps; poly(adp; proteins; regulation; response; ribose; ribosylation; streptomyces cache: cord-345712-gmzue6lj.txt plain text: cord-345712-gmzue6lj.txt item: #512 of 541 id: cord-346314-o9fjpqaj author: Jarboui, Mohamed Ali title: Nucleolar Protein Trafficking in Response to HIV-1 Tat: Rewiring the Nucleolus date: 2012-11-15 words: 10059 flesch: 29 summary: The proteasome regulates HIV-1 transcription by both proteolytic and nonproteolytic mechanisms Oncogenic activity of MCM7 transforming cluster Unzipped and loaded: the role of DNA helicases and RFC clamp-loading complexes in sister chromatid cohesion The XRCC genes: expanding roles in DNA double-strand break repair Role of the non-homologous DNA end joining pathway in the early steps of retroviral infection Lupus autoantigen Ku protein binds HIV-1 TAR RNA in vitro Effect of Ku80 depletion on the preintegrative steps of HIV-1 replication in human cells Identification of cellular cofactors for human immunodeficiency virus replication via a ribozyme-based genomics approach siRNA screening of a targeted library of DNA repair factors in HIV infection reveals a role for base excision repair in HIV integration The dynamics of HMG proteinchromatin interactions in living cells Retroviral cDNA integration: stimulation by HMG I family proteins HIV-1 cDNA integration: requirement of HMG I(Y) protein for function of preintegration complexes in vitro Activity of the human immunodeficiency virus type 1 cell cycle-dependent internal ribosomal entry site is modulated by IRES trans-acting factors Fuel feeds function: energy metabolism and the T-cell response Human immunodeficiency virus type 1, human protein interaction database at NCBI Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems The biological context of HIV-1 host interactions reveals subtle insights into a system hijack HIVhost interactions: a map of viral perturbation of the host system Cataloguing the HIV type 1 human protein interaction network Retroviral proteomics and interactomes: intricate balances of cell survival and viral replication Dual role of host cell factors in HIV-1 replication: restriction and enhancement of the viral cycle Decoding the multifaceted HIV-1 virus-host interactome Functions of Tat: the versatile protein of human immunodeficiency virus type 1 Chromatin dynamics associated with HIV-1 Tat-activated transcription Modifications in host cell cytoskeleton structure and function mediated by intracellular HIV-1 Tat protein are greatly dependent on the second coding exon Pathway analysis in HEK 293T cells overexpressing HIV-1 tat and nucleocapsid Expression profiles and pathway analysis in HEK 293 T cells overexpressing HIV-1 Tat and nucleocapsid using cDNA microarray Proliferative activity of extracellular HIV-1 Tat protein in human epithelial cells: expression profile of pathogenetically relevant genes Proteomics analysis of human astrocytes expressing the HIV protein Tat HIV-1 Tat reprograms immature dendritic cells to express chemoattractants for activated T cells and macrophages Gene expression profile of HIV-1 Tat expressing cells: a close interplay between proliferative and differentiation signals Modifications in the human T cell proteome induced by intracellular HIV-1 Tat protein expression Cell-type-specific proteome and interactome: using HIV-1 Tat as a test case Differentially expressed genes in HIV-1 tat-expressing CD4(+) T-cell line HIV-1 Tat assembles a multifunctional transcription elongation complex and stably associates with the 7SK snRNP The histone chaperone protein Nucleosome Assembly Protein-1 (hNAP-1) binds HIV-1 Tat and promotes viral transcription Genome-wide binding map of the HIV-1 Tat protein to the human genome Jurkat T cells and development of the T-cell receptor signalling paradigm Global survey of human T leukemic cells by integrating proteomics and transcriptomics profiling A genome-wide short hairpin RNA screening of jurkat T-cells for human proteins contributing to productive HIV-1 replication Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity DEDD and DEDD2 associate with caspase-8/10 and signal cell death Chaperones and multitasking proteins in the nucleolus: networking together for survival? Protein B23 is an important human factor for the nucleolar localization of the human immunodeficiency virus protein Tat Spatial association of HIV-1 tat protein and the nucleolar transport protein B23 in stably transfected Jurkat T-cells Specific complex of human immunodeficiency virus type 1 rev and nucleolar B23 proteins: dissociation by the Rev response element Effects of a highly basic region of human immunodeficiency virus Tat protein on nucleolar localization A region of basic amino-acid cluster in HIV-1 Tat protein is essential for trans-acting activity and nucleolar localization Intracellular trafficking and interactions of the HIV-1 Tat protein Phosphatidylinositol-(4,5)-bisphosphate enables efficient secretion of HIV-1 Tat by infected T-cells The ins and outs of HIV-1 Tat Tuning the transport properties of HIV-1 Tat arginine-rich motif in living cells In vivo study of HIV-1 Tat arginine-rich motif unveils its transport properties Direct interaction of the human I-mfa domain-containing protein Tat results in cytoplasmic sequestration and control of Tat activity The arginine-rich domains present in human immunodeficiency virus type 1 Tat and Rev function as direct importin betadependent nuclear localization signals The HIV-1 Tat nuclear localization sequence confers novel nuclear import properties Global enhancement of nuclear localization-dependent nuclear transport in transformed cells Intermolecular masking of the HIV-1 Rev NLS by the cellular protein HIC: novel insights into the regulation of Rev nuclear import Nuclear Factor 90, a cellular dsRNA binding protein inhibits the HIV Rev-export function Functional analysis of the interaction of the human immunodeficiency virus type 1 Rev nuclear export signal with its cofactors The ins and outs of HIV Rev The HIV-1 Rev protein The specificity of the CRM1-Rev nuclear export signal interaction is mediated by RanGTP Requirement of DDX3 DEAD box RNA helicase for HIV-1 Rev-RRE export function Mechanisms of receptor-mediated nuclear import and nuclear export The nuclear pore component Nup358 promotes transportin-dependent nuclear import A nucleolar TAR decoy inhibitor of HIV-1 replication Ribozyme-mediated inhibition of HIV 1 suggests nucleolar trafficking of HIV-1 RNA Constitutive expression of HIV-1 tat protein in human Jurkat T cells using a BK virus vector Gautier VW Proteomic profiling of the human T-cell nucleolus keywords: abundance; analysis; anti; cells; enrichment; expression; figure; fold; gene; human; jurkat; nuclear; nucleolar; nucleolus; pathway; proteins; replication; ribosomal; rna; tap; tat; tat expression; tat protein; virus cache: cord-346314-o9fjpqaj.txt plain text: cord-346314-o9fjpqaj.txt item: #513 of 541 id: cord-346819-11fkgzaa author: Khan, Mohd Imran title: Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight date: 2020-09-03 words: 4408 flesch: 48 summary: In this study, we have made an attempt to investigate the SARS-CoV-2 genome reported from 13 different countries, identification of mutations in major coronavirus proteins of these different SARS-CoV-2 genomes and compared with SARS-CoV. These thirteen complete genome sequences of SARS-CoV-2 showed high identity (>99%) to each other, while they shared 82% identity with SARS-CoV. Here, we performed a very systematic mutational analysis of SARS-CoV-2 genomes from different geographical locations, which enabled us to identify numerous unique features of this viral genome. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL (pro)) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates Structure of M(pro) from COVID-19 virus and discovery of its inhibitors Structure of the RNA-dependent RNA polymerase from COVID-19 virus Structure of SARS coronavirus spike receptor-binding domain complexed with receptor Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding Insight into the effect of inhibitor resistant S130G mutant on physico-chemical properties of SHV type beta-lactamase: a molecular dynamics study Comparative analysis of complete genome sequences of three avian coronaviruses reveals a novel group 3c coronavirus Identification of a novel coronavirus from a beluga whale by using a panviral microarray Coronavirus genomics and bioinformatics analysis COVID-2019: The role of the nsp2 and nsp3 in its pathogenesis The establishment of reference sequence for SARS-CoV-2 and variation analysis Characterization of the receptor-binding domain (RBD) of 2019 novel coronavirus: implication for development of RBD protein as a viral attachment inhibitor and vaccine The spike protein of SARS-CoV-a target for vaccine and therapeutic development Angiotensin-converting enzyme 2: a functional receptor for SARS coronavirus Can one predict protein stability? keywords: amino; analysis; coronavirus; cov; genome; mpro; mutation; protein; rna; sars; spike cache: cord-346819-11fkgzaa.txt plain text: cord-346819-11fkgzaa.txt item: #514 of 541 id: cord-346916-jj4l9ydl author: Girardi, Erika title: Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell date: 2020-08-23 words: 13150 flesch: 37 summary: genomic RNA Protein kinase r degradation is essential for rift valley fever virus infection and is regulated by SKP1-CUL1-F-box (SCF)FBXW11-NSs E3 ligase Viral encounters with 2',5'-oligoadenylate synthetase and RNase L during the interferon antiviral response New insights into the role of RNase L in innate immunity Molecular mechanisms for the adaptive switching between the OAS/RNase l and OASL/RIG-I pathways in birds and mammals Homologous 2',5'-phosphodiesterases from disparate RNA viruses antagonize antiviral innate immunity Attacked from all sides: RNA decay in antiviral defense The host nonsense-mediated mRNA decay pathway restricts Mammalian RNA virus replication Competing and noncompeting activities of miR-122 and the 5' exonuclease Xrn1 in regulation of hepatitis C virus replication Stabilization of hepatitis C virus RNA by an Ago2-miR-122 complex Zika virus produces noncoding RNAs using a multipseudoknot structure that confounds a cellular exonuclease The structural basis of pathogenic subgenomic flavivirus RNA (sfRNA) production RNA structures that resist degradation by Xrn1 produce a pathogenic Dengue virus RNA Full genome sequence and sfRNA interferon antagonist activity of zika virus from Recife, Brazil RNA structures required for production of subgenomic flavivirus RNA Dengue subgenomic RNA binds TRIM25 to inhibit interferon expression for epidemiological fitness A noncoding RNA produced by arthropod-borne flaviviruses inhibits the cellular exoribonuclease XRN1 and alters host mRNA stability A highly structured, nuclease-resistant, noncoding RNA produced by flaviviruses is required for pathogenicity An RNA pseudoknot is required for production of yellow fever virus subgenomic RNA by the host nuclease XRN1 Zika virus noncoding RNA suppresses apoptosis and is required for virus transmission by mosquitoes Noncoding flavivirus RNA displays RNA interference suppressor activity in insect and mammalian cells Viruses: overturning RNA turnover Stem-loop recognition by DDX17 facilitates miRNA processing and antiviral defense The zinc-finger antiviral protein recruits the RNA processing exosome to degrade the target mRNA CG dinucleotide suppression enables antiviral defence targeting non-self RNA KHNYN is essential for the zinc finger antiviral protein (ZAP) to restrict HIV-1 containing clustered CpG dinucleotides ZAP's stress granule localization is correlated with its antiviral activity and induced by virus replication RNA-binding activity of TRIM25 is mediated by its PRY/ SPRY domain and is required for ubiquitination TRIM25 enhances the antiviral action of zinc-finger antiviral protein (ZAP) MCPIP1 ribonuclease exhibits broad-spectrum antiviral effects through viral RNA binding and degradation MCPIP1 suppresses hepatitis C virus replication and negatively regulates virus-induced proinflammatory cytokine responses RNase L releases a small RNA from HCV RNA that refolds into a potent PAMP Activation and evasion of the antiviral 2'-5' oligoadenylate synthetase/ribonuclease L pathway by hepatitis C virus mRNA Essential function in vivo for Dicer-2 in host defense against RNA viruses in drosophila Cross-species comparative analysis of Dicer proteins during Sindbis virus infection RNA interference functions as an antiviral immunity mechanism in mammals Antiviral RNA interference in mammalian cells Flavivirus induces and antagonizes antiviral RNA interference in both mammals and mosquitoes The evolution of antiviral defense systems Human virus-derived small RNAs can confer antiviral immunity in mammals Induction and suppression of antiviral RNA interference by influenza A virus in mammalian cells Viruses and RNA interference: issues and controversies No evidence for viral small RNA production and antiviral function of Argonaute 2 in human cells RNase III nucleases from diverse kingdoms serve as antiviral effectors Making the mark: the role of adenosine modifications in the life cycle of RNA viruses Innate immune restriction and antagonism of viral RNA lacking 2‫-׳‬O methylation RNA modifications: what have we learned and where are we headed? Host factors in positive-strand RNA virus genome replication Human host factors required for influenza virus replication Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens Diverse roles of host RNA binding proteins in RNA virus replication CRISPR-Cas immunity in prokaryotes Antiviral immunity directed by small RNAs Combating emerging viral threats The global distribution and burden of dengue Virus: new clinical syndromes and its emergence in the western hemisphere Emergence of a novel human coronavirus threatening human health Sensing of RNA viruses: a review of innate immune receptors involved in recognizing RNA virus invasion The innate antiviral response in animals: an evolutionary perspective from flagellates to humans Discriminating self from non-self in nucleic acid sensing Toll-like receptor control of the adaptive immune responses Toll-like receptors in antiviral innate immunity Innate antiviral responses by means of TLR7-mediated recognition of single-stranded RNA Species-specific recognition of single-stranded RNA via toll-like receptor 7 and 8 Toll-like receptor 3 is an essential component of the innate stress response in virus-induced cardiac injury Human TLR3 recognizes dengue virus and modulates viral replication in vitro Zika virus depletes neural progenitors in human cerebral organoids through activation of the innate immune receptor TLR3 Toll-like receptor 3 in viral pathogenesis: friend or foe? RIG-I-like receptors: their regulation and roles in RNA sensing 5'-Triphosphate RNA is the ligand for RIG-I RIG-I-mediated antiviral responses to single-stranded RNA bearing 5'-phosphates Recognition of 5' triphosphate by RIG-I helicase requires short blunt double-stranded RNA as contained in panhandle of negative-strand virus 5'-triphosphate RNA requires base-paired structures to activate antiviral signaling via RIG-I Processing of genome 5' termini as a strategy of negative-strand RNA viruses to avoid RIG-I-dependent interferon induction Differential roles of MDA5 and RIG-I helicases in the recognition of RNA viruses Cell type-specific involvement of RIG-I in antiviral response RIG-I recognizes the 5' region of dengue and Zika virus genomes Balancing act: MDA5 in Antiviral Immunity and Autoinflammation MDA5 assembles into a polar helical filament on dsRNA Enterovirus 2Apro targets MDA5 and MAVS in infected cells MDA5 detects the double-stranded RNA replicative form in picornavirus-infected cells How flaviviruses activate and suppress the interferon response MDA5 is critical to host defense during infection with murine coronavirus LGP2 is a positive regulator of RIG-I-and MDA5-mediated antiviral responses The RNA helicase Lgp2 inhibits TLR-independent sensing of viral replication by retinoic acid-inducible gene-I Loss of DExD/H box RNA helicase LGP2 manifests disparate antiviral responses The RIG-I-like receptor LGP2 inhibits Dicer-dependent processing of long double-stranded RNA and blocks RNA interference in mammalian cells DEAD-box helicases: sensors, regulators, and effectors for antiviral defense Type 1 interferons and the virus-host relationship: a lesson in détente Interferon-inducible antiviral effectors Involvement of the interferon-regulated antiviral proteins PKR and RNase L in reovirus-induced shutoff of cellular translation Doublestranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses RNA dimerization promotes PKR dimerization and activation Viral double-stranded RNAs from vaccinia virus early or intermediate gene transcripts possess PKR activating function, resulting in NF-kappaB activation, when the K1 protein is absent or mutated Regulation of innate immunity through RNA structure and the protein kinase PKR Translational control in virus-infected cells A cap-to-Tail guide to mRNA translation strategies in virus-infected cells Viral noncoding RNAs: more surprises Inhibition of the protein kinase PKR by the internal ribosome entry site of hepatitis C virus keywords: antiviral; binding; cap; cells; cellular; dsrna; factors; fig; host; infection; initiation; interactions; mrna; pkr; protein; rbps; replication; ribosome; rig; rna; rnas; translation; viral; virus; viruses; vrna cache: cord-346916-jj4l9ydl.txt plain text: cord-346916-jj4l9ydl.txt item: #515 of 541 id: cord-346965-0oq2n0af author: Liu, Zhi-Ping title: Bridging protein local structures and protein functions date: 2008-04-18 words: 14492 flesch: 38 summary: Supplement 4: corrections and additions Kernel-based machine learning protocol for predicting DNA-binding proteins Inferring functional relationships of proteins from local sequence and spatial surface patterns CASTp: computed atlas of surface topography of proteins pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins Protein surface analysis for function annotation in high-throughput structural genomics pipeline Statistical analysis and prediction of protein-protein interfaces Flu virus proton channel analyzed: structures of key surface protein suggest different drug mechanisms Insights into protein-protein interfaces using a Bayesian network prediction method A tour of structural genomics Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces Identify catalytic triads of serine hydrolases by support vector machines The gene ontology annotation (GOA) database: sharing knowledge in Uniprot with gene ontology Ligand binding: functional site location, similarity and docking Predicting functionally important residues from sequence conservation Analysis and prediction of functionally important sites in proteins Prediction of interface residues in proteinprotein complexes by a consensus neural network method: test against NMR data Prediction of linear B-cell epitopes using amino acid pair antigenicity scale Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design Prediction of protein cellular attributes using pseudo amino acid composition (Erratum: ibid Structural bioinformatics and its impact to biomedical science A novel approach to predict active sites of enzyme molecules Predicting protein-protein interactions from sequences in a hybridization space MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM Recent progresses in protein subcellular location prediction Cell-PLoc: a package of web-servers for predicting subcellular localization of proteins in various organisms Prediction of protein structural classes Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS (Erratum: ibid High-throughput identification of interacting protein-protein binding sites Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families Predicting calciumbinding sites in proteins-a graph theory and geometry approach Practical limits of function prediction Using pseudo amino acid composition to predict transmembrane regions in protein: cellular automata and Lempel-Ziv complexity Analogue inhibitors by modifying oseltamivir based on the crystal neuraminidase structure for treating drug-resistant H5N1 virus Robust recognition of zinc binding sites in proteins Protein function in the post-genomic era Prediction of functionally important residues based solely on the computed energetics of protein structure Predicting DNA-binding proteins: approached from Chou's pseudo amino acid composition and other specific sequence features Prediction of protein-protein interaction sites in heterocomplexes with neural networks SURFACE: a database of protein surface regions for functional annotation Functional annotation by identification of local surface similarities: a novel tool for structural genomics HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces Using pseudo amino acid composition to predict protein subcellular location: approached with Lyapunov index, Bessel function, and Chebyshev filter Effective function annotation through catalytic residue conservation Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins Surprising similarities in structure comparison A method for localizing ligand binding pockets in protein structures SiteBase: a database for structurebased protein-ligand binding site comparison Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships Structural genomics: computational methods for structure analysis Exploiting 3D structural templates for detection of metal-binding sites in protein structures Uncovering network systems within protein structures Using a neural network and spatial clustering to predict the location of active sites in enzymes Distance-based identification of spatial motifs in proteins using constrained frequent subgraph mining LIGSITE csc : predicting ligand binding sites using the Connolly surface and degree of conservation LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins Protein structure comparison by alignment of distance matrices Mapping the protein universe An algorithm for predicting protein-protein interaction sites: abnormally exposed amino acid residues and secondary structure elements Global mapping of the protein structure space and application in structure-based inference of protein function Prediction of functional sites in proteins using conserved functional group analysis PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins PDBSite: a database of the 3D structure of protein functional sites A new bioinformatic approach to detect common 3D sites in protein structures Principles of protein-protein interactions Searching for functional sites in protein structures Protein-RNA interactions: a structural analysis Using electrostatic potentials to predict DNA-binding sites on DNAbinding proteins Quantitative assessment of relationship between sequence similarity and function similarity Shape variation in protein binding pockets and their ligands KEGG: An approach for clustering protein pockets into similar groups Analysis of protein surface patterns by pocket similarity network Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity An overview of the structures of protein-DNA complexes Amino acidbase interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level Protein-protein interaction: structurally conserved residues distinguish between binding sites and exposed protein surfaces A combined algorithm for genome-wide prediction of protein function Statistical models for discerning protein structures containing the DNA-binding helix-turn helix motif Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons SCOP: a structural classification of proteins database for the investigation of sequences and structures On the nature of cavities on protein surfaces: application to the identification of drug-binding sites ProMate: a structure based prediction program to identify the location of protein-protein binding sites Predicted protein-protein interaction sites from local sequence information CATH-a hierarchic classification of protein domain structures SSAP: sequential structure alignment program for protein structure comparison From protein structure to function Inference of protein function from protein structure Prediction of functional sites by analysis of sequence and structure conservation Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks Automatic prediction of protein function and detection of functional sites from structure The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data Molecular shape comparisons in searches for active sites and functional similarity Twilight zone of protein sequence alignments The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution A structural perspective on protein-protein interactions Computational methods of analysis of protein-protein interactions Integrating structure, bioinformatics, and enzymology to discover function-BioH, a new carboxylesterase from Escherichia coli A new method to detect related function among proteins independent of sequence and fold homology Structure and mechanism of the M2 proton channel of influenza A virus Predicting enzyme function from sequence: a systematic appraisal Network-based prediction of protein function EzyPred: a top-down approach for predicting enzyme functional classes and subclasses Nuc-PLoc: a new web-server for predicting protein subnuclear localization by fusing PseAA composition and PsePSSM PseAAC: a flexible web-server for generating various kinds of protein pseudo amino acid composition Using pseudo amino acid composition to predict protein subcellular location: approached with amino acid composition distribution Protein structure alignment by incremental combinatorial extension (CE) of the optimal path SiteEngines: recognition and comparison of binding sites and protein-protein interfaces Structural alignment of protein-DNA interfaces: insights into the determinants of binding specificity Hierarchical protein structure alignment using both secondary structure and atomic representations Identifying structural motifs in proteins Predicting metal-binding site residues in low-resolution structural models Annotation in three dimensions. keywords: acid; algorithm; amino; binding; dna; et al; features; functions; information; interaction; method; network; prediction; protein; protein function; protein structures; protein surface; residues; sequence; similarity; sites; structures; surface cache: cord-346965-0oq2n0af.txt plain text: cord-346965-0oq2n0af.txt item: #516 of 541 id: cord-347661-q9lgliph author: Zevenhoven-Dobbe, Jessika C. title: Production of Monospecific Rabbit Antisera Recognizing Nidovirus Proteins date: 2007-11-28 words: 6884 flesch: 45 summary: key: cord-347661-q9lgliph authors: Zevenhoven-Dobbe, Jessika C.; Wassenaar, Alfred L. M.; van der Meer, Yvonne; Snijder, Eric J. title: Production of Monospecific Rabbit Antisera Recognizing Nidovirus Proteins date: 2007-11-28 journal: SARS- and Other Coronaviruses DOI: 10.1007/978-1-59745-181-9_16 sha: doc_id: 347661 cord_uid: q9lgliph The importance of monospecific antisera for the experimental analysis of viral proteins is undisputed. Usually, metabolically labeled protein lysates (e.g., 35 S-methionine-labeled) are used for immunoprecipitation studies and samples are run on SDS-PAGE gels that can then be used for autoradiography. keywords: antigen; antisera; antiserum; cells; immunization; min; pbs; peptides; protein; rabbit; sds; target; use cache: cord-347661-q9lgliph.txt plain text: cord-347661-q9lgliph.txt item: #517 of 541 id: cord-347710-ff64y6ef author: Wan, Qianya title: Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development date: 2020-07-13 words: 36727 flesch: 38 summary: First, Hsp90 works as a classic chaperone protein to stabilize virus proteins. 57, 473 Except for promoting viral protein translation by binding with the viral IRES sequence, hnRNPs can directly bind with virus proteins to facilitate virus replication. keywords: a71; activation; activity; antiviral; apoptosis; atp; binding; c virus; cells; chaperone; complex; diseases; dna; domain; entry; expression; factor; family; folding; formation; function; gene; hbv; hcv; heat; heat shock; hepatitis; hnrnp; hnrnp a1; host; hsc70; hsp27; hsp90; human; infection; influenza; influenza virus; inhibitors; interaction; kinase; mrna; nuclear; nucleus; polymerase; protein; response; rna; role; shock protein; splicing; stress; terminal; transcription; translation; type; viral; virus; virus infection; virus replication; virus rna; virus type; viruses cache: cord-347710-ff64y6ef.txt plain text: cord-347710-ff64y6ef.txt item: #518 of 541 id: cord-347714-vxxhglx7 author: Abitogun, Folagbade title: COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding date: 2020-10-14 words: 3709 flesch: 30 summary: Obtaining these antigenic epitopes using the immune-informatics approach will help inform which epitopes to use in the construct of protein vaccines against SARS-CoV-2 using proteins other than the spike protein. Homology modelling of protein structures and complexes LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins IntFOLD: An integrated server for modelling protein structures and functions from amino acid sequences The I-TASSER Suite: protein structure and function prediction FALCON: keywords: analysis; coronavirus; cov-2; epitopes; hla; proteins; residues; sars; server; structural; vaccine cache: cord-347714-vxxhglx7.txt plain text: cord-347714-vxxhglx7.txt item: #519 of 541 id: cord-348360-20eq5meh author: Esposito, Dominic title: Optimizing high-yield production of SARS-CoV-2 soluble spike trimers for serology assays date: 2020-06-04 words: 3454 flesch: 43 summary: Until stable cell lines are developed to increase the titer of this secreted protein in mammalian cell culture, the low yield of spike protein produced from transient transfection of HEK293 cells will be a limiting factor for these assays. To improve the yield of spike protein and support the high demand for antigens in serology assays, we investigated several recombinant protein expression variables by altering the incubation temperature, harvest time, chromatography strategy, and final protein manipulation. keywords: buffer; expression; production; protein; sars; serology; spike; yield cache: cord-348360-20eq5meh.txt plain text: cord-348360-20eq5meh.txt item: #520 of 541 id: cord-348972-r94fhpe0 author: Gussow, Ayal B. title: Machine-learning approach expands the repertoire of anti-CRISPR protein families date: 2020-07-29 words: 9657 flesch: 49 summary: We show that this method is significantly predictive of Acrs, compile a collection of 2500 previously undetected predicted Acrs families and examine the top candidates in detail, including experimental validation. Consequently, we removed protein families with an average directon size of more than five genes. keywords: acrs; anti; candidate; cas; crispr; data; directon; families; genes; genomes; model; proteins; set; type; virus cache: cord-348972-r94fhpe0.txt plain text: cord-348972-r94fhpe0.txt item: #521 of 541 id: cord-349774-898tmq14 author: Zhang, Haiyang title: Proteasome activator PA28γ-dependent degradation of coronavirus disease (COVID-19) nucleocapsid protein date: 2020-06-16 words: 3178 flesch: 48 summary: Moreover, the stability of nCoV N protein in PA28γ-WT was lower than that in the PA28γ-KO cell line over time (Fig.1D) . Taken together, the data show that endogenous PA28γ may have an effect on the degradation of nCoV N protein through interaction. keywords: cells; degradation; ncov; pa28γ; proteasome; protein; sars cache: cord-349774-898tmq14.txt plain text: cord-349774-898tmq14.txt item: #522 of 541 id: cord-350286-n7ylgqfu author: Giri, Rajanish title: When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses date: 2020-04-03 words: 15857 flesch: 51 summary: Evaluation of intrinsic disorder in non-structural proteins of Bat CoV. Table 7 : Predicted MoRF residues in Human SARS proteins. Supplementary Table 10 : Predicted nucleotide-binding residues in Human SARS proteins. keywords: analysis; bat cov; binding; coronavirus; cov; cov-2; disorder; domain; figure; human; mean; protein; regions; residues; rna; sars; sars cov; sequence; structure; syndrome; table; terminal; viral; viruses cache: cord-350286-n7ylgqfu.txt plain text: cord-350286-n7ylgqfu.txt item: #523 of 541 id: cord-350309-j4oh1z8m author: Liu, D. X. title: Coronavirus envelope protein: A small membrane protein with multiple functions date: 2007-05-29 words: 3406 flesch: 42 summary: Retention of the avian coronavirus infectious bronchitis virus envelope protein in the pre-Golgi compartments and physical interaction between the envelope and membrane proteins Differential maturation and subcellular localization of severe acute respiratory syndrome coronavirus surface proteins Characterization of the coronavirus mouse hepatitis virus strain A59 small membrane protein E Biochemical evidence for the presence of mixed membrane topologies of the severe acute respiratory syndrome coronavirus envelope protein expressed in mammalian cells The transmembrane oligomers of coronavirus protein E Membrane topology of coronavirus E protein A highly unusual palindromic transmembrane helical hairpin formed by SARS coronavirus E protein SARS coronavirus E protein in phospholipid bilayers: an X-ray study Model of a putative pore: the pentameric alpha-helical bundle of SARS coronavirus E protein in lipid bilayers Coronavirus pseudoparticles formed with recombinant M and E proteins induce alpha interferon synthesis by leukocytes The production of recombinant infectious DI-particles of a murine coronavirus in the absence of helper virus Assembly of human severe acute respiratory syndrome coronavirus-like particles Nucleocapsid-independent assembly of coronavirus-like particles by co-expression of viral envelope protein genes Release of coronavirus E protein in membrane vesicles from virusinfected cells and E protein-expressing cells Generation of synthetic severe acute respiratory syndrome coronavirus pseudoparticles: implications for assembly and vaccine production The transmembrane domain of the infectious bronchitis virus E protein is required for efficient virus release Analysis of constructed E gene mutants of mouse hepatitis virus confirms a pivotal role for E protein in coronavirus assembly The small envelope protein E is not essential for murine coronavirus replication Role of the coronavirus E viroporin protein transmembrane domain in virus assembly Visions & Reflections (Minireview) keywords: cells; coronavirus; cov; e protein; membrane; mhv; protein; sars cache: cord-350309-j4oh1z8m.txt plain text: cord-350309-j4oh1z8m.txt item: #524 of 541 id: cord-350423-yaeduwvb author: James, Claire D. title: Viral Interactions with PDZ Domain-Containing Proteins—An Oncogenic Trait? date: 2016-01-18 words: 10646 flesch: 31 summary: Perhaps not surprisingly considering the wide remit of PDZ protein functions, deregulation of a number of PDZ proteins has been linked to tumourigenesis [2] . What is striking is that the diverse viruses target a common subset of PDZ proteins that are intimately involved in controlling cell polarity and the structure and function of intercellular junctions, including tight junctions. keywords: binding; cell; dlg1; domain; function; hpv; human; interaction; papillomavirus; pbm; pdz; pdz proteins; polarity; protein; tax; type; virus; viruses cache: cord-350423-yaeduwvb.txt plain text: cord-350423-yaeduwvb.txt item: #525 of 541 id: cord-350558-qfdp4ov9 author: Shaban, Mohammed Samer title: Inhibiting coronavirus replication in cultured cells by chemical ER stress date: 2020-08-26 words: 5088 flesch: 45 summary: Pearson correlation matrix confirmed a 91 progressive loss of correlation between mRNA levels and protein levels for this pathway over a time 92 course from 3 h to 24 h p.i. The ER is critically involved in surveying the quality and fidelity of membrane and secreted protein 40 synthesis, as well as the folding, assembly, transport and degradation of these proteins (Wang & 41 Kaufman, 2016). keywords: anti; cells; cov; data; fig; infection; p.i; pathways; protein; replication; stress; thapsigargin; virus cache: cord-350558-qfdp4ov9.txt plain text: cord-350558-qfdp4ov9.txt item: #526 of 541 id: cord-350935-p6euuop3 author: Doğan, Tunca title: CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations date: 2020-09-15 words: 7070 flesch: 40 summary: In CROssBAR knowledge graphs (CROssBAR-KG), biological components/terms (i.e., drugs/compounds, genes/proteins, bio-processes/pathways, phenotypes/diseases) are represented as nodes, and their known or predicted pairwise relationships are annotated as edges (a protein and its coding gene is treated as one merged term/entry/node). Currently, CROssBAR knowledge graphs do not include PubChem data due to both elevated computational demand (the sizes of PubChem collections are large) and high redundancy (a large portion of bioactivity data points in PubChem and ChEMBL databases are shared). keywords: biomedical; compound; covid-19; crossbar; data; database; disease; genes; graph; knowledge; nodes; proteins; terms cache: cord-350935-p6euuop3.txt plain text: cord-350935-p6euuop3.txt item: #527 of 541 id: cord-351559-az4pgi9k author: Turjya, Rafeed Rahman title: Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection date: 2020-06-29 words: 2444 flesch: 26 summary: There 122 are direct RNA-RNA interactions for 4 genes, and RNA-protein interactions for the rest 123 ( Figure 2 ). 777 MOV10 Is a 5' to 3' RNA helicase contributing to UPF1 mRNA target degradation by 778 translocation along 3' UTRs 780 Identification of novel argonaute-associated proteins APOBEC3G inhibits 783 microRNA-mediated repression of translation by interfering with the interaction between 784 MicroRNA silencing through RISC recruitment of eIF6 Virus Escape and Manipulation of Cellular 788 Nonsense-Mediated mRNA Decay Provides Antiviral Activity against RNA Viruses by Enhancing RIG-I-MAVS-Independent 791 IFN Induction Not applicable. keywords: cell; cov-2; genes; infection; lncrnas; protein; rna; sars cache: cord-351559-az4pgi9k.txt plain text: cord-351559-az4pgi9k.txt item: #528 of 541 id: cord-352172-g0jiaenw author: Stoevesandt, Oda title: Protein microarrays: high-throughput tools for proteomics date: 2014-01-09 words: 7470 flesch: 28 summary: In contrast to screening systems such as yeast two-hybrid, the in vitro nature of protein arrays allows for the control of the interaction conditions, protein concentrations, PTMs and specific cofactor requirements [2] . In situ synthesis of protein array (see Figure Recently, a novel system has been introduced that converts a reusable DNA array into multiple protein array copies ( Figure 2C ) keywords: ana; antibody; binding; cancer; cell; detection; dna; expression; functional; interactions; lysis; methods; microarrays; profiling; protein; proteome; screening; surface; throughput cache: cord-352172-g0jiaenw.txt plain text: cord-352172-g0jiaenw.txt item: #529 of 541 id: cord-352371-t54zftal author: Kumar, Ravindra title: Prediction of endoplasmic reticulum resident proteins using fragmented amino acid composition and support vector machine date: 2017-09-04 words: 6623 flesch: 48 summary: Both types of non-ERRPs were downloaded using the criteria earlier used to download ER proteins. It has been observed that ER proteins are rich in transmembrane domain (Schuldiner & Weissman, 2013; Scott et al., 2004) . keywords: acid; amino; composition; dataset; errps; prediction; proteins; sequence; signal cache: cord-352371-t54zftal.txt plain text: cord-352371-t54zftal.txt item: #530 of 541 id: cord-352481-iq3wor3w author: Postic, Guillaume title: An information gain-based approach for evaluating protein structure models date: 2020-08-18 words: 6521 flesch: 46 summary: Applications to HIV-1-protease inhibitor design Consistency in structural energetics of protein folding and peptide recognition An empirical energy function for threading protein sequence through the folding motif An empirical energy potential with a reference state for protein fold and sequence recognition Protein threading using PROSPECT: Design and evaluation An automatic method for CASP9 free modeling structure prediction assessment Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0 Ranking the quality of protein structure models using sidechain based network properties MetaMQAP: In this article, we present a conceptually new method for ranking protein structure models by quality, which is (i) independent of any physics-based explanation and (ii) relevant to statistics and to a general definition of information gain. keywords: models; native; potentials; protein; quality; score; scoring; structures; tig cache: cord-352481-iq3wor3w.txt plain text: cord-352481-iq3wor3w.txt item: #531 of 541 id: cord-354030-8tfg881h author: Dong, Rong title: Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches date: 2020-07-28 words: 7986 flesch: 46 summary: The pdb file of vaccine protein and receptor complex (TLR3, MHC-I, and MHC-II) were used to start the molecular dynamic (MD) simulations. The sequence homology of final vaccine protein to human protein sequence shown that there were no significant alignments ( Figure S4 ). keywords: amino; binding; cell; cell epitopes; complex; cov-2; epitopes; figure; immunoinformatics; mhc; model; prediction; protein; sars; sequence; server; structure; table; vaccine; virus cache: cord-354030-8tfg881h.txt plain text: cord-354030-8tfg881h.txt item: #532 of 541 id: cord-354050-kcn67stj author: Shi, Guoli title: More than meets the I: the diverse antiviral and cellular functions of interferon-induced transmembrane proteins date: 2017-11-21 words: 6879 flesch: 31 summary: It was reported that elevated levels of IFITM3 protein in memory CD8+ T lymphocytes, which kill virus-infected cells and serve as important targets themselves for IAV infection in the lung, promotes their survival during infection and enables long-term defense against future viral exposures [65] . A recent and comprehensive study now links an additional variant in the IFITM3 locus to severe influenzaassociated illness in three independent cohorts, albeit the SNP identified is distinct from rs12252-C. Known as rs34481144-A, it is found in the 5' untranslated region and is linked to lower IFITM3 protein levels in cells keywords: activity; cell; entry; env; fusion; ifitm; infection; interferon; membrane; proteins; restriction; transmembrane; virion; virus; viruses cache: cord-354050-kcn67stj.txt plain text: cord-354050-kcn67stj.txt item: #533 of 541 id: cord-354547-eomm1sl5 author: Wang, Jibin title: Interaction of the Coronavirus Infectious Bronchitis Virus Membrane Protein with β-Actin and Its Implication in Virion Assembly and Budding date: 2009-03-16 words: 6349 flesch: 47 summary: IBV M protein was transiently expressed in H1299 cells grown on 4-well chamber slides (IWAKI). When expressed alone, M protein accumulates in the Golgi complex in the form of homomultimeric complexes [8, 9] . keywords: actin; budding; cells; coronavirus; fig; ibv; interaction; panel; protein; rna; virus cache: cord-354547-eomm1sl5.txt plain text: cord-354547-eomm1sl5.txt item: #534 of 541 id: cord-354950-kmpbdvof author: Demurtas, Olivia C. title: Antigen Production in Plant to Tackle Infectious Diseases Flare Up: The Case of SARS date: 2016-02-05 words: 8662 flesch: 42 summary: M protein forms homo-oligomers and interacts with S, E, and N proteins (Hogue and Machamer, 2008) . N protein has been recognized as the preferred target for detection of SARS-CoV infection by reverse transcription-polymerase chain reaction (RT-PCR; Suresh et al., 2008) . keywords: cells; coronavirus; cov; et al; expression; figure; gene; infection; n protein; plant; ppvx; protein; recombinant; sars; sera; syndrome cache: cord-354950-kmpbdvof.txt plain text: cord-354950-kmpbdvof.txt item: #535 of 541 id: cord-355327-d3gcfepx author: Fan, Samuel W title: Conformational changes in redox pairs of protein structures date: 2009-08-01 words: 9870 flesch: 41 summary: Emerging evidence supports the concept of two distinct types of disulfides in protein structures which have different functional roles. The Redox Pairs dataset contains 18,003 pairs of protein structures consisting of 4333 protein chains, of which 1238 (28.57%) are high-resolution structures (<2.2 Å). keywords: activity; binding; changes; cys; dataset; different; disorder; disulfide; group; morphing; pairs; proteins; redox; reduction; residues; sequence; sites; state; structure; transitions cache: cord-355327-d3gcfepx.txt plain text: cord-355327-d3gcfepx.txt item: #536 of 541 id: cord-355377-b0rcg3rt author: van der Vlag, R. title: Analytical Methods in Protein-Templated Dynamic Combinatorial Chemistry date: 2017-06-29 words: 9859 flesch: 49 summary: Another disadvantage are the large amounts of protein used (e.g., 30 mg HEWL 11 or 6-10 mg BSA 4 per DCL) to ensure a sufficiently high concentration of binding inhibitors for proper detection by MS. Since the first report of DCC applied to the discovery of binders for a protein, this elegant tool has been employed on a range of protein targets in early stage of medicinal-chemistry projects. keywords: acylhydrazones; aldehydes; analysis; binding; dcc; dcl; dcls; enzyme; inhibitors; library; ligand; nmr; protein; scheme; target cache: cord-355377-b0rcg3rt.txt plain text: cord-355377-b0rcg3rt.txt item: #537 of 541 id: cord-355477-7xd93aqv author: SATIJA, NAMITA title: The Molecular Biology of SARS Coronavirus date: 2007-04-23 words: 4952 flesch: 46 summary: A bound to the amino-terminal domain of HIV-1 capsid The nucleocapsid protein of SARS coronavirus has a high binding affinity to the human cellular heterogeneous nuclear ribonucleoprotein A1 Crystal structure of human UP1, the domain of hnRNP A1that contains two RNA-recognition motifs The nucleocapsid protein of coronavirus mouse hepatitis virus interacts with the cellular heterogeneous nuclear ribonucleoprotein A1 in vitro and in vivo Activation of AP-1 signal transduction pathway by SARS coronavirus nucleocapsid protein The nucleocapsid protein of sars-coronavirus inhibits the activity of cyclin-CDK complex and blocks S phase progression in mammalian cells The SARS coronavirus nucleocapsid protein induces actin reorganization and apoptosis in COS-1 cells in the absence of growth factors Nuclear/nucleolar localization properties of C-terminal nucleocapsid protein of SARS coronavirus The severe acute respiratory syndrome coronavirus nucleocapsid protein is phosphorylated and localizes in the cytoplasm by 14-3-3-mediated translocation Phosphorylation of the porcine reproductive and respiratory syndrome virus nucleocapsid protein Intracellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein: absence of nucleolar accumulation during infection and after expression as a recombinant protein in vero cells Peptide domain involved in the interaction between membrane protein and nucleocapsid protein of SARS-associated coronavirus Characterization of severe acute respiratory syndrome coronavirus membrane protein Differential maturation and subcellular localization of severe acute respiratory syndrome coronavirus surface proteins S, M and E Biochemical and functional characterization of the membrane association and membrane permeabilizing activity of the severe acute respiratory syndrome coronavirus envelope protein The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells The severe acute respiratory syndrome (SARS) coronavirus 3a protein may function as a modulator of the trafficking properties of the spike protein The severe acute respiratory syndrome coronavirus 3a protein up-regulates expression of fibrinogen in lung epithelial cells The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells Overexpression of 7a, a protein specifically encoded by severe acute respiratory syndrome coronavirus, induces apoptosis via a caspase-dependent pathway Severe acute respiratory syndromeassociated coronavirus 3a protein forms an ion channel and modulates virus release Carboxyl terminus of severe acute respiratory coronavirus nucleocapsid protein: self-association analysis and nucleic acid binding characteristics Nucleocapsid amino acids 211 to 254, in particular, tetrad glutamines, are essential for the interaction between the nucleocapsid and membrane proteins of SARS-associated coronavirus Coronavirus nucleocapsid protein is an RNA chaperone A first step in understanding SARS pathogenesis Mechanisms and enzymes involved in SARS coronavirus genome expression Molecular biology of severe acute respiratory syndrome coronavirus A 193 amino acid fragment of SARS coronavirus S protein efficiently binds angiotensin converting enzyme 2 Mass spectrometric characterization of proteins from the SARS virus: a preliminary report Proteomic analysis on structural proteins of severe acute respiratory syndrome coronavirus Differential maturation and subcellular localization of severe acute respiratory syndrome coronavirus surface proteins S, M and E Structure of SARS coronavirus spike receptor-binding domain complexed with receptor Profile of antibodies to the nucleocapsid protein of the severe acute respiratory syndrome (SARS)-associated coronavirus in probable SARS patients Diagnosis of severe acute respiratory syndrome (SARS) by detection of SARS coronavirus nucleocapsid antibodies in an antigencapturing enzyme-linked immunosorbent assay Assessment of immunoreactive synthetic peptides from the structural proteins of severe acute respiratory syndrome coronavirus Mapping of antigenic sites on the nucleocapsid protein of the severe acute respiratory syndrome coronavirus Antigenic structure of transmissible gastroenteritis virus nucleoprotein Location of antibody epitopes within the mouse hepatitis virus nucleocapsid protein Localization of linear B-cell epitopes on infectious bronchitis virus nucleocapsid protein The epitope study on the SARS-CoV nucleocapsid protein Structure of the N-terminal RNAbinding domain of the SARS CoV nucleocapsid protein Assembly of severe acute respiratory syndrome coronavirus RNA packaging signal into virus-like particles is nucleocapsid dependent The nucleocapsid protein of the SARS coronavirus is capable of self-association through a C-terminal 209 amino acid interaction domain Recombinant severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein forms a dimer through its C-terminal domain Nucleocapsid protein of SARS coronavirus tightly binds to human cyclophilin A Crystal structure of human cyclophilin keywords: cells; coronavirus; cov; covs; domain; nucleocapsid; protein; rna; sars; syndrome; terminal cache: cord-355477-7xd93aqv.txt plain text: cord-355477-7xd93aqv.txt item: #538 of 541 id: cord-355913-fhvt1ht1 author: Burrell, Christopher J. title: Virus Replication date: 2016-11-11 words: 9867 flesch: 41 summary: The situation is quite different for RNA viruses as these are unique having genetic information coded as RNA. For RNA viruses, the regulation of transcription is, on the whole, not as complex as is the case for DNA viruses. keywords: acid; cell; dna; example; genes; genome; host; membrane; mrna; particles; proteins; replication; rna; rna viruses; synthesis; transcription; viruses cache: cord-355913-fhvt1ht1.txt plain text: cord-355913-fhvt1ht1.txt item: #539 of 541 id: cord-355924-8sk9al0n author: Allam, Loubna title: Targeting the GRP78-Dependant SARS-CoV-2 Cell Entry by Peptides and Small Molecules date: 2020-10-21 words: 4764 flesch: 44 summary: respiratory syndrome coronavirus The tetraspanin CD9 facilitates MERS-coronavirus entry by scaffolding host cell receptors and proteases Gene expression and in situ protein profiling of candidate SARS-CoV-2 receptors in human airway epithelial cells and lung tissue SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues Preliminary virtual screening studies to identify GRP78 inhibitors which may interfere with SARS-CoV-2 infection Alteration and analyses of viral entry with library-derived peptides Molecular screening and docking analysis of LMTK3and AKT1 combined inhibitors Effects of polyphenol compounds on influenza A virus replication and definition of their mechanism of action The antimicrobial and antiviral activity of polyphenols from almond (Prunus dulcis L.) skin In silico inhibition studies of AXL kinase by curcumin and its natural derivatives Curcumin-synthetic analogs library screening by docking and quantitative structure-activity relationship studies for AXL tyrosine kinase inhibition in cancers Probing the ATP site of GRP78 with nucleotide triphosphate analogs Three-dimensional structure prediction of the human LMTK3 catalytic domain in DYG-in conformation Open Babel: an open chemical toolbox AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading The ClusPro web server for protein-protein docking ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT Natural product-derived phytochemicals as potential agents against coronaviruses: a review Potential effects of curcumin in the treatment of COVID-19 infection Coronavirus disease 2019 (COVID-19): a perspective from China Repurposing of known anti-virals as potential inhibitors for SARS-CoV-2 main protease using molecular docking analysis GRP78 is an important host factor for Japanese encephalitis virus entry and replication in mammalian cells HSPA5 is an essential host factor for Ebola virus infection â��)â��Epigallocatechin gallate overcomes resistance to etoposide-induced cell death by targeting the molecular chaperone glucose-regulated protein 78 Glucose-regulated protein 78 substratebinding domain alters its conformation upon EGCG inhibitor binding to nucleotide-binding domain: molecular dynamics studies Adenosine-derived inhibitors of 78 kDa glucose regulated protein (Grp78) ATPase: insights into isoform selectivity Natural products may interfere with SARS-CoV-2 attachment to the host cell Anti-infective properties of the golden spice curcumin Identification of potent COVID-19 main protease (Mpro) inhibitors from natural polyphenols: an in silico strategy unveils a hope against CORONA An in vitro study of theaflavins extracted from black tea to neutralize bovine rotavirus and bovine coronavirus infections Specific plant terpenoids and lignoids possess potent antiviral activities against severe acute respiratory syndrome coronavirus Inhibition of enveloped viruses infectivity by curcumin GRP78, a coreceptor for coxsackievirus A9, interacts with major histocompatibility complex class I molecules which mediate virus internalization Japanese encephalitis virus co-opts the ER-stress response protein GRP78 for viral infectivity The residues (ILE-13, SER-12, and THR-9) of satpdb14438 interacted with GRP78 residues THR-434, VAL-429, and THR-458. keywords: binding; cov-2; grp78; infection; interaction; peptides; protein; sars; spike; virus cache: cord-355924-8sk9al0n.txt plain text: cord-355924-8sk9al0n.txt item: #540 of 541 id: cord-356019-k7gs1ohp author: Makhzoum, Abdullah title: Recent advances on host plants and expression cassettes' structure and function in plant molecular pharming date: 2013-08-20 words: 8929 flesch: 35 summary: Moreover, protein expression in plant aerial parts could affect the growth and development of the host plant. Different ORFeome projects have thus been generated using Gateway technology for protein expression and functional analysis, such as the yeast ORFeome keywords: accumulation; cells; chloroplast; expression; gateway; gene; growth; human; leaves; level; maize; pharming; plant; production; promoter; proteins; rice; seeds; system; technology; tobacco; transgenic; yield cache: cord-356019-k7gs1ohp.txt plain text: cord-356019-k7gs1ohp.txt item: #541 of 541 id: cord-356064-q56jnhss author: Bartel, Sebastian title: Proteome analysis of vaccinia virus IHD-W-infected HEK 293 cells with 2-dimensional gel electrophoresis and MALDI-PSD-TOF MS of on solid phase support N-terminally sulfonated peptides date: 2011-08-01 words: 6185 flesch: 38 summary: The regulation of eIF-4H may contribute to an enhancement in protein biosynthesis which is required by the virus' need for protein expression. In contrast to the negative control, protein expression is enhanced by an infection with active and UV-inactivated viruses. keywords: analysis; apoptosis; cells; expression; identification; ihd; infection; peptides; protein; proteome; psd; spectra; spitc; vacv; virus cache: cord-356064-q56jnhss.txt plain text: cord-356064-q56jnhss.txt