# bib

id: cord-273107-xc61osdx
author: Qureshi, Abid
date: 2014-01-01
extension: .txt
mime: text/plain
words: 2371
sentence: 100
flesch: 41
cache: cache/cord-273107-xc61osdx.txt
txt: txt/cord-273107-xc61osdx.txt
title:
  AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses

summary:
  Antiviral peptides (AVPs) are being regarded as such new promising entities to combat the viral infections. AVPs are a subset of antimicrobial peptides (AMPs) which act as the first line of defence in many organisms as innate immune response and are the hosts' defence peptides generated in response to pathogenic disease condition (8) (9) (10) .


id: cord-007755-o2r8ktie
author: Kokoszka, Malgorzata E.
date: 2014-10-20
extension: .txt
mime: text/plain
words: 2927
sentence: 133
flesch: 52
cache: cache/cord-007755-o2r8ktie.txt
txt: txt/cord-007755-o2r8ktie.txt
title:
  Mapping Protein–Protein Interactions with Phage-Displayed Combinatorial Peptide Libraries and Alanine Scanning

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.


id: cord-001677-p6ikd8ns
author: Hansra, Satyender
title: Exploration of New Sites in Adenovirus Hexon for Foreign Peptides Insertion
date: 2015-05-29
extension: .txt
mime: text/plain
words: 2935
sentence: 134
flesch: 45
cache: cache/cord-001677-p6ikd8ns.txt
txt: txt/cord-001677-p6ikd8ns.txt
summary:
  In order to access new sites in hAd5 hexon, tailored for the incorporation of foreign peptide sequences, we genetically inserted a 15 amino acid (aa) residue peptide into HVR7, HVR8 or HVR9 region of the hAd5 hexon. Peptide sequence corresponding to the PRRSV epitope is underlined.


id: cord-260392-hj9s5cnu
author: Lin, Peng
title: A novel and exploitable antifungal peptide from kale (Brassica alboglabra) seeds
date: 2008-05-30
extension: .txt
mime: text/plain
words: 3322
sentence: 144
flesch: 48
cache: cache/cord-260392-hj9s5cnu.txt
txt: txt/cord-260392-hj9s5cnu.txt
summary:
  key: cord-260392-hj9s5cnu authors: Lin, Peng; Ng, Tzi Bun title: A novel and exploitable antifungal peptide from kale (Brassica alboglabra) seeds date: 2008-05-30 journal: Peptides DOI: 10.1016/j.peptides.2008.05.020 sha: doc_id: 260392 cord_uid: hj9s5cnu The aim of this study was to purify and characterize antifungal peptides from kale seeds in view of the paucity of information on antifungal peptides from the family Brassicaceae, and to compare its characteristics with those of published Brassica antifungal peptides. Buffer only without antifungal peptide served as a control.


id: cord-340970-389t032s
author: Choy, Wai-Yan
date: 2004-06-01
extension: .txt
mime: text/plain
words: 3535
sentence: 115
flesch: 41
cache: cache/cord-340970-389t032s.txt
txt: txt/cord-340970-389t032s.txt
title:
  Synthetic Peptide Studies on the Severe Acute Respiratory Syndrome (SARS) Coronavirus Spike Glycoprotein: Perspective for SARS Vaccine Development

summary:
  We focused on using synthetic peptides for developing antibodies against SARS-CoV, which aimed to block viral invasion by eliciting an immune response specific to the native SARS-CoV S protein. Conclusions: Synthetic peptides can elicit specific antibodies to SARS-CoV.


id: cord-262748-v4xue7ha
author: Xu, Yongtao
title: Identification of Peptide Inhibitors of Enveloped Viruses Using Support Vector Machine
date: 2015-12-04
extension: .txt
mime: text/plain
words: 4645
sentence: 188
flesch: 34
cache: cache/cord-262748-v4xue7ha.txt
txt: txt/cord-262748-v4xue7ha.txt
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] .


id: cord-000947-psguw47w
author: Feng, Jianyu
date: 2013-04-24
extension: .txt
mime: text/plain
words: 4721
sentence: 232
flesch: 51
cache: cache/cord-000947-psguw47w.txt
txt: txt/cord-000947-psguw47w.txt
title:
  A Study of the Mechanism of the Chaperone-like Function of an scFv of Human Creatine Kinase by Computer Simulation

summary:
  programs for checking the quality of protein structures solved by NMR A method to identify protein sequences that fold into a known three-dimensional structure ElliPro: a new structure-based tool for the prediction of antibody epitopes ZDOCK: First set of peptides covered HCK sequence was spotted in squares A1 to M9.


id: cord-320693-de1lmzl1
author: Hu, Han
title: Antiviral activity of Piscidin 1 against pseudorabies virus both in vitro and in vivo
date: 2019-07-31
extension: .txt
mime: text/plain
words: 5060
sentence: 259
flesch: 48
cache: cache/cord-320693-de1lmzl1.txt
txt: txt/cord-320693-de1lmzl1.txt
summary:
  Residual virus was calculated according to the following formula, residual infectivity = b/a × 100% (a represent TCID50 of residual virus non-treated by the AMPs (control), b represent TCID50 of residual virus after treated by AMPs). Although vaccination can suppress development of the disease, vaccines cannot eliminate virus infection.


id: cord-285443-9y2kkmby
author: Pessi, Antonello
title: Cholesterol‐conjugated peptide antivirals: a path to a rapid response to emerging viral diseases
date: 2014-10-20
extension: .txt
mime: text/plain
words: 5049
sentence: 188
flesch: 34
cache: cache/cord-285443-9y2kkmby.txt
txt: txt/cord-285443-9y2kkmby.txt
summary:
  Emerging and reemerging diseases: a historical perspective Emerging viral diseases The World Health Report Global trends in emerging infectious diseases Middle East respiratory syndrome coronavirus (MERS-CoV): announcement of the coronavirus study group World struggles to stop Ebola Identification of a novel coronavirus in patients with severe acute respiratory syndrome Characterization of a novel coronavirus associated with severe acute respiratory syndrome SARS: systematic review of treatment effects Mechanisms of viral membrane fusion and its inhibition Design of recombinant protein-based SARS-CoV entry inhibitors targeting the heptad-repeat regions of the spike protein S2 domain Analysis of a peptide inhibitor of paramyxovirus (NDV) fusion using biological assays, NMR, and molecular modeling Inhibition of Henipavirus fusion and infection by heptad-derived peptides of the Nipah virus fusion glycoprotein Development of antiviral fusion inhibitors: short modified peptides derived from the transmembrane glycoprotein of feline immunodeficiency virus Peptide inhibitors targeting virus-cell fusion in class I enveloped viruses Downsizing human, bacterial, and viral proteins to short water-stable alpha helices that maintain biological potency Peptides corresponding to the heptad repeat sequence of human parainfluenza virus fusion protein are potent inhibitors of virus infection A synthetic peptide corresponding to a conserved heptad repeat domain is a potent inhibitor of Sendai virus-cell fusion: an emerging similarity with functional domains of other viruses Antiviral activity of membrane fusion inhibitors that target gp40 of the feline immunodeficiency virus envelope protein Peptide-based inhibitors of the HIV envelope protein and other class I viral fusion proteins Inhibition of Ebola virus entry by a C-peptide targeted to endosomes Peptides from conserved regions of paramyxovirus fusion (F) proteins are potent inhibitors of viral fusion Inhibition of Hendra virus fusion Inhibition of measles virus infection and fusion with peptides corresponding to the leucine zipper region of the fusion protein Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides Identification of a minimal peptide derived from heptad repeat (HR) 2 of spike protein of SARS-CoV and combination of HR1-derived peptides as fusion inhibitors Interaction between heptad repeat 1 and 2 regions in spike protein of SARS-associated coronavirus: implications for virus fusogenic mechanism and identification of fusion inhibitors LearnCoil-VMF: computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins MultiCoil2: predicting coiled coils and their oligomerization states from sequence in the twilight zone MultiCoil: a program for predicting two-and three-stranded coiled coils The complete genome sequence of severe acute respiratory syndrome coronavirus strain HKU-39849 (HK-39) Structural characterization of the SARS-coronavirus spike S fusion protein core Structures and polymorphic interactions of two heptad-repeat regions of the SARS virus S2 protein Structural characterization of the fusion-active complex of severe acute respiratory syndrome (SARS) coronavirus Crystal structure of severe acute respiratory syndrome coronavirus spike protein fusion core Sensitivity of HIV-1 to entry inhibitors correlates with envelope/coreceptor affinity, receptor density, and fusion kinetics A quantitative and kinetic fusion protein-triggering assay can discern distinct steps in the Nipah virus membrane fusion cascade Kinetic dependence of paramyxovirus entry inhibition Broad antiviral activity and crystal structure of HIV-1 fusion inhibitor sifuvirtide Short-peptide fusion inhibitors with high potency against wild-type and enfuvirtide-resistant HIV-1 Design of helical, oligomeric HIV-1 fusion inhibitor peptides with potent activity against enfuvirtide-resistant virus Design of a novel HIV-1 fusion inhibitor that displays a minimal interface for binding affinity Remodeling of gp41-C34 peptide leads to highly effective inhibitors of the fusion of HIV-1 with target cells Inhibition of HIV type 1 infectivity by constrained alpha-helical peptides: implications for the viral fusion mechanism Short constrained peptides that inhibit HIV-1 entry Hydrocarbon doublestapling remedies the proteolytic instability of a lengthy peptide therapeutic Design and evaluation of sifuvirtide, a novel HIV-1 fusion inhibitor Lipid rafts are involved in SARS-CoV entry into Vero E6 cells Cholesterol enhances mouse hepatitis virus-mediated cell fusion A single point mutation controls the cholesterol dependence of Semliki Forest virus entry and exit Cholesterol removal by methyl-beta-cyclodextrin inhibits poliovirus entry The major cellular sterol regulatory pathway is required for Andes virus infection Lipid rafts play an important role in the early stage of severe acute respiratory syndrome-coronavirus life cycle Cholesterol-rich lipid rafts are required for release of infectious human respiratory syncytial virus particles Ebola virus entry requires the cholesterol transporter Niemann-Pick C1 Cholesterol dependence of varicella-zoster virion entry into target cells Influenza virus hemagglutinin concentrates in lipid raft microdomains for efficient viral fusion Plasma membrane rafts play a critical role in HIV-1 assembly and release Membrane raft microdomains mediate lateral assemblies required for HIV-1 infection Role for human immunodeficiency virus type 1 membrane cholesterol in viral internalization Role of cholesterol in human immunodeficiency virus type 1 envelope protein-mediated fusion with host cells Nef induces multiple genes involved in cholesterol synthesis and uptake in human immunodeficiency virus type 1-infected T cells Human immunodeficiency virus impairs reverse cholesterol transport from macrophages Nef increases the synthesis of and transports cholesterol to lipid rafts and HIV-1 progeny virions Nef mobilizes lipid rafts in macrophages through a pathway that competes with ABCA1-dependent cholesterol efflux The HIV lipidome: a raft with an unusual composition Alterations in cholesterol metabolism restrict HIV-1 trans infection in nonprogressors New clues to understanding HIV nonprogressors: low cholesterol blocks HIV trans infection Evidence for budding of human immunodeficiency virus type 1 selectively from glycolipid-enriched membrane lipid rafts Galactosylceramide domain microstructure: impact of cholesterol and nucleation/growth conditions Lipid composition and fluidity of the human immunodeficiency virus Lipid composition and fluidity of the human immunodeficiency virus envelope and host cell plasma membranes Role of lipid rafts in virus replication


id: cord-269462-7yozebv2
author: Vitiello, Mariateresa
date: 2010-07-02
extension: .txt
mime: text/plain
words: 5206
sentence: 185
flesch: 41
cache: cache/cord-269462-7yozebv2.txt
txt: txt/cord-269462-7yozebv2.txt
title:
  Viral Fusion Peptides Induce Several Signal Transduction Pathway Activations That Are Essential for Interleukin-10 and Beta-Interferon Production

summary:
  The deciphering of intracellular signaling pathways that are activated by the interaction between viral fusion peptides and cellular membranes are important for the understanding of both viral replication strategies and host defense mechanisms. All assays were carried out using U937 cells (3 ! 10 6 cells/ml) stimulated with viral fusion peptides (10 M ) and incubated for 24 h at 37 ° in 5% CO 2 .


id: cord-293072-giakcaki
author: Xu, Wan-Xiang
date: 2017-10-12
extension: .txt
mime: text/plain
words: 5335
sentence: 157
flesch: 42
cache: cache/cord-293072-giakcaki.txt
txt: txt/cord-293072-giakcaki.txt
title:
  A simpler and more cost-effective peptide biosynthetic method using the truncated GST as carrier for epitope mapping

summary:
  Design all 16/18mer peptides with an overlap of 8 aa residues covering the full-length of the target protein or a longer segment sequence for the first round of antigenic peptide mapping, as well as design a set of 8mer peptides with overlapping 7 aa residues and covering each reactive 16/18mer peptide sequence for the second round of precise BCE motif identification. In order to know how many BCEs are there among three neighboring reactive 18mer-peptides of P32-34 (Fig 4A and 4B) , which were blotted in first round of antigenic peptide mapping in our study on epitome decoding of huZP4 protein, we first expressed a set of 8mer-peptides (P110-120) covering the full-length sequence of reactive P32 according to procedures of steps 1 to 8 in the protocol, and then they were subjected to SDS-PAGE, and transferred onto 0.2 μm nitrocellulose membrane.


id: cord-351321-6d2mn5ok
author: Gouveia, Duarte
date: 2020-06-19
extension: .txt
mime: text/plain
words: 6251
sentence: 229
flesch: 46
cache: cache/cord-351321-6d2mn5ok.txt
txt: txt/cord-351321-6d2mn5ok.txt
title:
  Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window

summary:
  By using a short LC gradient focusing on the region of interest identified in our previous study, we tested the detection of the virus in samples containing different quantities of viral peptides, as well as COVID-19 clinical samples, paving the way for the development of time-efficient viral diagnostic tests based on an alternative platform. This was repeated several times to obtain a one third dilution cascade of viral peptides.


id: cord-002394-n85ptr5p
author: Reddy, Vijayalakshmi
date: 2017-01-26
extension: .txt
mime: text/plain
words: 6105
sentence: 247
flesch: 46
cache: cache/cord-002394-n85ptr5p.txt
txt: txt/cord-002394-n85ptr5p.txt
title:
  Molecular Mimicry between Chikungunya Virus and Host Components: A Possible Mechanism for the Arthritic Manifestations

summary:
  Mouse experiments to evaluate the role of CHIKV peptides in causing tissue damage by molecular mimicry On the other hand, mice that received two doses of CHIKV specific peptides but no virus (Groups 3 & 4) exhibited myositis, muscle necrosis, vasculitis and hyperplasia of the marrow (immune mediated inflammatory muscle and marrow reactive changes) and an overall inflammation score of 3+ (Fig 8) .


id: cord-337812-arivkkj0
author: Chu, Ling-Hon Matthew
date: 2006-03-07
extension: .txt
mime: text/plain
words: 6887
sentence: 209
flesch: 43
cache: cache/cord-337812-arivkkj0.txt
txt: txt/cord-337812-arivkkj0.txt
title:
  Rapid peptide-based screening on the substrate specificity of severe acute respiratory syndrome (SARS) coronavirus 3C-like protease by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

summary:
  For the synthesis of peptide substrates, we deliberately applied the novel cartridge replacement strategy, which was based on the flexibility on modifying the solid-phase peptide synthesis process, in which each amino acid cartridge can be filled with different contents of amino acids in defined ratios, to generate the desired combinations of mixed peptide substrates according to experimental needs. The sequence of peptide substrate used in this study was based on one of the SARS-CoV 3CL pro cleavage sites on the SARS-CoV BJ01 polyprotein pp1ab (residues 3232-3247) ( Table 1) .


id: cord-337897-hkvll3xh
author: Yang, Zheng Rong
title: Peptide Bioinformatics- Peptide Classification Using Peptide Machines
date: 2009
extension: .txt
mime: text/plain
words: 7635
sentence: 379
flesch: 49
cache: cache/cord-337897-hkvll3xh.txt
txt: txt/cord-337897-hkvll3xh.txt
summary:
  We then generate validation peptides using one fold and generate training peptides from the remaining folds. In building a computer model for a real application, there are two important issues for model validation in addition to model parameter estimation.


id: cord-284523-lknyehsa
author: da Mata, Élida Cleyse Gomes
title: Antiviral activity of animal venom peptides and related compounds
date: 2017-01-06
extension: .txt
mime: text/plain
words: 7093
sentence: 275
flesch: 38
cache: cache/cord-284523-lknyehsa.txt
txt: txt/cord-284523-lknyehsa.txt
summary:
  (6) The peptides hecate and TVS-LAO act in the post-translation process, in the cleavage of the GAG/POL protein precursor thus interfering in the assembly of the viral capsid and in the organization of the polymerase complex with viral nucleic acid, or (ii) production of cytokines that stimulate the action of T cytotoxic cells, and NK cells, and even host cell expression of the major histocompatibility complex molecules, in order to present viral peptides to the other cells of the immune system [16] . key: cord-284523-lknyehsa authors: da Mata, Élida Cleyse Gomes; Mourão, Caroline Barbosa Farias; Rangel, Marisa; Schwartz, Elisabeth Ferroni title: Antiviral activity of animal venom peptides and related compounds date: 2017-01-06 journal: J Venom Anim Toxins Incl Trop Dis DOI: 10.1186/s40409-016-0089-0 sha: doc_id: 284523 cord_uid: lknyehsa Viruses exhibit rapid mutational capacity to trick and infect host cells, sometimes assisted through virus-coded peptides that counteract host cellular immune defense.


id: cord-003033-nlaiurau
author: Ansari, Junaid
title: Therapeutic Potential of Annexin A1 in Ischemia Reperfusion Injury
date: 2018-04-16
extension: .txt
mime: text/plain
words: 6929
sentence: 248
flesch: 27
cache: cache/cord-003033-nlaiurau.txt
txt: txt/cord-003033-nlaiurau.txt
summary:
  Mitochondrial damage-associated molecular patterns and vascular function Formyl peptide receptor-like 2 is expressed and functional in plasmacytoid dendritic cells, tissue-specific macrophage subpopulations, and eosinophils ogic mechanisms of acute ischemic stroke: An overview with emphasis on therapeutic significance beyond thrombolysis Ischemia-reperfusion injury in stroke Ischemic stroke and neuroprotection Inflammatory mechanisms in ischemic stroke: Role of inflammatory cells The science of stroke: Mechanisms in search of treatments Toll-like receptors in ischemia-reperfusion injury Thromboinflammation in Stroke Brain Damage Brain dendritic cells in ischemic stroke: Time course, activation state, and origin Temporal profile of ischemic tissue damage, neutrophil response, and vascular plugging following permanent and transient (2H) middle cerebral artery occlusion in the rat MMP-9-positive neutrophil infiltration is associated to blood-brain barrier breakdown and basal lamina type IV collagen degradation during hemorrhagic transformation after human ischemic stroke Targeting formyl peptide receptor 2 reduces leukocyte-endothelial interactions in a murine model of stroke Activation of the annexin 1 counter-regulatory circuit affords protection in the mouse brain microcirculation Lipocortin-1 is an endogenous inhibitor of ischemic damage in the rat brain The restorative role of annexin A1 at the blood-brain barrier Identification of an essential endogenous regulator of blood-brain barrier integrity, and its pathological and therapeutic implications Bacterial lipopolysaccharide selectively up-regulates the function of the chemotactic peptide receptor formyl peptide receptor 2 in murine microglial cells Antioxidants in the prevention of myocardial ischemia/reperfusion injury Myocardial ischemia-reperfusion injury: A neglected therapeutic target Pathogenesis of myocardial ischemia-reperfusion injury and rationale for therapy Myocardial reperfusion injury Matrix-dependent mechanism of neutrophil-mediated release and activation of matrix metalloproteinase 9 in myocardial ischemia/reperfusion The role of neutrophils in myocardial ischemia-reperfusion injury Annexin 1 peptides protect against experimental myocardial ischemia-reperfusion: Analysis of their mechanism of action Formyl-peptide receptor is not involved in the protection afforded by annexin 1 in murine acute myocardial infarct Lipocortin 1 reduces myocardial ischemia-reperfusion injury by affecting local leukocyte recruitment Annexin-1 peptide Anx-1(2-26) protects adult rat cardiac myocytes from cellular injury induced by simulated ischaemia Reperfusion-induced myocardial dysfunction is prevented by endogenous annexin-A1 and its N-terminal-derived peptide Ac-ANX-A1(2-26) Endogenous Annexin-A1 Regulates Haematopoietic Stem Cell Mobilisation and Inflammatory Response Post Myocardial Infarction in Mice In Vivo Small-molecule-biased formyl peptide receptor agonist compound 17b protects against myocardial ischaemia-reperfusion injury in mice Update on ischemia-reperfusion injury in kidney transplantation: Inhibition by a soluble P-selectin ligand Annexin 1 mimetic peptide protects against renal ischemia/reperfusion injury in rats Annexin A1 protein attenuates cyclosporine-induced renal hemodynamics changes and macrophage infiltration in rats Update on Diabetic Nephropathy: Core Curriculum Annexin A1 attenuates microvascular complications through restoration of Akt signalling in a murine model of type 1 diabetes Human intestinal ischemia-reperfusion-induced inflammation characterized: Experiences from a new translational model TLR2 modulates antibodies required for intestinal ischemia/reperfusion-induced damage and inflammation Mesenchymal stromal cell therapy for the treatment of intestinal ischemia: Defining the optimal cell isolate for maximum therapeutic benefit Potential roles of neutrophils in regulating intestinal mucosal inflammation of inflammatory bowel disease Leukocyte antiadhesive actions of annexin 1: ALXR-and FPR-related anti-inflammatory mechanisms Annexin A1-containing extracellular vesicles and polymeric nanoparticles promote epithelial wound repair Annexin-1 modulates repair of gastric mucosal injury Annexin A1, formyl peptide receptor, and NOX1 orchestrate epithelial repair Annexin-A1 peptide down-regulates the leukocyte recruitment and up-regulates interleukin-10 release into lung after intestinal ischemia-reperfusion in mice Annexin A1 regulates intestinal mucosal injury, inflammation, and repair Pleiotropic roles of formyl peptide receptors Ac2-26, an Annexin A1 Peptide, Attenuates Ischemia-Reperfusion-Induced Acute Lung Injury Neutrophil NADPH-oxidase activation by an annexin AI peptide is transduced by the formyl peptide receptor (FPR), whereas an inhibitory signal is generated independently of the FPR family receptors Enhancing the interaction between annexin-1 and formyl peptide receptors regulates microglial activation to protect neurons from ischemia-like injury Cathepsin G-dependent modulation of platelet thrombus formation in vivo by blood neutrophils Identification of neutrophil granule protein cathepsin G as a novel chemotactic agonist for the G protein-coupled formyl peptide receptor Mouse cathelin-related antimicrobial peptide chemoattracts leukocytes using formyl peptide receptor-like 1/mouse formyl peptide receptor-like 2 as the receptor and acts as an immune adjuvant The soluble D2D3(88-274) fragment of the urokinase receptor inhibits monocyte chemotaxis and integrin-dependent cell adhesion Defective polymorphonuclear leukocyte formyl peptide receptor(s) in juvenile periodontitis N-formyl-methionyl-leucyl-phenylalanine (fMLP) promotes osteoblast differentiation via the N-formyl peptide receptor 1-mediated signaling pathway in human mesenchymal stem cells from bone marrow Formylated humanin activates both formyl peptide receptor-like 1 and 2 T20/DP178, an ectodomain peptide of human immunodeficiency virus type 1 gp41, is an activator of human phagocyte N-formyl peptide receptor The HIV-1 cell entry inhibitor T-20 potently chemoattracts neutrophils by specifically activating the N-formylpeptide receptor T21/DP107, A synthetic leucine zipper-like domain of the HIV-1 envelope gp41, attracts and activates human phagocytes by using G-protein-coupled formyl peptide receptors N36, a synthetic N-terminal heptad repeat domain of the HIV-1 envelope protein gp41, is an activator of human phagocytes Lipoxins and novel 15-epi-lipoxin analogs display potent anti-inflammatory actions after oral administration LL-37, the neutrophil granule-and epithelial cell-derived cathelicidin, utilizes formyl peptide receptor-like 1 (FPRL1) as a receptor to chemoattract human peripheral blood neutrophils, monocytes, and T cells Synthetic peptide MMK-1 is a highly specific chemotactic agonist for leukocyte FPRL1 Human mitochondria-derived N-formylated peptides are novel agonists equally active on FPR and FPRL1, while Listeria monocytogenes-derived peptides preferentially activate FPR Pituitary adenylate cyclase-activating polypeptide 27 is a functional ligand for formyl peptide receptor-like 1 Internalization of PrP106-126 by the formyl-peptide-receptor-like-1 in glial cells A novel nonpeptide ligand for formyl peptide receptor-like 1 Regulatory effects of deoxycholic acid, a component of the anti-inflammatory traditional Chinese medicine Niuhuang, on human leukocyte response to chemoattractants Cross-talk between fMLP and vitronectin receptors triggered by urokinase receptor-derived SRSRY peptide A seven-transmembrane, G protein-coupled receptor, FPRL1, mediates the chemotactic activity of serum amyloid A for human phagocytic cells Activation of the chemotactic peptide receptor FPRL1 in monocytes phosphorylates the chemokine receptor CCR5 and attenuates cell responses to selected chemokines Utilization of two seven-transmembrane, G protein-coupled receptors, formyl peptide receptor-like 1 and formyl peptide receptor, by the synthetic hexapeptide WKYMVm for human phagocyte activation Boc-MLF and Boc-FLFLF are antagonists that preferentially inhibit activity triggered through the formyl peptide receptor Characterization of chenodeoxycholic acid as an endogenous antagonist of the G-coupled formyl peptide receptors N-terminal residues of the chemotaxis inhibitory protein of Staphylococcus aureus are essential for blocking formylated peptide receptor but not C5a receptor Peptides derived from HIV-1, HIV-2, Ebola virus, SARS coronavirus and coronavirus 229E exhibit high affinity binding to the formyl peptide receptor The immunosuppressant cyclosporin A antagonizes human formyl peptide receptor through inhibition of cognate ligand binding A new staphylococcal anti-inflammatory protein that antagonizes the formyl peptide receptor-like 1 N-terminus urea-substituted chemotactic peptides: New potent agonists and antagonists toward the neutrophil fMLF receptor The endogenous opioid spinorphin blocks fMet-Leu-Phe-induced neutrophil chemotaxis by acting as a specific antagonist at the N-formylpeptide receptor subtype FPR Identification of peptides that antagonize formyl peptide receptor-like 1-mediated signaling


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
extension: .txt
mime: text/plain
words: 7324
sentence: 332
flesch: 38
cache: cache/cord-343791-0vykwml5.txt
txt: txt/cord-343791-0vykwml5.txt
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.


id: cord-103837-iuvigqdx
author: Knierman, Michael D.
title: The Human Leukocyte Antigen Class II Immunopeptidome of SARS-CoV-2 Spike Glycoprotein
date: 2020-11-13
extension: .txt
mime: text/plain
words: 8585
sentence: 305
flesch: 46
cache: cache/cord-103837-iuvigqdx.txt
txt: txt/cord-103837-iuvigqdx.txt
summary:
  The donor ID is listed on X-axis and the total number of spike protein peptides from that particular donor denoted on the Y-axis. (A) Prevalence of peptide clusters across donors.


id: cord-003020-q69f57el
author: Farhadi, Tayebeh
title: Computer-aided design of amino acid-based therapeutics: a review
date: 2018-05-14
extension: .txt
mime: text/plain
words: 8674
sentence: 434
flesch: 36
cache: cache/cord-003020-q69f57el.txt
txt: txt/cord-003020-q69f57el.txt
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.


id: cord-262253-3ovqhypt
author: Iqbal, Umar H.
title: The Use of Antimicrobial and Antiviral Drugs in Alzheimer’s Disease
date: 2020-07-12
extension: .txt
mime: text/plain
words: 8842
sentence: 382
flesch: 41
cache: cache/cord-262253-3ovqhypt.txt
txt: txt/cord-262253-3ovqhypt.txt
summary:
  Abeta42 is essential for parenchymal and vascular amyloid deposition in mice Abeta40 inhibits amyloid deposition in vivo Subacute meningoencephalitis in a subset of patients with AD after Abeta42 immunization Clinical effects of Abeta immunization (AN1792) in patients with AD in an interrupted trial A subset of NSAIDs lower amyloidogenic Abeta42 independently of cyclooxygenase activity Substrate-targeting gamma-secretase modulators Effect of tarenflurbil on cognitive decline and activities of daily living in patients with mild Alzheimer disease: A randomized controlled trial A phase 3 trial of semagacestat for treatment of Alzheimer's disease Inositol stereoisomers stabilize an oligomeric aggregate of Alzheimer amyloid beta peptide and inhibit abeta -induced toxicity A phase 2 randomized trial of ELND005, scyllo-inositol, in mild to moderate Alzheimer disease Alzheimer's Amyloid-β is an Antimicrobial Peptide: A Review of the Evidence Characterizing the preclinical stages of Alzheimer's disease and the prospect of presymptomatic intervention Amyloid β deposition, neurodegeneration, and cognitive decline in sporadic Alzheimer's disease: A prospective cohort study Blood-based biomarkers for Alzheimer disease: Mapping the road to the clinic Diagnostic Value of Cerebrospinal Fluid Biomarkers (Phospho-Tau181, total-Tau, Aβ42, and Aβ40) in Prodromal Stage of Alzheimer's Disease and Dementia with Lewy Bodies Plasma β-amyloid in Alzheimer's disease and vascular disease Serum neurofilament light in familial Alzheimer disease: A marker of early neurodegeneration Detection of misfolded Aβ oligomers for sensitive biochemical diagnosis of Alzheimer's disease Seeding selectivity and ultrasensitive detection of tau aggregate conformers of Alzheimer disease Inflammation as a central mechanism in Alzheimer's disease. Aβ peptides are produced through a two-step cleavage process, in which APP is metabolized into smaller fragments.


id: cord-320497-e5pb83mj
author: Zunszain, Patricia A.
date: 2010-01-15
extension: .txt
mime: text/plain
words: 9966
sentence: 333
flesch: 49
cache: cache/cord-320497-e5pb83mj.txt
txt: txt/cord-320497-e5pb83mj.txt
title:
  Insights into Cleavage Specificity from the Crystal Structure of Foot-and-Mouth Disease Virus 3C Protease Complexed with a Peptide Substrate

summary:
  However, peptide cleavage assays previously showed that incorporation of Glu at this position only reduces the cleavage rate by a factor of 2, 8 consistent with the common occurrence of P1-Glu in FMDV 3C pro substrates. However, there is little sequence conservation at this position in FMDV 3C pro substrates, and the most common alternative P3′ residues (Tyr, Ala and Ile) would not maintain this interaction.


id: cord-003948-npijn7co
author: Esfandiyari, Reza
date: 2019-10-23
extension: .txt
mime: text/plain
words: 3246
sentence: 145
flesch: 39
cache: cache/cord-003948-npijn7co.txt
txt: txt/cord-003948-npijn7co.txt
title:
  Performance evaluation of antimicrobial peptide ll-37 and hepcidin and β-defensin-2 secreted by mesenchymal stem cells

summary:
  Antimicrobial peptides exert various mechanisms such as changing cell membrane permeability which leads to inhibition or death of bacterial cells. mesenchymal stem cells (MSCs) are key to produce antimicrobial peptides and to inhibit the growth of pathogens.


id: cord-254404-lrsqrc2u
author: Yañez-Guerra, Luis Alfonso
title: Echinoderms provide missing link in the evolution of PrRP/sNPF-type neuropeptide signalling
date: 2020-06-24
extension: .txt
mime: text/plain
words: 9753
sentence: 300
flesch: 34
cache: cache/cord-254404-lrsqrc2u.txt
txt: txt/cord-254404-lrsqrc2u.txt
summary:
  Phyla in which sNPF-type peptides/precursors and sNPF-type receptors have been identified are labelled with red-filled squares. The grey square for sNPF in M. expansa, for which only transcriptome sequence data are available, indicates that sNPFtype peptides and sNPF-type receptor(s) are likely to be present in this species because sNPF-type peptides and sNPF-type receptors have been identified in another platyhelminth species, S. mediterranea, for which a genome sequence is available.


id: cord-002141-9mxi4dzi
author: Memczak, Henry
title: Anti-Hemagglutinin Antibody Derived Lead Peptides for Inhibitors of Influenza Virus Binding
date: 2016-07-14
extension: .txt
mime: text/plain
words: 8796
sentence: 402
flesch: 47
cache: cache/cord-002141-9mxi4dzi.txt
txt: txt/cord-002141-9mxi4dzi.txt
summary:
  The antibody derived peptide PeB and its mutant variant PeB GF are promising hemagglutinin binding peptides, which both could have potential for application in viral diagnostics and therapeutics. A more epitope-oriented accession to binding peptides is the search for paratope-derived peptides from variable regions of specific antibodies [24] .


id: cord-284690-ogu1gmcb
author: da Cunha, Nicolau B.
date: 2016-11-23
extension: .txt
mime: text/plain
words: 9495
sentence: 354
flesch: 29
cache: cache/cord-284690-ogu1gmcb.txt
txt: txt/cord-284690-ogu1gmcb.txt
title:
  The next generation of antimicrobial peptides (AMPs) as molecular therapeutic tools for the treatment of diseases with social and economic impacts

summary:
  Overview: global and local impact of antibiotic resistance The emergence of peptides in the pharmaceutical business: from exploration to exploitation Mechanisms and consequences of bacterial resistance to antimicrobial peptides Antibiotic strategies in the era of multidrug resistance The expanding scope of antimicrobial peptide structures and their modes of action The antifungal plant defensin AhPDF1.1b is a beneficial factor involved in adaptive response to zinc overload when it is expressed in yeast cells Engineered cationic antimicrobial peptides to overcome multidrug resistance by ESKAPE pathogens Magnifection: a new platform for expressing recombinant vaccines in plants CRISPR/Cas9 for genome editing: progress, implications and challenges Antimicrobial peptides targeting Grampositive bacteria Gram-positive bacterial cell envelopes: the impact on the activity of antimicrobial peptides Antimicrobial peptides and their pore/ion channel properties in neutralization of pathogenic microbes Understanding bacterial resistance to antimicrobial peptides: from the surface to deep inside Induced bacterial cross-resistance toward host antimicrobial peptides: a worrying phenomenon New edge of antibiotic development: antimicrobial peptides and corresponding resistance Correlation of cell membrane lipid profiles with daptomycin resistance in methicillin-resistant Staphylococcus aureus Cardiolipin prevents membrane translocation and permeabilization by daptomycin Heterogeneity of mprF sequences in methicillin-resistant Staphylococcus aureus clinical isolates: role in cross-resistance between daptomycin and host defense antimicrobial peptides Daptomycin resistance in enterococci is associated with distinct alterations of cell membrane phospholipid content D-Alanylation of teichoic acids promotes group A Streptococcus antimicrobial peptide resistance, neutrophil survival, and epithelial cell invasion Lipopolysaccharide endotoxins Antimicrobial peptide resistance of Vibrio cholerae results from an LPS modification pathway related to nonribosomal peptide synthetases A metalloproteinase karilysin present in the majority of Tannerella forsythia isolates inhibits all pathways of the complement system A group B streptococcal pilus protein promotes phagocyte resistance and systemic virulence Protein GRAB of Streptococcus pyogenes regulates proteolysis at the bacterial surface by binding a2-macroglobulin Bacterial biofilm: structure, function, and antimicrobial resistance Peptide therapeutics: current status and future directions Antimicrobial and host-defense peptides as new anti-infective therapeutic strategies Antimicrobial peptides (AMPs) as drug candidates: a patent review Quality specifications for peptide drugs: a regulatorypharmaceutical approach Antimicrobial peptides stage a comeback Future directions for peptide therapeutics development Rational design of engineered cationic antimicrobial peptides consisting exclusively of arginine and tryptophan, and their activity against multidrug-resistant pathogens Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria? Antimicrobial peptides in toroidal and cylindrical pores Novel engineered peptides of a phage lysin as effective antimicrobials against multidrug resistant, Acinetobacter baumannii Antimicrobial peptides: versatile biological properties Interaction-site prediction for protein complexes: a critical assessment Biopharmaceutical production in plants: problems, solutions and opportunities N-glycosylation of plant recombinant pharmaceuticals Production and glycosylation of plant-made pharmaceuticals: the antibodies as a challenge Expression of rat b(1,4)-N-acetylglucosaminyltransferase III in Nicotiana tabacum remodels the plant-specific N-glycosylation End-tagging of ultra-short antimicrobial peptides by W/ F stretches to facilitate bacterial killing Engineered chimeric peptides as antimicrobial surface coating agents toward infection-free implants D-Enantiomeric peptides that eradicate wildtype and multi-drug resistant biofilms and protect against lethal Pseudomonas aeruginosa infections Membrane insertion and orientation of polyalanine peptides: a (15)N solid-state NMR spectroscopy investigation Structural and functional characterization of a multifunctional alanine-rich peptide analogue from Pleuronectes americanus Chemistry for peptide and protein PEGylation PEG-peptide conjugates Efficient backbone cyclization of linear peptides by a recombinant asparaginyl endopeptidase Global analysis of peptide cyclization efficiency The effects of the C-terminal amidation of mastoparans on their biological actions and interactions with membrane-mimetic systems Characterization of antimicrobial peptides toward the development of novel antibiotics Antifungal plant defensins: mechanisms of action and production Lanthipeptides: chemical synthesis versus in vivo biosynthesis as tools for pharmaceutical production Chemical synthesis of proteins Synthetic therapeutic peptides: science and market Dengue fever virus and Japanese encephalitis virus synthetic peptides, with motifs to fit HLA class I haplotypes prevalent in human populations in endemic regions, can be used for application to skin Langerhans cells to prime antiviral CD8+ cytotoxic T cells (CTLs): a novel approach to the protection of humans Expression systems for heterologous production of antimicrobial peptides Current scenario of peptide-based drugs: the key roles of cationic antitumor and antiviral peptides A review of antimicrobial peptides and their therapeutic potential as anti-infective drugs Plant antimicrobial peptides Engineering viral expression vectors for plants: the 'full virus' and the 'deconstructed virus' strategies Plant viral vectors for delivery by Agrobacterium Viral vectors for the expression of proteins in plants Expanding the genetic editing tool kit: ZFNs, TALENs, and CRISPR-Cas9 The CRISPR-Cas system for plant genome editing: advances and opportunities The CRISPR/Cas9 system for plant genome editing and beyond Development and applications of CRISPR-Cas9 for genome engineering Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering Antimicrobial Resistance: Tackling a Crisis for the Health and Wealth of Nations. key: cord-284690-ogu1gmcb authors: da Cunha, Nicolau B.; Cobacho, Nicole B.; Viana, Juliane F.C.; Lima, Loiane A.; Sampaio, Kamila B.O.; Dohms, Stephan S.M.; Ferreira, Arthur C.R.; de la Fuente-Núñez, César; Costa, Fabrício F.; Franco, Octávio L.; Dias, Simoni C. title: The next generation of antimicrobial peptides (AMPs) as molecular therapeutic tools for the treatment of diseases with social and economic impacts date: 2016-11-23 journal: Drug Discov Today DOI: 10.1016/j.drudis.2016.10.017 sha: doc_id: 284690 cord_uid: ogu1gmcb Anti-infective drugs have had a key role in the contemporary world, contributing to dramatically decrease mortality rates caused by infectious diseases worldwide.


id: cord-009743-2rntyccn
author: Wang, Ke‐Ming
date: 2008-09-10
extension: .txt
mime: text/plain
words: 4644
sentence: 193
flesch: 44
cache: cache/cord-009743-2rntyccn.txt
txt: txt/cord-009743-2rntyccn.txt
title:
  Characterization of inhibitory mechanism and antifungal activity between group‐1 and group‐2 phytocystatins from taro (Colocasia esculenta)

summary:
  Expressed recombinant FL, Nt and Ct peptides were further purified from the E. coli and analyzed by 12.5% SDS ⁄ To determine whether the connection between the Nt and Ct peptides is important for inhibitory capacity of the FL peptide, equal amounts of Nt and Ct peptides were mixed and the inhibitory capacity of the mixture was then compared with that of only the Nt or FL peptides.


id: cord-001726-d7iwkatn
author: Henry, Kevin A.
date: 2015-08-04
extension: .txt
mime: text/plain
words: 10454
sentence: 231
flesch: 13
cache: cache/cord-001726-d7iwkatn.txt
txt: txt/cord-001726-d7iwkatn.txt
title:
  Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold

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.


id: cord-000128-t74b5j2j
author: Laufer, S.D
date: 2008-12-17
extension: .txt
mime: text/plain
words: 11965
sentence: 487
flesch: 34
cache: cache/cord-000128-t74b5j2j.txt
txt: txt/cord-000128-t74b5j2j.txt
title:
  Peptide-Mediated Cellular Delivery of Oligonucleotide-Based Therapeutics In Vitro: Quantitative Evaluation of Overall Efficacy Employing Easy to Handle Reporter Systems

summary:
  The versatility of oligonucleotides as potential therapeutics Gene therapy with viral vectors Gene therapy: twenty-first century medicine A pilot study of in vivo liver-directed gene transfer with an adenoviral vector in partial ornithine transcarbamylase deficiency LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1 Fatal systemic inflammatory response syndrome in a ornithine transcarbamylase deficient patient following adenoviral gene transfer Gene therapy put on hold as third child develops cancer TAT peptide on the surface of liposomes affords their efficient intracellular delivery even at low temperature and in the presence of metabolic inhibitors Comparison between the interactions of adenovirus-derived peptides with plasmid DNA and their role in gene delivery mediated by liposomepeptide-DNA virus-like nanoparticles Vectors based on reducible polycations facilitate intracellular release of nucleic acids Cell transfection in vitro and in vivo with nontoxic TAT peptide-liposome-DNA complexes HIV-1 Tat protein transduction domain peptide facilitates gene transfer in combination with cationic liposomes Unique features of a pH-sensitive fusogenic peptide that improves the transfection efficiency of cationic liposomes A versatile reducible polycation-based system for efficient delivery of a broad range of nucleic acids Tat peptide-mediated intracellular delivery of pharmaceutical nanocarriers Evaluation of transportan 10 in PEI mediated plasmid delivery assay Efficient gene transfer by histidylated polylysine/pDNA complexes Branched co-polymers of histidine and lysine are efficient carriers of plasmids A novel transfecting peptide comprising a tetrameric nuclear localization sequence Highly branched HK peptides are effective carriers of siRNA Macro-branched cell-penetrating peptide design for gene delivery Protein transduction by lipidic peptide dendrimers Tat-Conjugated PAMAM Dendrimers as Delivery Agents for Antisense and siRNA Oligonucleotides Design, synthesis, and characterization of pH-sensitive PEG-PE conjugates for stimuli-sensitive pharmaceutical nanocarriers: the effect of substitutes at the hydrazone linkage on the ph stability of PEG-PE conjugates Smart drug carriers: PEGylated TATpmodified pH-sensitive liposomes Octaarginine-modified multifunctional envelope-type nanoparticles for gene delivery Multiblock reducible copolypeptides containing histidine-rich and nuclear localization sequences for gene delivery Intracellular siRNA and precursor miRNA trafficking using bioresponsive copolypeptides Cellular uptake of the tat protein from human immunodeficiency virus Autonomous functional domains of chemically synthesized human immunodeficiency virus tat transactivator protein alpha-2,8-Polysialic acid is the neuronal surface receptor of antennapedia homeobox peptide Tat-mediated delivery of heterologous proteins into cells Prochiantz A. Downregulation of amyloid precursor protein inhibits neurite outgrowth in vitro In vivo protein transduction: delivery of a biologically active protein into the mouse Cellpenetrating peptides Cell-penetrating peptides: mechanism and kinetics of cargo delivery Handbook of Cell-Penetrating Peptides Cell penetrating peptides: intracellular pathways and pharmaceutical perspectives Cell-penetrating peptides: from molecular mechanisms to therapeutics Cell-penetrating peptides for drug delivery across membrane barriers Recent Developments in Peptidebased Nucleic Acid Delivery Conjugates of oligonucleotides and analogues with cell penetrating peptides as gene silencing agents Delivery of proteins and nucleic acids using a non-covalent peptide-based strategy Peptide-based Nanoparticle for ex vivo and in vivo drug delivery Cell internalization of the third helix of the Antennapedia homeodomain is receptor-independent A new peptide vector for efficient delivery of oligonucleotides into mammalian cells To illustrate current limitations of non-viral nucleic acid delivery systems, we present own data as an example and discuss options of how to enhance trafficking of molecules entrapped in cellular compartments.


id: cord-013952-zp4q3ztr
author: Moll, Gert N.
title: Biosynthesis of lanthionine-constrained agonists of G protein-coupled receptors
date: 2020-10-30
extension: .txt
mime: text/plain
words: 3940
sentence: 186
flesch: 38
cache: cache/cord-013952-zp4q3ztr.txt
txt: txt/cord-013952-zp4q3ztr.txt
summary:
  [29] . Following the elucidation of the precursor sequence of the lanthipeptide gallidermin, as early as 1988, it was recognized that the introduction of (methyl)lanthionines into therapeutic peptides, such as agonistic peptide hormones might constitute a valuable opportunity to discover specific and stable lanthionine-containing therapeutics Mechanistic understanding of lanthipeptide biosynthetic enzymes Mechanistic aspects of lanthipeptide leaders Biosynthesis, immunity, regulation, mode of action and engineering of the model lantibiotic nisin In vitro activity of the nisin dehydratase NisB Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB Structure and mechanism of the lantibiotic cyclase involved in nisin biosynthesis Requirements of the engineered leader peptide of nisin for inducing modification, export, and cleavage Prepeptide sequence of epidermin, a ribosomally synthesized antibiotic with four sulphide-rings Nist, the transporter of the lantibiotic nisin, can transport fully modified, dehydrated, and unmodified prenisin and fusions of the leader peptide with non-lantibiotic peptides Lantibiotic structures as guidelines for the design of peptides that can be modified by lantibiotic enzymes Post-translational modification of therapeutic peptides by NisB, the dehydratase of the lantibiotic nisin Production of dehydroamino acid-containing peptides by Lactococcus lactis Nisc, the cyclase of the lantibiotic nisin, can catalyze cyclization of designed nonlantibiotic peptides Sec-mediated transport of posttranslationally dehydrated peptides in Lactococcus lactis Translocation of a thioether-bridged azurin peptide fragment via the sec pathway in Lactococcus lactis Investigation of the substrate specificity of lacticin 481 synthetase by using nonproteinogenic amino acids Production of lantipeptides in Escherichia coli Lanthionine introduction into nukacin ISK-1 prepeptide by co-expression with modification enzyme NukM in Escherichia coli Mechanistic dissection of the enzyme complexes involved in biosynthesis of lacticin 3147 and nisin High-throughput screening for substrate specificity-adapted mutants of the nisin dehydratase NisB Structural characterization of lacticin 3147, a two-peptide lantibiotic with synergistic activity Activity and export of engineered nisin-(1-22) analogs Bacterial display and screening of posttranslationally thioether-stabilized peptides Substrate specificity of the secreted nisin leader peptidase NisP Structural characterization of four prochlorosins: a novel class of lantipeptides produced by planktonic marine cyanobacteria Use of lantibiotic synthetases for the preparation of bioactive constrained peptides Acute respiratory distress syndrome leads to reduced ratio of ACE/ACE2 activities and is prevented by angiotensin-(1-7) or an angiotensin II receptor antagonist Does activation of the protective renin-angiotensin system have therapeutic potential in COVID-19?


id: cord-315115-f61xcnuw
author: Wang, Guangshun
date: 2020-08-07
extension: .txt
mime: text/plain
words: 12172
sentence: 676
flesch: 46
cache: cache/cord-315115-f61xcnuw.txt
txt: txt/cord-315115-f61xcnuw.txt
title:
  Bioinformatic Analysis of 1000 Amphibian Antimicrobial Peptides Uncovers Multiple Length-Dependent Correlations for Peptide Design and Prediction

summary:
  Toll and beyond Antimicrobial peptides of multicellular organisms Host defense peptides: Front-line immunomodulators Design and synthesis of antimicrobial peptides Complete sequence-specific 1 H nuclear magnetic resonance assignments for the alpha-amylase polypeptide inhibitor tendamistat from Streptomyces tendae Three-dimensional NMR spectroscopy of a protein in solution Rational design of alpha-helical antimicrobial peptides: Do's and don'ts Solution NMR studies of amphibian antimicrobial peptides: Linking structure to function? Correlation of three-dimensional structures with the antibacterial activity of a group of peptides designed based on a nontoxic bacterial membrane anchor Prolines are not essential residues in the barrel-stave model for ion channels induced by alamethicin analogues High-resolution conformation of gramicidin A in a lipid bilayer by solid-state NMR Mode of action of membrane active antimicrobial peptides Detergent-like actions of linear amphipathic cationic antimicrobial peptides Describing the mechanism of antimicrobial peptide action with the interfacial activity model Anionic Lipid Clustering Model Membrane Thinning and Thickening Induced by Membrane-Active Amphipathic Peptides. Front Membrane Permeabilization Mechanisms Membrane pores induced by magainin Decoding the functional roles of cationic side chains of the major antimicrobial region of human cathelicidin LL-37 Sublethal concentrations of pleurocidin-derived antimicrobial peptides inhibit macromolecular synthesis in Escherichia coli Molecular mechanisms of LL-37-induced receptor activation: An overview APD3: The antimicrobial peptide database as a tool for research and education APD2: The updated antimicrobial peptide database and its application in peptide design APD: The Antimicrobial Peptide Database Purification and characterization of antimicrobial peptides from the skin of the North American green frog Rana clamitans Peptides with antimicrobial activity from four different families isolated from the skins of the North American frogs Rana luteiventris, Rana berlandieri and Rana pipiens Induction of synthesis of an antimicrobial peptide in the skin of the freeze-tolerant frog, Rana sylvatica, in response to environmental stimuli Anti-infection peptidomics of amphibian skin Peptidomic approach identifies cruzioseptins, a new family of potent antimicrobial peptides in the splendid leaf frog Cruziohyla calcarifer Evidence from peptidomic analysis of skin secretions that the red-legged frogs, Rana aurora draytonii and Rana aurora aurora, are distinct species Peptidomic analysis in the discovery of therapeutically valuable peptides in amphibian skin secretions A proposed nomenclature for antimicrobial peptides from frogs of the genus Leptodactylus Defensins of vertebrate animals Structure and biology of cathelicidins Cathelicidin-DM is an antimicrobial peptide from Duttaphrynus melanostictus and Has Wound-Healing Therapeutic Potential Antimicrobial peptides and wound healing: Biological and therapeutic considerations Gold-nanoparticles coated with the antimicrobial peptide esculentin-1a(1-21)NH 2 as a reliable strategy for antipseudomonal drugs Targeting the fungal cell wall: Current therapies and implications for development of alternative antifungal agents Chytridiomycosis causes amphibian mortality associated with population declines in the rain forests of Australia and Central America The role of amphibian antimicrobial peptides in protection of amphibians from pathogens linked to global amphibian declines Urbańczyk-Lipkowska, Z. Natural Antimicrobial Peptides as Inspiration for Design of a New Generation Antifungal Compounds Design of Antimicrobial Peptides: Progress Made with Human Cathelicidin LL-37 Antiviral peptides as promising therapeutic drugs Inhibition of HIV infection by caerin 1 antimicrobial peptides Natural antimicrobial peptides as promising anti-HIV candidates Identification of novel human immunodeficiency virus type 1-inhibitory peptides based on the antimicrobial peptide database An Amphibian Host Defense Peptide Is Virucidal for Human H1 Hemagglutinin-Bearing Influenza Viruses The Amphibian Antimicrobial Peptide Temporin B Inhibits In Vitro Herpes Simplex Virus 1 Infection Amphibian antimicrobial peptides and Protozoa: Lessons from parasites Anti-Trypanosoma cruzi activity without cytotoxicity to mammalian cells Antimalarial activities of dermaseptin S4 derivatives Antimicrobial peptides: A new class of antimalarial drugs? Anticancer efficacy of Magainin2 and analogue peptides Agents from amphibians with anticancer properties.


id: cord-000264-o80duxhs
author: Chandramouli, Kondethimmanahalli
title: Proteomics: Challenges, Techniques and Possibilities to Overcome Biological Sample Complexity
date: 2009-12-08
extension: .txt
mime: text/plain
words: 12282
sentence: 448
flesch: 24
cache: cache/cord-000264-o80duxhs.txt
txt: txt/cord-000264-o80duxhs.txt
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] .


id: cord-012391-53hgrs40
author: Miazga-Karska, Malgorzata
title: Anti-Acne Action of Peptides Isolated from Burdock Root—Preliminary Studies and Pilot Testing
date: 2020-04-27
extension: .txt
mime: text/plain
words: 6464
sentence: 272
flesch: 45
cache: cache/cord-012391-53hgrs40.txt
txt: txt/cord-012391-53hgrs40.txt
summary:
  Briefly, 0.5 µL of peptide sample was mixed with the same volume of matrix saturated solution containing α-cyano-4-hydroxycinnamic acid (HCCA, Bruker, Bremen, Germany) and 2,5-dihydroxy benzoic acid (DHB, Bruker, Bremen, Germany). Other authors also report favorable, high SI values of tested antimicrobial peptides (AMPs) from plants and the possibilities of their application in the cosmetics, medical, food, or agriculture industries


id: cord-022779-himray6q
title: Abstracts of oral presentations
date: 2005-06-10
extension: .txt
mime: text/plain
words: 3624
sentence: 149
flesch: 39
cache: cache/cord-022779-himray6q.txt
txt: txt/cord-022779-himray6q.txt
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.


id: cord-274101-vm9nh8lc
author: Perez Espitia, Paula Judith
date: 2012-02-29
extension: .txt
mime: text/plain
words: 12728
sentence: 456
flesch: 31
cache: cache/cord-274101-vm9nh8lc.txt
txt: txt/cord-274101-vm9nh8lc.txt
title:
  Bioactive Peptides: Synthesis, Properties, and Applications in the Packaging and Preservation of Food

summary:
  Current EU approved additives and their E numbers Defensins: antimicrobial peptides of innate immunity Immunomodulatory peptides obtained by the enzymatic hydrolysis of whey proteins Principles of mass transfer Development of cellulose acetate-based antimicrobial food packaging materials for controlled release of lysozyme Polymer surface modification for the attachment of bioactive compounds Development and characterization of an antimicrobial packaging film coating containing nisin for inhibition of Listeria monocytogenes Antimicrobial plastic film: physico-chemical characterization and nisin desorption modeling Innovative multilayer antimicrobial films made with Nisaplin ® or nisin and cellulosic ethers: physico-chemical characterization, bioactivity and nisin desorption kinetics Simulating diffusion model and determining diffusivity of potassium sorbate through plastics to develop antimicrobial packaging films The role of cationic antimicrobial peptides in innate host defences Antimicrobial and host-defense peptides as new anti-infective therapeutic strategies Antimicrobial activities of amphiphilic peptides covalently bonded to a water-insoluble resin A coating for use as an antimicrobial and antioxidative packaging material incorporating nisin and [alpha]-tocopherol Studies on anticancer activities of antimicrobial peptides The antibacterial activity of magainin I immobilized onto mixed thiols self-assembled monolayers Proteomics for studying cancer cells and the development of chemoresistance Antifungal properties and mode of action of psacotheasin, a novel knottin-type peptide derived from Psacothea hilaris Antifungal activity of synthetic peptide derived from halocidin, antimicrobial peptide from the tunicate, Halocynthia aurantium Peptide antimicrobial agents Chemical synthesis of peptides and proteins Properties of nisin-incorporated polymer coatings as antimicrobial packaging materials Bioactive peptides: production and functionality Thermal, mechanical and water vapor barrier properties of sodium caseinate films containing antimicrobials and their inhibitory action on Listeria monocytogenes Antifungal mechanism of SMAP-29 (1-18) isolated from sheep myeloid mRNA against Trichosporon beigelii Antitumor activity of the antimicrobial peptide magainin II against bladder cancer cell lines Virucidal activity of a scorpion venom peptide variant mucroporin-M1 against measles, SARS-CoV and influenza H5N1 viruses Recombinant production of antimicrobial peptides in Escherichia coli: a review Peptide-derivatized dendrimers inhibit human cytomegalovirus infection by blocking virus binding to cell surface heparan sulfate Sínteses química e enzimática de peptídeos: princípios básicos e aplicações High-pressure processing and antimicrobial biodegradable packaging to control Listeria monocytogenes during storage of cooked ham Development and characterization of an active polyethylene film containing Lactobacillus curvatus CRL705 In animals, antimicrobial peptides are produced mainly in those tissues exposed to adverse conditions such as skin, eyes, and lungs, which are more likely to be in contact with microorganisms (Zasloff 2002; Papo and Shai 2003) .


id: cord-003084-y4w3plro
author: McClorey, Graham
title: Cell-Penetrating Peptides to Enhance Delivery of Oligonucleotide-Based Therapeutics
date: 2018-05-05
extension: .txt
mime: text/plain
words: 8144
sentence: 240
flesch: 25
cache: cache/cord-003084-y4w3plro.txt
txt: txt/cord-003084-y4w3plro.txt
summary:
  Drug Des Functional correction in mouse models of muscular dystrophy using exon-skipping tricyclo-DNA oligomers Elucidation of muscle-binding peptides by phage display screening Effects of systemic multiexon skipping with peptide-conjugated morpholinos in the heart of a dog model of Duchenne muscular dystrophy Improved cell-penetrating peptide-PNA conjugates for splicing redirection in HeLa cells and exon skipping in mdx mouse muscle Pip5 transduction peptides direct high efficiency oligonucleotide-mediated dystrophin exon skipping in heart and phenotypic correction in mdx mice Arginine-rich cell-penetrating peptide dramatically enhances AMO-mediated ATM aberrant splicing correction and enables delivery to brain and cerebellum Nusinersen versus Sham Control in Later-Onset Spinal Muscular Atrophy Nusinersen versus Sham Control in Infantile-Onset Spinal Muscular Atrophy Dystrophin isoform induction in vivo by antisense-mediated alternative splicing Antisense-induced myostatin exon skipping leads to muscle hypertrophy in mice following octa guanidine morpholino oligomer treatment Dual myostatin and dystrophin exon skipping by morpholino nucleic acid oligomers conjugated to a cell-penetrating peptide is a promising therapeutic strategy for the treatment of duchenne muscular dystrophy Systemic Antisense Therapeutics for Dystrophin and Myostatin Exon Splice Modulation Improve Muscle Pathology of Adult mdx Mice Bi-specific splice-switching PMO oligonucleotides conjugated via a single peptide active in a mouse model of Duchenne muscular dystrophy Advances in the delivery of antisense oligonucleotides for combating bacterial infectious diseases A new peptide vector for efficient delivery of oligonucleotides into mammalian cells Mechanisms and optimization of in vivo delivery of lipophilic siRNAs Recent developments in retro peptides and proteins-An ongoing topochemical exploration Highly branched HK peptides are effective carriers of siRNA Peptide Nanoparticle Delivery of Charge-Neutral Splice-Switching Morpholino Oligonucleotides Cell-Specific siRNA Delivery Suppresses HIV-1 Infection in Humanized Mice Building cell selectivity into CPP-mediated strategies In vivo characterization of activatable cell penetrating peptides for targeting protease activity in cancer Enhancing siRNA-based cancer therapy using a new pH-responsive activatable cell-penetrating peptide-modified liposomal system Structure and topology of the influenza virus fusion peptide in lipid bilayers Many of the early identified CPPs derive from peptide sequences found in naturally occurring protein elements that exhibited inherent translocating properties.


id: cord-353815-w35spqqt
author: Huan, Yuchen
date: 2020-10-16
extension: .txt
mime: text/plain
words: 12289
sentence: 399
flesch: 27
cache: cache/cord-353815-w35spqqt.txt
txt: txt/cord-353815-w35spqqt.txt
title:
  Antimicrobial Peptides: Classification, Design, Application and Research Progress in Multiple Fields

summary:
  Archiv Activity and characterization of a pH-sensitive antimicrobial peptide Influence of pH on the activity of thrombin-derived antimicrobial peptides Effects of antimicrobial peptides on growth performance and small intestinal function in broilers under chronic heat stress Grouper (Epinephelus coioides) antimicrobial peptide epinecidin-1 exhibits antiviral activity against foot-andmouth disease virus in vitro A cancer vaccine based on the marine antimicrobial peptide pardaxin (GE33) for control of bladder-associated tumors Acquired resistance to the rice blast in transgenic rice accumulating the antimicrobial peptide thanatin Characterization and antimicrobial evaluation of SpPR-AMP1, a proline-rich antimicrobial peptide from the mud crab The vast structural diversity of antimicrobial peptides Predicting the minimal inhibitory concentration for antimicrobial peptides with rana-box domain The antibacterial peptide pyrrhocoricin inhibits the ATPase actions of DnaK and prevents chaperone-assisted protein folding Conformational fine-tuning of pore-forming peptide potency and selectivity Gain-of-function analogues of the pore-forming peptide melittin selected by orthogonal high-throughput screening Comparative analysis of two attacin genes from Hyphantria cunea The human anionic antimicrobial peptide dermcidin induces proteolytic defence mechanisms in Staphylococci Antimicrobial peptides: possible anti-infective agents Dalbavancin and telavancin in the treatment of infective endocarditis: a literature review Antimicrobial peptides: application informed by evolution Transcriptome analysis of Streptococcus pneumoniae treated with the designed antimicrobial peptides Intracellular targeting mechanisms by antimicrobial peptides Diptericinlike protein: an immune response gene regulated by the anti-bacterial gene induction pathway in drosophila De novo generation of short antimicrobial peptides with simple amino acid composition The antimicrobial peptides and their potential clinical applications Exploring small cationic peptides of different origin as potential antimicrobial agents in aquaculture Interactions of the antimicrobial peptide nisin Z with conventional antibiotics and the use of nanostructured lipid carriers to enhance antimicrobial activity Two optimized antimicrobial peptides with therapeutic potential for clinical antibiotic-resistant Staphylococcus aureus Membrane active antimicrobial peptides: translating mechanistic insights to design Mechanism of antifungal activity of antimicrobial peptide APP, a cell-penetrating peptide derivative, against Candida albicans: intracellular DNA binding and cell cycle arrest Membrane interactions of proline-rich antimicrobial peptide, Chex1-Arg20, multimers Effects of the peptide H-OOWW-NH2 and its derived lipopeptide C12-OOWW-NH2 on controlling of citrus postharvest green mold Implicit membrane investigation of the stability of antimicrobial peptide β-barrels and arcs Control of sour rot in citrus fruit by three insect antimicrobial peptides Effects of rabbit sacculus rotundus antimicrobial peptides on the intestinal mucosal immunity in chickens Effect of an antifungal peptide from oyster enzymatic hydrolysates for control of gray mold (Botrytis cinerea) on harvested strawberries Biological activity and structural aspects of PGLa interaction with membrane mimetic systems Membrane pore-formation correlates with the hydrophilic angle of histidine-rich amphipathic peptides with multiple biological activities The first antimicrobial peptide from sea amphibian Regulation of cell division in E. coli Antimicrobial packaging based on ε-polylysine bioactive film for the control of mycotoxigenic fungi in vitro and in bread Nucleation and growth of pores in 1,2-Dimyristoyl-sn-glycero-3-phosphocholine (DMPC) / cholesterol bilayer by antimicrobial peptides melittin, its mutants and cecropin P1 In vitro and MD simulation study to explore physicochemical parameters for antibacterial peptide to become potent anticancer peptide Antimicrobial peptides of the vaginal innate immunity and their role in the fight against sexually transmitted diseases The value of antimicrobial peptides in the age of resistance Influence of self-assembly on the performance of antimicrobial peptides Kappacin, a novel antibacterial peptide from bovine milk Temporins, small antimicrobial peptides with leishmanicidal activity The host antimicrobial peptide Bac71-35 binds to bacterial ribosomal proteins and inhibits protein synthesis


id: cord-332003-67e9fchy
author: Boisguérin, Prisca
title: Delivery of therapeutic oligonucleotides with cell penetrating peptides()
date: 2015-06-29
extension: .txt
mime: text/plain
words: 13090
sentence: 483
flesch: 35
cache: cache/cord-332003-67e9fchy.txt
txt: txt/cord-332003-67e9fchy.txt
summary:
  key: cord-332003-67e9fchy authors: Boisguérin, Prisca; Deshayes, Sébastien; Gait, Michael J.; O'Donovan, Liz; Godfrey, Caroline; Betts, Corinne A.; Wood, Matthew J.A.; Lebleu, Bernard title: Delivery of therapeutic oligonucleotides with cell penetrating peptides() date: 2015-06-29 journal: Among the many proposed tools for delivery, cell penetrating peptides (CPPs) have appeared as an easy to implement strategy and have led to encouraging data at least in murine models of human diseases, as will be reviewed later in this chapter.


id: cord-013364-pq9obtrc
author: Capasso, Domenica
title: Selective Targeting of αvβ5 Integrin in HepG2 Cell Line by RGDechi15D Peptide
date: 2020-09-19
extension: .txt
mime: text/plain
words: 6563
sentence: 265
flesch: 41
cache: cache/cord-013364-pq9obtrc.txt
txt: txt/cord-013364-pq9obtrc.txt
summary:
  Here we demonstrated the ability of the peptide to diminish both adhesion and invasion of HepG2 cells, an in vitro model system for hepatocellular carcinoma, to reduce the cell proliferation through an apoptotic process, and to interfere with the PI3K pathway. Data indicate that HepG2 cells show an average surface expression of 1.7 × 10 4 ± 1000 αvβ5 (Figure 1 ), while they do not present a significant amount of αvβ3 receptors.


id: cord-011184-ohdukhqt
author: Patil, Shital P.
title: Plant-Derived Bioactive Peptides: A Treatment to Cure Diabetes
date: 2019-07-22
extension: .txt
mime: text/plain
words: 7642
sentence: 265
flesch: 37
cache: cache/cord-011184-ohdukhqt.txt
txt: txt/cord-011184-ohdukhqt.txt
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.


id: cord-023200-3caevjvh
author: Falanga, Annarita
title: Membranotropic peptides mediating viral entry
date: 2018-02-13
extension: .txt
mime: text/plain
words: 6066
sentence: 221
flesch: 36
cache: cache/cord-023200-3caevjvh.txt
txt: txt/cord-023200-3caevjvh.txt
summary:
  [70, 71] As for enveloped virus fusion peptides, the amphipathic a-helix seems to be a key structural motif also for non-enveloped viruses. [3] On the other hand, the entry of non-enveloped viruses, which lacking the outer viral membrane are unable to take advantage of the cellular mechanism of membrane fusion, involves the activation of viral lytic factors that induce cell membrane rupture.


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
extension: .txt
mime: text/plain
words: 4797
sentence: 188
flesch: 41
cache: cache/cord-048360-n9sih438.txt
txt: txt/cord-048360-n9sih438.txt
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.


id: cord-103421-46owvqw8
author: Saunders, Jaclyn K.
date: 2020-05-21
extension: .txt
mime: text/plain
words: 5735
sentence: 203
flesch: 33
cache: cache/cord-103421-46owvqw8.txt
txt: txt/cord-103421-46owvqw8.txt
title:
  METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies - Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses

summary:
  The software program METATRYP v 2 and associated interactive web portals enables users to identify the frequency of shared tryptic peptides among taxonomic groups and evaluate the occurrence of specific tryptic peptides within complex communities. The software program METATRYP v 2 and associated interactive web portals enables users to identify the frequency of shared tryptic peptides among taxonomic groups and evaluate the occurrence of specific tryptic peptides within complex communities.


id: cord-346816-xys0g8b8
author: Shichijo, S.
date: 2004-10-20
extension: .txt
mime: text/plain
words: 1147
sentence: 33
flesch: 38
cache: cache/cord-346816-xys0g8b8.txt
txt: txt/cord-346816-xys0g8b8.txt
title:
  Assessment of synthetic peptides of severe acute respiratory syndrome coronavirus recognized by long‐lasting immunity

summary:
  Identification of a novel coronavirus in patients with severe acute respiratory syndrome A novel coronavirus associated with severe acute respiratory syndrome Characterization of a novel coronavirus associated with severe acute respiratory syndrome Assessment of immunoreactive synthetic peptides from the structural proteins of severe acute respiratory syndrome coronavirus Severe acute respiratory syndrome vaccine development: experiences of vaccination against avian infectious bronchitis coronavirus Effects of a SARS-associated coronavirus vaccine in monkeys Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus Expression of the monoclonal antibody against nucleocapsid antigen of SARS-associated coronavirus in autopsy tissues from SARS patients New multiplexed flow cytometric assay to measure anti-peptide antibody: a novel tool for monitoring immune responses to peptides used for immunization Analysis of false-positive associated with antibody tests for SARS-CoV in SLE patients Antibodies to SARS-like virus hint at repeated infections Dynamic observation IgG and IgM antibodies in patients with severe acute respiratory syndrome Microbiologic characteristics, serologic responses, and clinical manifestations in severe acute respiratory syndrome Detection of the anti-SARS coronavirus-specific antibody levels in 156 SARS patients Multiplexed quantification of human IgG, IgA, and IgM with the FlowMetrix TM system Severe acute respiratory syndrome (SARS) IgG reactive to CTL-directed epitopes of selfantigens is either lacking or unbalanced in atopic dermatitis patients Assessment of SARS peptides recognized by long-lasting immunity The authors thank Dr Nguyen Le Hang, Ms. Nguyen Thu Ha and Pham Phuong Thuy for supporting the co-ordination and implementation of this research project in Vietnam, and Drs Masamichi Koujiro and Akira Yamada of Kurume University School of Medicine, Asahi-machi, Kurume, Fukuoka, Japan, for co-ordinating this research. The method for the preparation of immobilized peptides was the same as the method used for ELISA plate preparation, as described in the legend of Fig. 4 .


id: cord-022499-7d58f1k3
author: Mall, Sanjay
title: Transmembrane α helices
date: 2004-01-07
extension: .txt
mime: text/plain
words: 12227
sentence: 399
flesch: 45
cache: cache/cord-022499-7d58f1k3.txt
txt: txt/cord-022499-7d58f1k3.txt
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) .


id: cord-314604-w61sqy17
author: Crone, Niek S. A.
title: Modulation of Coiled-Coil Binding Strength and Fusogenicity through Peptide Stapling
date: 2020-02-14
extension: .txt
mime: text/plain
words: 6645
sentence: 225
flesch: 43
cache: cache/cord-314604-w61sqy17.txt
txt: txt/cord-314604-w61sqy17.txt
summary:
  In this study, a library of nine stapled peptides was prepared by modifying peptide K via cysteine alkylation. The effectiveness of E/ K-based membrane fusion is partially attributed to the membrane interactions of peptide K, which are theorized to induce membrane curvature and therefore accelerate the transition from membrane docking to hemifusion.


id: cord-321417-6code4oh
author: Benincasa, Monica
date: 2003-12-20
extension: .txt
mime: text/plain
words: 4581
sentence: 169
flesch: 42
cache: cache/cord-321417-6code4oh.txt
txt: txt/cord-321417-6code4oh.txt
title:
  In vitro and in vivo antimicrobial activity of two α-helical cathelicidin peptides and of their synthetic analogs

summary:
  Despite a wealth of published in vitro activity studies of antimicrobial peptides against antibiotic-resistant clinical isolates, there are only a few published reports of their in vivo activity. A highly potent PG-1 analog proved effective in reducing oral microflora in humans, suggesting that antimicrobial peptides may be useful for treatment of oral infections [14] .


id: cord-305755-6jup93v4
author: Gouveia, Duarte
date: 2020-07-22
extension: .txt
mime: text/plain
words: 6718
sentence: 255
flesch: 45
cache: cache/cord-305755-6jup93v4.txt
txt: txt/cord-305755-6jup93v4.txt
title:
  Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window

summary:
  By using a short LC gradient focusing on the region of interest identified in our previous study, we tested the detection of the virus in samples containing different quantities of viral peptides, as well as COVID-19 clinical samples, paving the way for the development of time-efficient viral diagnostic tests based on an alternative platform. This was repeated several times to obtain a one-third dilution cascade of viral peptides.


id: cord-300189-gsp1dozg
author: Franci, Gianluigi
date: 2017-02-14
extension: .txt
mime: text/plain
words: 6375
sentence: 210
flesch: 39
cache: cache/cord-300189-gsp1dozg.txt
txt: txt/cord-300189-gsp1dozg.txt
title:
  Infectivity inhibition by overlapping synthetic peptides derived from the gH/gL heterodimer of herpes simplex virus type 1

summary:
  Inhibitory activity of gH peptides. In fact, the two proteins need each other to fold correctly and gL is a powerful scaffolding protein for gH. The inability of gH peptides derived from the H1 domain to function as inhibitors of infectivity can be explained by the fact that the formation of the highly stable complex between the two glycoproteins happens during the maturation and egress from the infected cell; therefore, the structure is already definitive when the heterodimer becomes expressed on the mature virion envelope.


id: cord-295207-0p6x4lwx
author: Melnik, Lilia I
title: Peptide inhibition of human cytomegalovirus infection
date: 2011-02-22
extension: .txt
mime: text/plain
words: 4770
sentence: 189
flesch: 38
cache: cache/cord-295207-0p6x4lwx.txt
txt: txt/cord-295207-0p6x4lwx.txt
summary:
  WWIHS score-positive sequences may also interact with hydrophobic surfaces within proteins, and are often sequestered within pre-fusion forms of viral fusion proteins. Previous studies have suggested that synthetic peptides corresponding to or overlapping with sequences in viral fusion proteins that have positive WWIHS scores can sometimes serve as viral entry inhibitors [35] [36]


id: cord-024193-khdvj6t5
author: Zhang, Hong
title: Peptide Arrays
date: 2012-01-17
extension: .txt
mime: text/plain
words: 11364
sentence: 387
flesch: 35
cache: cache/cord-024193-khdvj6t5.txt
txt: txt/cord-024193-khdvj6t5.txt
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) .


id: cord-277716-6gsmkmk5
author: Doll, Tais A. P. F.
title: Design and optimization of peptide nanoparticles
date: 2015-10-24
extension: .txt
mime: text/plain
words: 5895
sentence: 243
flesch: 50
cache: cache/cord-277716-6gsmkmk5.txt
txt: txt/cord-277716-6gsmkmk5.txt
summary:
  [28] . Natural supramolecular building blocks: from virus coat proteins to viral nanoparticles Atomic-level models of the bacterial carboxysome shell Development of the vault particle as a platform technology Natural strategies for the spatial optimization of metabolism in synthetic biology Towards an artificial cell Biological containers: protein cages as multifunctional nanoplatforms Drug delivery systems: entering the mainstream Micellar nanocontainers distribute to defined cytoplasmic organelles Immunodrugs: therapeutic VLP-based vaccines for chronic diseases Developments in virus-like particle-based vaccines for infectious diseases and cancer A nonadjuvanted polypeptide nanoparticle vaccine confers long-lasting protection against rodent malaria Conformation-specific display of 4E10 and 2F5 epitopes on self-assembling protein nanoparticles as a potential HIV vaccine A novel vaccine using nanoparticle platform to present immunogenic M2e against avian influenza infection Peptide nanoparticles as novel immunogens: design and analysis of a prototypic severe acute respiratory syndrome vaccine Coiled coils: a highly versatile protein folding motif Self-assembly of coiled coils in synthetic biology: inspiration and progress Peptide and protein building blocks for synthetic biology: from programming biomolecules to self-organized biomolecular systems Designing heterodimeric two-stranded alphahelical coiled-coils: the effect of chain length on protein folding, stability and specificity Improving coiled-coil stability by optimizing ionic interactions Design of a minimal protein oligomerization domain by a structural approach Optimizing the design of protein nanoparticles as carriers for vaccine applications Optimizing the refolding conditions of self-assembling polypeptide nanoparticles that serve as repetitive antigen display systems Phase I malaria vaccine trial with a long synthetic peptide derived from the merozoite surface protein 3 antigen A mechanism for toxin insertion into membranes is suggested by the crystal structure of the channel-forming domain of colicin E1 Atomic structure of a tryptophan-zipper pentamer Design of a minimal protein oligomerization domain by a structural approach Improved methods for building protein models in electron density maps and the location of errors in these models Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • A disulfide bond has been introduced by double mutations T15C and S23C in peptide 3, peptide 6, and peptide 8 to see how this constraint affects the peptide conformation.


id: cord-007735-ejvv2lxv
author: Bowdish, D. M. E.
title: Immunomodulatory Properties of Defensins and Cathelicidins
date: 2006
extension: .txt
mime: text/plain
words: 13937
sentence: 405
flesch: 28
cache: cache/cord-007735-ejvv2lxv.txt
txt: txt/cord-007735-ejvv2lxv.txt
summary:
  In humans, the major classes of host defence peptides include the α- and β-defensins and the cathelicidin, hCAP-18/LL-37. Interest in the immunomodulatory functions of these peptides is increasing, and indeed many peptides and proteins with similar characteristics to host defence peptides have been found to have either antimicrobial or immunomodulatory properties in addition to their primary functions.


id: cord-347661-q9lgliph
author: Zevenhoven-Dobbe, Jessika C.
title: Production of Monospecific Rabbit Antisera Recognizing Nidovirus Proteins
date: 2007-11-28
extension: .txt
mime: text/plain
words: 6884
sentence: 243
flesch: 45
cache: cache/cord-347661-q9lgliph.txt
txt: txt/cord-347661-q9lgliph.txt
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.


id: cord-280383-hi7z3nob
author: Huang, Jian
title: SAROTUP: Scanner and Reporter of Target-Unrelated Peptides
date: 2010-03-21
extension: .txt
mime: text/plain
words: 3417
sentence: 148
flesch: 53
cache: cache/cord-280383-hi7z3nob.txt
txt: txt/cord-280383-hi7z3nob.txt
summary:
  It is also possible that a SAROTUP predicted target unrelated peptide is actually target-specific. In the 11 panels of peptides SAROTUP scanned, there were target-unrelated peptides in 3 panels from cetuximab, 80R, and b12 test case, respectively (Table 3 ).


id: cord-018401-josb16pi
author: Kumaraswamy, Priyadharshini
title: Hierarchical Self-Assembled Peptide Nano-ensembles
date: 2014-03-01
extension: .txt
mime: text/plain
words: 13493
sentence: 544
flesch: 41
cache: cache/cord-018401-josb16pi.txt
txt: txt/cord-018401-josb16pi.txt
summary:
  A bioactive self-assembled membrane to promote angiogenesis Morphology of self-assembled structures formed by short peptides from the amyloidogenic protein tau depends on the solvent in which the peptides are dissolved Time-lapse atomic force microscopy in the characterization of amyloid-like fibril assembly and oligomeric intermediates Using the bending beam model to estimate the elasticity of diphenylalanine nanotubes Nanostructured films from hierarchical self-assembly of amyloidogenic proteins Transthyretin fibrillogenesis entails the assembly of monomers: a molecular model for in vitro assembled transthyretin amyloid-like fibrils Self-assembled peptide nanotubes as an etching material for the rapid fabrication of silicon wires Confined conversion of CuS nanowires to CuO nanotubes by annealinginduced diffusion in nanochannels Electrochemical determination of dopamine based on selfassembled peptide nanostructure Natural tri-to hexapeptides self-assemble in water to amyloid beta-type fiber aggregates by unexpected alpha-helical intermediate structures William Thomas Astbury 1898-1961 Hierarchical self-assembly of Tjernberg peptide at nanoscale Conformational transition of amyloid beta-peptide Connecting macroscopic observables and microscopic assembly events in amyloid formation using coarse grained simulations Peptide self-assembly at the nanoscale: a challenging target for computational and experimental biotechnology Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences Stability of diphenylalanine peptide nanotubes in solution Molecular dynamics simulation of the α-helix to β-sheet transition in coiled protein filaments: evidence for a critical filament length scale Rigid self-assembled hydrogel composed of a modified aromatic dipeptide From the globular to the fibrous state: protein structure and structural conversion in amyloid formation Amyloid fibrillogenesis: themes and variations Protein misfolding and disease; protein refolding and therapy The correctly-folded state of proteins: Is it a metastable state? Direct conversion of an oligopeptide from a ß-sheet to an a-helix: a model for amyloid formation Identification of a penta-and hexapeptide of islet amyloid polypeptide (IAPP) with amyloidogenic and cytotoxic properties Conformational transitions and fibrillation mechanism of human calcitonin as studied by high-resolution solid-state 13C NMR Charge attraction and beta propensity are necessary for amyloid fibril formation from tetrapeptides Self-assembly of a modified amyloid peptide fragment: pH responsiveness and nematic phase formation Controlling amyloid growth in multiple dimensions Templating molecular arrays in amyloid's crossbeta grooves Effect of PEG crystallization on the self-assembly of PEG/peptide copolymers containing amyloid peptide fragments Molecular self-assembly of peptide nanostructures: mechanism of association and potential uses Puramatrix: Self-assembling peptide nanofiber scaffolds Rational design and application of responsive alpha-helical peptide hydrogels Lipid-like self-assembling peptides Production of self-assembling biomaterials for tissue engineering Light harvesting antenna on an amyloid scaffold Dual-surface modification of the tobacco mosaic virus Neural stem cells encapsulated in a functionalized self-assembling peptide hydrogel for brain tissue engineering Fine-tuning the pH trigger of self-assembly Artificial transmembrane ion channels from self-assembling peptide nanotubes Self-assembling chimeric polypeptidedoxorubicin conjugate nanoparticles that abolish tumours after a single injection A novel vaccine using nanoparticle platform to present immunogenic M2e against avian influenza infection Peptide nanoparticles as novel immunogens: design and analysis of a prototypic severe acute respiratory syndrome vaccine Development of an electrochemical metal-ion biosensor using self-assembled peptide nanofibrils Self-assembled diphenylalanine nanowires for cellular studies and sensor applications An auto-biotinylated bifunctional protein nanowire for ultra-sensitive molecular biosensing Remote electronic control of DNA hybridization through inductive coupling to an attached metal nanocrystal antenna Design of metal-binding sites onto self-assembled peptide fibrils Self-assembling peptide-based nanostructures for regenerative medicine Self-assembly of collagen-mimetic peptide amphiphiles into biofunctional nanofiber Self-assembling functionalized nanopeptides for immediate hemostasis and accelerative liver tissue regeneration However, there are certain limitations associated with this technique, too, such as a limited resolution, strong dependency of the quality of predictions on the size of the peptide, and the limited number of peptide residues for which such predictions could be made.


id: cord-298019-gf2asni1
author: Galdiero, Stefania
title: gH625: A milestone in understanding the many roles of membranotropic peptides
date: 2014-10-12
extension: .txt
mime: text/plain
words: 8593
sentence: 283
flesch: 31
cache: cache/cord-298019-gf2asni1.txt
txt: txt/cord-298019-gf2asni1.txt
summary:
  Selfoligomerization of membrane embedded fusion peptides has been proposed to be responsible of inhibition [52, 53] . The preference of tryptophan for membrane interfaces Use of hydrophobic moment plot methodology to aid the identification of oblique orientated α-helices Antimicrobial peptides and viral fusion peptides: how different they are? Antimicrobial peptides: promising compounds against pathogenic microorganisms Membrane fusion and fission: enveloped viruses Recent progress of cellpenetrating peptides as new carriers for intracellular cargo delivery Mechanism of membrane fusion by viral envelope proteins Viral membrane fusion Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 A resolution Retrovirus envelope domain at 1.7 angstrom resolution Crystal structure of the Ebola virus membrane fusion subunit, GP2, from the envelope glycoprotein ectodomain Structure of the parainfluenza virus 5 F protein in its metastable, prefusion conformation Structural basis for coronavirus-mediated membrane fusion.


id: cord-009492-lhwhkada
author: Kašička, Václav
title: Recent developments in CE and CEC of peptides
date: 2007-11-28
extension: .txt
mime: text/plain
words: 17950
sentence: 649
flesch: 36
cache: cache/cord-009492-lhwhkada.txt
txt: txt/cord-009492-lhwhkada.txt
summary:
  Being a hybrid electrokinetic and chromatographic technique, CEC of peptides profits from the high selectivity of numerous stationary phases developed for peptide separation by HPLC and from the low dispersion of electroosmotically driven motion of a mobile phase. The current state-of-the-art in this rapidly growing area of CEC including its application for peptide separations is summarized in the recent reviews [139, 140] .


id: cord-316474-407bthqj
author: Huang, Jian
title: Bioinformatics Resources and Tools for Phage Display
date: 2011-01-18
extension: .txt
mime: text/plain
words: 6415
sentence: 293
flesch: 49
cache: cache/cord-316474-407bthqj.txt
txt: txt/cord-316474-407bthqj.txt
summary:
  Mimotope sequence might be very similar or even identical to one part of its template sequence, indicating the location of the protein-protein interaction site [2, 25] . Eyes and tools are often used to align mimotope sequence to its template.


id: cord-331633-ix5un6c9
author: Teixeira, Maria C.
title: Nanomedicines for the Delivery of Antimicrobial Peptides (AMPs)
date: 2020-03-20
extension: .txt
mime: text/plain
words: 9145
sentence: 393
flesch: 27
cache: cache/cord-331633-ix5un6c9.txt
txt: txt/cord-331633-ix5un6c9.txt
summary:
  Furthermore, nanomaterials can be used for antimicrobial drug delivery, and the incorporation of antimicrobial nanomaterials in medical devices and implants can prevent microbial adhesion and infection Antimicrobial drug delivery using polymeric NPs offers several advantages: (i) structural stability in biological fluids and under harsh and various conditions for preparation; (ii) precisely tuneable properties, such as size, zeta-potentials, and drug release profiles, by manipulating polymer lengths, surfactants, and organic solvents used for NP preparation [67] , and (iii) facile and versatile surface functionalization for conjugating drugs and targeting ligands [68] .


id: cord-340971-e42g37la
author: Lehrer, Robert I.
title: Defensins and Other Antimicrobial Peptides and Proteins
date: 2007-05-09
extension: .txt
mime: text/plain
words: 10475
sentence: 361
flesch: 29
cache: cache/cord-340971-e42g37la.txt
txt: txt/cord-340971-e42g37la.txt
summary:
  Since the intestinal epithelium stem cells reside in the intestinal crypts, secretion of Paneth cell defensins into the crypt lumen (Figure 6. 3) could provide a protective barrier for this vital proliferative compartment. However, unlike the myeloid defensins, Paneth cell defensins are stored as propeptides, exclusively so in humans (Porter et al. 1998; Ouellette et al. 2000; Ghosh et al. 2002) .


id: cord-291534-c6cjxq07
author: Gwyer Findlay, Emily
title: Cationic Host Defence Peptides: Potential as Antiviral Therapeutics
date: 2013-05-07
extension: .txt
mime: text/plain
words: 8792
sentence: 323
flesch: 33
cache: cache/cord-291534-c6cjxq07.txt
txt: txt/cord-291534-c6cjxq07.txt
summary:
  A/PR/8/34 hemagglutinin (H1 subtype) alpha-Defensin inhibits influenza virus replication by cell-mediated mechanism(s) Role of protein kinase C betaII in influenza virus entry via late endosomes Interactions of alpha-, beta-, and theta-defensins with influenza A virus and surfactant protein D Mechanism of adenovirus neutralization by human alpha-defensins Epithelial defensins impair adenoviral infection: implication for adenovirus-mediated gene therapy Human alpha-defensins block papillomavirus infection Human alpha-defensins inhibit BK virus infection by aggregating virions and blocking binding to host cells Insight into the mechanisms of adenovirus capsid disassembly from studies of defensin neutralization Human alpha-defensin 1 (HNP-1) inhibits adenoviral infection in vitro Adenovirus-directed ocular innate immunity: the role of conjunctival defensin-like chemokines (IP-10, I-TAC) and phagocytic human defensin-alpha Critical determinants of human alpha-defensin 5 activity against nonenveloped viruses Direct evidence from single-cell analysis that human {alpha}-defensins block adenovirus uncoating to neutralize infection Enhanced expression of murine beta-defensins (MBD-1, -2,-3, and -4) in upper and lower airway mucosa of influenza virus infected mice Human epithelial beta-defensins 2 and 3 inhibit HIV-1 replication Rhinovirus increases human beta-defensin-2 and -3 mRNA expression in cultured bronchial epithelial cells Human rhinovirus infection induces airway epithelial cell production of human beta-defensin 2 both in vitro and in vivo Role of human beta-defensin-2 during tumor necrosis factor-alpha/NF-kappaB-mediated innate antiviral response against human respiratory syncytial virus Oral human beta-defensin 2 in HIV-infected subjects with long-term use of antiretroviral therapy Human betadefensins suppress human immunodeficiency virus infection: potential role in mucosal protection Cutting edge: human beta defensin 3-a novel antagonist of the HIV-1 coreceptor CXCR4 beta-Defensin genomic copy number is associated with HIV load and immune reconstitution in subsaharan Africans Increased levels of human betadefensins mRNA in sexually HIV-1 exposed but uninfected individuals Modulation of human beta-defensin-1 (hBD-1) in plasmacytoid dendritic cells (PDC), monocytes, and epithelial cells by influenza virus, Herpes simplex virus, and Sendai virus and its possible role in innate immunity Recombinant mouse beta-defensin 2 inhibits infection by influenza A virus by blocking its entry Antiviral activity of recombinant mouse beta-defensin 3 against influenza A virus in vitro and in vivo Cytokine (tumor necrosis factor, IL-6, and IL-8) production by respiratory syncytial virus-infected human alveolar macrophages Antiviral activity of human beta-defensin 3 against vaccinia virus Selective killing of vaccinia virus by LL-37: implications for eczema vaccinatum Cytokine milieu of atopic dermatitis, as compared to psoriasis, skin prevents induction of innate immune response genes A cyclic antimicrobial peptide produced in primate leukocytes by the ligation of two truncated alpha-defensins Retrocyclin: a primate peptide that protects cells from infection by T-and M-tropic strains of HIV-1 Evaluation of a theta-defensin in a murine model of herpes simplex virus type 1 keratitis. The human antimicrobial peptide LL-37 is a multifunctional modulator of innate immune responses The cationic antimicrobial peptide LL-37 modulates dendritic cell differentiation and dendritic cellinduced T cell polarization Plasmacytoid dendritic cells sense self-DNA coupled with antimicrobial peptide Antimicrobial protein hCAP18/LL-37 is highly expressed in breast cancer and is a putative growth factor for epithelial cells An angiogenic role for the human peptide antibiotic LL-37/hCAP-18 Secondary necrosis of apoptotic neutrophils induced by the human cathelicidin LL-37 is not proinflammatory to phagocytosing macrophages The human cathelicidin LL-37 preferentially promotes apoptosis of infected airway epithelium Direct inactivation of viruses by human granulocyte defensins Human alpha-and beta-defensins block multiple steps in herpes simplex virus infection Theta defensins protect cells from infection by herpes simplex virus by inhibiting viral adhesion and entry Multivalent binding of carbohydrates by the human alpha-defensin, HD5 Defensins inhibit HIV replication in vitro Contribution of human alpha-defensin 1, 2, and 3 to the anti-HIV-1 activity of CD8 antiviral factor Retraction of an interpretation Alpha-defensins in the prevention of HIV transmission among breastfed infants Multifaceted mechanisms of HIV-1 entry inhibition by human alpha-defensin Human neutrophil alpha-defensin 4 inhibits HIV-1 infection in vitro Dual role of alpha-defensin-1 in anti-HIV-1 innate immunity Alphadefensins block the early steps of HIV-1 infection: interference with the binding of gp120 to CD4 Alpha-defensins inhibit HIV infection of macrophages through upregulation of CC-chemokines Contribution of immune activation to the pathogenesis and transmission of human immunodeficiency virus type 1 infection Defensins induce the recruitment of dendritic cells in cervical human papillomavirus-associated (pre)neoplastic lesions formed in vitro and transplanted in vivo Human defensins 5 and 6 enhance HIV-1 infectivity through promoting HIV attachment Antibacterial peptides in bronchoalveolar lavage fluid Elevated concentrations of defensins in bronchoalveolar lavage fluid in diffuse panbronchiolitis Production of beta-defensins by human airway epithelia Innate defense against influenza A virus: activity of human neutrophil defensins and interactions of defensins with surfactant protein D Human neutrophil defensins increase neutrophil uptake of influenza A virus and bacteria and modify virus-induced respiratory burst responses Carbohydrate-binding molecules inhibit viral fusion and entry by crosslinking membrane glycoproteins The antigenic structure of the influenza virus


id: cord-031957-df4luh5v
author: dos Santos-Silva, Carlos André
date: 2020-09-02
extension: .txt
mime: text/plain
words: 16639
sentence: 632
flesch: 34
cache: cache/cord-031957-df4luh5v.txt
txt: txt/cord-031957-df4luh5v.txt
title:
  Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era

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.


id: cord-269756-tid8a464
author: Basso, Luis G. M.
title: SARS-CoV fusion peptides induce membrane surface ordering and curvature
date: 2016-11-28
extension: .txt
mime: text/plain
words: 12265
sentence: 388
flesch: 41
cache: cache/cord-269756-tid8a464.txt
txt: txt/cord-269756-tid8a464.txt
summary:
  I viral membrane fusion Mechanisms of Virus Membrane Fusion Proteins Virus membrane-fusion proteins: more than one way to make a hairpin Structure and function of membrane fusion peptides Are fusion peptides a good model to study viral cell fusion? Structural and dynamic characterization of the interaction of the putative fusion peptide of the S2 SARS-CoV virus protein with lipid membranes A second SARS-CoV S2 glycoprotein internal membrane-active peptide. Calorimetric and Monolayer Studies Interaction of the C2 domain from protein kinase C epsilon with model membranes Network formation of lipid membranes: Triggering structural transitions by chain melting Some aspects of the phase behavior of charged lipids Lipid bilayer pre-transition as the beginning of the melting process Membrane fusion between liposomes composed of acidic phospholipids and neutral phospholipids induced by melittin: A differential scanning calorimetric study Effects of the antimalarial drug primaquine on the dynamic structure of lipid model membranes Interaction of a peptide model of a hydrophobic transmembrane alpha-helical segment of a membrane protein with phosphatidylethanolamine bilayers: differential scanning calorimetric and Fourier transform infrared spectroscopic studies Nature of the thermal pretransition of synthetic phospholipids: dimyristolyl-and dipalmitoyllecithin Thermal analysis of lipids, proteins and biological membranes.


id: cord-316792-89f8g0m8
author: Herzig, Volker
title: Animal toxins — Nature’s evolutionary-refined toolkit for basic research and drug discovery
date: 2020-06-12
extension: .txt
mime: text/plain
words: 12772
sentence: 469
flesch: 35
cache: cache/cord-316792-89f8g0m8.txt
txt: txt/cord-316792-89f8g0m8.txt
summary:
  One therapeutic area in which venom peptides have been successfully used to identify new drug targets is chronic pain In addition to venom peptides, non-peptidic marine toxins have proven to be invaluable tools for elucidating diverse pain pathways.


id: cord-307909-7vbxyns0
author: Ronda, Luca
date: 2020-09-02
extension: .txt
mime: text/plain
words: 9360
sentence: 332
flesch: 37
cache: cache/cord-307909-7vbxyns0.txt
txt: txt/cord-307909-7vbxyns0.txt
title:
  Rational Design of a User-Friendly Aptamer/Peptide-Based Device for the Detection of Staphylococcus aureus

summary:
  Figure 6 shows the image acquired by a scanner/reader of SA23 fluorescent aptamer spotted on a glass slide coated with ns-ZrO 2 for various concentrations, namely 1, 2, 4 and 8 µM. The isotherms showing the adhesion of SA23 aptamer on different substrates are reported in Figure 7 . Circular dichroism experiments were carried out on λ-Cro peptide mutants optimized to interact with the double strand portion of SA23 aptamer in 20 mM phosphate buffer, pH 7.4.


id: cord-287123-ldkuwcc7
author: He, Hui-Qiong
title: The Formyl Peptide Receptors: Diversity of Ligands and Mechanism for Recognition
date: 2017-03-13
extension: .txt
mime: text/plain
words: 13841
sentence: 529
flesch: 35
cache: cache/cord-287123-ldkuwcc7.txt
txt: txt/cord-287123-ldkuwcc7.txt
summary:
  The fibrinolytic receptor for urokinase activates the g protein-coupled chemotactic receptor fprl1/lxa4r Identification of fam3d as a new endogenous chemotaxis agonist for the formyl peptide receptors Distinct signaling cascades elicited by different formyl peptide receptor 2 (fpr2) agonists The synthetic peptide trp-lys-tyr-met-val-d-met inhibits human monocyte-derived dendritic cell maturation via formyl peptide receptor and formyl peptide receptor-like 2 Synthetic peptide mmk-1 is a highly specific chemotactic agonist for leukocyte fprl1 A novel peptide agonist of formyl-peptide receptor-like 1 (alx) displays anti-inflammatory and cardioprotective effects Tethered ligand library for discovery of peptide agonists Design, synthesis and characterization of fmlf-mimicking aapeptides Characterization of quin-c1 for its anti-inflammatory property in a mouse model of bleomycin-induced lung injury Stable formyl peptide receptor agonists that activate the neutrophil nadph-oxidase identified through screening of a compound library A non-peptide receptor inhibitor with selectivity for one of the neutrophil formyl peptide receptors, fpr 1 Molecular docking of 2-(benzimidazol-2-ylthio)-n-phenylacetamide-derived small-molecule agonists of human formyl peptide receptor 1 Further studies on 2-arylacetamide pyridazin-3(2H)-ones: Design, synthesis and evaluation of 4,6-disubstituted analogs as formyl peptide receptors (fprs) agonists High-throughput screening for small-molecule activators of neutrophils: Identification of novel n-formyl peptide receptor agonists Gastrin-releasing peptide/neuromedin b receptor antagonists pd176252, pd168368, and related analogs are potent agonists of human formyl-peptide receptors Lipoxins and aspirin-triggered 15-epi-lipoxins are the first lipid mediators of endogenous anti-inflammation and resolution The lipoxin receptor alx: Potent ligand-specific and stereoselective actions in vivo Lipoxins: Update and impact of endogenous pro-resolution lipid mediators Resolution of inflammation: State of the art, definitions and terms Identification, cloning, and functional characterization of a murine lipoxin a4 receptor homologue gene Lipoxin a(4) metabolites/analogues from two commercial sources have no effects on tnf-alpha-mediated priming or activation through the neutrophil formyl peptide receptors What formyl peptide receptors, if any, are triggered by compound 43 and lipoxin a4? a and formyl peptide receptor-like 1 genes in synovial tissue is associated with matrix metalloproteinase production in patients with inflammatory arthritis Opposing regulation of interleukin-8 and nf-kappab responses by lipoxin a4 and serum amyloid a via the common lipoxin a receptor Differential production of leukotriene b4 or prostaglandin e2 by wkymvm or serum amyloid a via formyl peptide receptor-like 1 Serum amyloid a opposes lipoxin a(4) to mediate glucocorticoid refractory lung inflammation in chronic obstructive pulmonary disease Serum amyloid a mediates human neutrophil production of reactive oxygen species through a receptor independent of formyl peptide receptor like-1 Endogenous acute phase serum amyloid a lacks pro-inflammatory activity, contrasting the two recombinant variants that activate human neutrophils through different receptors Serum amyloid a1 isoforms display different efficacy at toll-like receptor 2 and formyl peptide receptor 2 An il-23r/il-22 circuit regulates epithelial serum amyloid a to promote local effector th17 responses Th17 cell induction by adhesion of microbes to intestinal epithelial cells Pleiotropic roles of formyl peptide receptors Beta amyloid peptide (abeta42) is internalized via the g-protein-coupled receptor fprl1 and forms fibrillar aggregates in macrophages Humanin, a newly identified neuroprotective factor, uses the g protein-coupled formylpeptide receptor-like-1 as a functional receptor N-formylated humanin activates both formyl peptide receptor-like 1 and 2 An annexin 1 n-terminal peptide activates leukocytes by triggering different members of the formyl peptide receptor family Neutrophil nadph-oxidase activation by an annexin ai peptide is transduced by the formyl peptide receptor (fpr), whereas an inhibitory signal is generated independently of the fpr family receptors Mouse cathelin-related antimicrobial peptide chemoattracts leukocytes using formyl peptide receptor-like 1/mouse formyl peptide receptor-like 2 as the receptor and acts as an immune adjuvant Fprl1-mediated induction of superoxide in ll-37-stimulated imr90 human fibroblast Ll-37 inhibits serum amyloid a-induced il-8 production in human neutrophils Human endogenous antibiotic ll-37 stimulates airway epithelial cell proliferation and wound closure The pro-inflammatory peptide ll-37 promotes ovarian tumor progression through recruitment of multipotent mesenchymal stromal cells Leucine leucine-37 uses formyl peptide receptor-like 1 to activate signal transduction pathways, stimulate oncogenic gene expression, and enhance the invasiveness of ovarian cancer cells The expression of beta-defensin-2, 3 and ll-37 induced by candida albicans phospholipomannan in human keratinocytes Leukotriene b4/antimicrobial peptide ll-37 proinflammatory circuits are mediated by blt1 and fpr2/alx and are counterregulated by lipoxin a4 and resolvin e1


id: cord-252147-bvtchcbt
author: Domingo-Espín, Joan
title: Engineered Biological Entities for Drug Delivery and Gene Therapy: Protein Nanoparticles
date: 2011-11-15
extension: .txt
mime: text/plain
words: 17227
sentence: 611
flesch: 30
cache: cache/cord-252147-bvtchcbt.txt
txt: txt/cord-252147-bvtchcbt.txt
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.


id: cord-348432-6jgao58w
author: Conticello, Vincent
title: Biomaterials Made from Coiled-Coil Peptides
date: 2017-01-19
extension: .txt
mime: text/plain
words: 9197
sentence: 337
flesch: 37
cache: cache/cord-348432-6jgao58w.txt
txt: txt/cord-348432-6jgao58w.txt
summary:
  The structure of α-helical coiled coils A role for protein misfolding in immunogenicity of biopharmaceuticals The genome sequence of the SARS-associated coronavirus Peptide-based stimuli-responsive biomaterials Coiled-coil peptide motifs as thermoresponsive valves for mesoporous silica nanoparticles Functionalized α-helical peptide hydrogels for neural tissue engineering The NMR-rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope SARS: clinical virology and pathogenesis Coiled coil peptides as universal linkers for the attachment of recombinant proteins to polymer therapeutics Reversible hydrogels from selfassembling artificial proteins Peptide nanoparticles as novel immunogens: design and analysis of a prototypic severe acute respiratory syndrome vaccine Polymer therapeutics with a coiled coil motif targeted against murine BCL1 leukemia Structure-based design of peptides that self-assemble into regular polyhedral nanoparticles Effects of protein aggregates: an immunologic perspective Immune responses to coiled coil supramolecular biomaterials A self-assembling peptide acting as an immune adjuvant A self-assembling peptide polynanoreactor Self-assembling peptide nanotubes Self-assembled 20-nm 64Cu-micelles enhance accumulation in rat glioblastoma Tuning the erosion rate of artificial protein hydrogels through control of network topology Hydrogels in regenerative medicine Peptide-assembled optically responsive nanoparticle complexes CC+: a relational database of coiled-coil structures Platinum (IV) coiled coil nanotubes selectively kill human glioblastoma cells Computational design of water-soluble α-helical barrels Switchable electrostatic interactions between gold nanoparticles and coiled coil peptides direct colloid assembly Open-and-shut cases in coiled-coil assembly: alpha-sheets and alpha-cylinders Hybrid hydrogels assembled from synthetic polymers and coiled-coil protein domains Engineered pullalan-collagen composite dermal hydrogels improve early cutaneous wound healing CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies Coiled-coil based drug-free macromolecular therapeutics: in vivo efficacy Genetically engineered block copolymers: influence of the length and structure of the coiled-coil blocks on hydrogel self-assembly Rational design of helical nanotubes from selfassembly of coiled-coil lock washers Polypeptideengineered physical hydrogels designed from the coiled-coil region of cartilage oligomeric matrix protein for three-dimensional cell culture Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy Coiled-coils: stability, specificity, and drug delivery potential Rational design of a reversible pH-responsive switch for peptide self-assembly Coiled-coil forming peptides for the induction of silver nanoparticles Biomedical applications of electrostatic layer-by-layer nanoassembly of polymers, enzymes, and nanoparticles Controlling self-assembly of a peptide-based material via metal-ion induced registry shift Hybrid polymer therapeutics incorporating bioresponsive, coiled coil peptide linkers Cell uptake and trafficking behavior of non-covalent, coiled-coil based polymer-drug conjugates Growth factor tethering to protein nanoparticles via coiled-coil formation for targeted drug delivery Rational design and application of responsive alphahelical peptide hydrogels Synthetic virus-like particles from self-assembling coiled-coil lipopeptides and their use in antigen display to the immune system Modular design of self-assembling peptide-based nanotubes How to untwist an α-helix: structural principles of an α-helical barrel1 Intermediate filament structure: the bottom-up approach Drug-free macromolecular therapeutics -a new paradigm in polymeric nanomedicines Monoclonal antibody analysis of neutralization and antibody-dependent enhancement of feline infectious peritonitis virus Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus assembly and functions Evaluation of modified vaccinia virus ankara based recombinant SARS vaccine in ferrets Virus-templated self-assembled single-walled carbon nanotubes for highly efficient electron collection in photovoltaic devices Design of a selective metal ion switch for self-assembly of peptide-based fibrils Reconstruction of helical filaments and tubes Structural plasticity of helical nanotubes based on coiled-coil assemblies Hydrogels: structure starts to gel A pH-responsive coiled-coil peptide hydrogel Fabrication and optimization of alginate hydrogel constructs for use in 3D neural cell cuture Delivery of basic fibroblast growth factor with a pH-responsive, injectable hydrogel to improve angiogenesis in infarcted myocardium Layer-by-layer self-assembly of polymer films and capsules through coiled-coil peptides Probing designability via a generalized model of helical bundle geometry Historical review: another 50th anniversary -new periodicities in coiled coils Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China Lyophilized silk fibroin hydrogels for the sustained local delivery of therapeutic monoclonal antibodies Recent explorations in electrostatic multilayer thin film assembly A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants Crystal structure of an isoleucine-zipper trimer Programmable assembly of nanoarchitectures using genetically engineered viruses 3-D self-assembling leucine zipper hydrogel with tunable properties for tissue engineering Engineered coiled-coil protein microfibers Tunable conformation-dependent engineered protein-gold nanoparticle nanocomposites Multifactorial optimization of endothelial cell growth using modular synthetic extracellular matrices Hydrogel biomaterials: a smart future Smart self-assembled hybrid hydrogel biomaterials Crystal structure of the bacterial membrane protein


id: cord-257494-242k58ll
author: Bastos, Paulo
date: 2017-01-17
extension: .txt
mime: text/plain
words: 17385
sentence: 608
flesch: 26
cache: cache/cord-257494-242k58ll.txt
txt: txt/cord-257494-242k58ll.txt
title:
  Human Antimicrobial Peptides in Bodily Fluids: Current Knowledge and Therapeutic Perspectives in the Postantibiotic Era

summary:
  A new skin-specific proteinase inhibitor that is a target for crosslinking by transglutaminase Peptide hormones and their analogues: Distribution, clearance from the circulation, and inactivation in vivo Discovery of JANUVIA (Sitagliptin), a selective dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes Human antimicrobial peptides and proteins Antimicrobial peptides: Properties and applicability Structures of human host defense cathelicidin LL-37 and its smallest antimicrobial peptide KR-12 in lipid micelles Human antimicrobial peptides (AMPs) represent approximately 10% of all curated AMPs catalogued to date.


id: cord-289161-d7shmb2o
author: Harrison, Patrick L.
title: Antimicrobial peptides from scorpion venoms
date: 2014-09-15
extension: .txt
mime: text/plain
words: 12113
sentence: 393
flesch: 34
cache: cache/cord-289161-d7shmb2o.txt
txt: txt/cord-289161-d7shmb2o.txt
summary:
  Improvement of the efficacy of linear undecapeptides against plant-pathogenic bacteria by incorporation of D-amino acids Two peptides, TsAP-1 and TsAP-2, from the venom of the Brazilian yellow scorpion, Tityus serrulatus: evaluation of their antimicrobial and anticancer activities Vejovine, a new antibiotic from the scorpion venom of Vaejovis mexicanus The solution conformation of the antibacterial peptide cecropin A: a nuclear magnetic resonance and dynamical simulated annealing study Inhibitory activity and mechanism of two scorpion venom peptides against herpes simplex virus type 1 Broad activity against porcine bacterial pathogens displayed by two insect antimicrobial peptides moricin and cecropin B Peptide antimicrobial agents PEGylation of therapeutic proteins Effects of net charge and the number of positively charged residues on the biological activity of amphipathic alpha-helical cationic antimicrobial peptides Enantiomer-specific bioactivities of peptidomimetic analogues of mastoparan and mitoparan: characterization of inverso mastoparan as a highly efficient cell penetrating peptide Antimicrobial and cytolytic peptides of venomous arthropods Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study Mechanism of structural transformations induced by antimicrobial peptides in lipid membranes Antibiotic activity and structural analysis of the scorpion-derived antimicrobial peptide IsCT and its analogs Virucidal activity of a scorpion venom peptide variant mucroporin-M1 against measles, SARS-CoV and influenza H5N1 viruses Activity of the anti-MRSA carbapenem razupenem (PTZ601) against Enterobacteriaceae with defined resistance mechanisms Membrane pores induced by magainin Membrane interactions and biological activity of antimicrobial peptides from Australian scorpion Characterization of the venom from the Australian scorpion Urodacus yaschenkoi: molecular mass analysis of components, cDNA sequences and peptides with antimicrobial activity Membrane interactions and biological activity of antimicrobial peptides from Australian scorpion Transcriptome analysis of the venom gland of the scorpion Scorpiops jendeki: implication for the evolution of the scorpion venom arsenal Molecular diversity of toxic components from the scorpion Heterometrus petersii venom revealed by proteomic and transcriptome analysis Spontaneous membrane-translocating peptides by orthogonal high-throughput screening Relationship of membrane curvature to the formation of pores by magainin 2 A novel amphipathic linear peptide with both insect toxicity and antimicrobial activity from the venom of the scorpion Isometrus maculatus Antibacterial and antifungal properties of alpha-helical, cationic peptides in the venom of scorpions from southern Africa Pegylation of antimicrobial peptides maintains the active peptide conformation, model membrane interactions, and antimicrobial activity while improving lung tissue biocompatibility following airway delivery Plectasin is a peptide antibiotic with therapeutic potential from a saprophytic fungus Mass fingerprinting of toxic fractions from the venom of the Indian red scorpion, Mesobuthus tamulus: biotope-specific variation in the expression of venom peptides A novel class of antimicrobial peptides from the scorpion Heterometrus spinifer Orientation and pore-forming mechanism of a scorpion pore-forming peptide bound to magnetically oriented lipid bilayers Induction of morphological changes in model lipid membranes and the mechanism of membrane disruption by a large scorpionderived pore-forming peptide A repertoire of novel antibacterial diastereomeric peptides with selective cytolytic activity Subtype specificity interaction of bactridines with mammalian, insect and bacterial sodium channels under voltage clamp conditions Interaction of D-amino acid incorporated analogues of pardaxin with membranes Gene cloning and functional characterization of four novel antimicrobial-like peptides from scorpions of the family Vaejovidae Amino acid substitutions in an alpha-helical antimicrobial arachnid peptide affect its chemical properties and biological activity towards pathogenic bacteria but improves its therapeutic index Comparative venom gland transcriptome analysis of the scorpion Lychas mucronatus reveals intraspecific toxic gene diversity and new venomous components Omiganan pentahydrochloride (MBI 226), a topical 12-amino-acid cationic peptide: spectrum of antimicrobial activity and measurements of bactericidal activity Transcriptome analysis of the venom gland of the Mexican scorpion Hadrurus gertschi (Arachnida: Scorpiones) Mass spectrometry analysis, amino acid sequence and biological activity of venom components from the Brazilian scorpion Opisthacanthus cayaporum Cloning and characterization of cDNA sequences encoding for new venom peptides of the Brazilian scorpion Opisthacanthus cayaporum Influence of C-terminal amidation on the antimicrobial and hemolytic activities of cationic a-helical peptides Hadrurin, a new antimicrobial peptide from the venom of the scorpion Hadrurus aztecus Purification and characterization of Heteroscorpine-1 (HS-1) toxin from Heterometrus laoticus scorpion venom All-D amino acid-containing channel-forming antibiotic peptides Investigating the effects of L-to Damino acid substitution and deamidation on the activity and membrane interactions of antimicrobial peptide anoplin An albumin-conjugated peptide exhibits potent anti-HIV activity and long in vivo half-life A new natural alpha-helical peptide from the venom of the scorpion Heterometrus petersii kills HCV Emerging themes and therapeutic prospects for anti-infective peptides Cloning and functional characterization of a new antimicrobial peptide gene StCT1 from the venom of the scorpion Scorpiops tibetanus Epitope-specific tolerance induction with an engineered immunoglobulin Antimicrobial peptides of multicellular organisms Scorpion venom peptides without disulfide bridges Cloning and characterization of a novel cDNA sequence encoding the precursor of a novel venom peptide (BmKbpp) related to a bradykinin-potentiating peptide from Chinese scorpion Buthus martensii Karsch Characterization of BmKbpp, a multifunctional peptide from the Chinese scorpion Mesobuthus martensii Karsch: gaining insight into a new mechanism for the functional diversification of scorpion venom peptides Identification and functional characterization of novel scorpion venom peptides with no disulfide bridge from Buthus martensii Karsch Three new antimicrobial peptides from the scorpion Pandinus imperator Imcroporin, a new cationic antimicrobial peptide from the venom of the scorpion Isometrus maculates Mucroporin-M1 inhibits hepatitis B virus replication by activating the mitogen-activated protein kinase (MAPK) pathway and down-regulating HNF4a in vitro and in vivo Evidence for the existence of insect defensin-like peptide in scorpion venom The scorpine family of defensins: gene structure, alternative polyadenylation and fold recognition Diversity of long-chain toxins in Tityus zulianus and Tityus discrepans venoms (Scorpiones, Buthidae): molecular, immunological, and mass spectral analyses The tale of a resting gland: transcriptome of a replete venom gland from the scorpion Hottentotta judaicus Mass fingerprinting of the venom and transcriptome of venom gland of scorpion Venom proteomic and venomous glands transcriptomic analysis of the Egyptian scorpion Scorpio maurus palmatus (Arachnida: Scorpionidae) Snapshots of scorpion venomics Intraspecific variation in the Egyptian Scorpion Scorpio maurus palmatus venom collected from different biotopes Antimicrobial/cytolytic peptides from the venom of the North African scorpion, Androctonus amoreuxi: biochemical and functional characterization of natural peptides and a single site-substituted analog Profiling the resting venom gland of the scorpion Tityus stigmurus through a transcriptomic survey Pore formation of phospholipid membranes by the action of two hemolytic arachnid peptides of different size The hemolytic activity of six arachnid cationic peptides is affected by the phosphatidylcholine-to-sphingomyelin ratio in lipid bilayers Lipid dependence of antimicrobial peptide activity is an unreliable experimental test for different pore models Refined structure of charybdotoxin: common motifs in scorpion toxins and insect defensins Isolation, molecular cloning and functional characterization of a novel beta-toxin from the Venezuelan scorpion, Tityus zulianus Nanostructures as promising tools for delivery of antimicrobial peptides Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria? Discovery and development of a synthetic peptide derived from lactoferrin for clinical use Prote) omics in snake venom research-A mere academic exercise Snake venomics: from the inventory of toxins to biology StCT2, a new antibacterial peptide characterized from the venom of the scorpion Scorpiops tibetanus Improved protease stability of the antimicrobial peptide Pin2 substituted with D-amino acids Treatment of health-care-associated infections caused by Gram-negative bacteria: a consensus statement Purification and characterization of a scorpion defensin, a 4kDa antibacterial peptide presenting structural similarities with insect defensins and scorpion toxins Scorpine, an anti-malaria and anti-bacterial agent purified from scorpion venom Characterization of unique amphipathic antimicrobial peptides from venom of the scorpion Pandinus imperator Mucroporin, the first cationic host defense peptide from the venom of Lychas mucronatus Purification, structure-function analysis, and molecular characterization of novel linear peptides from scorpion Opisthacanthus madagascariensis Natural and synthetic cathelicidin peptides with anti-microbial and anti-biofilm activity against Staphylococcus aureus Identification of immunogenic HLA-B7 Achilles' heel epitopes within highly conserved regions of HIV Antibacterial activity of six novel peptides from Tityus discrepans scorpion venom.


id: cord-339879-92esdjy9
author: Delhalle, Sylvie
title: Phages and HIV-1: From Display to Interplay
date: 2012-04-13
extension: .txt
mime: text/plain
words: 22095
sentence: 779
flesch: 39
cache: cache/cord-339879-92esdjy9.txt
txt: txt/cord-339879-92esdjy9.txt
summary:
  The multimerization of human immunodeficiency virus type I Vif protein: A requirement for Vif function in the viral life cycle Potent suppression of viral infectivity by the peptides that inhibit multimerization of human immunodeficiency virus type 1 (HIV-1) Vif proteins An immunodominant neutralization epitope on the -thumb‖ subdomain of human immunodeficiency virus type 1 reverse transcriptase revealed by phage display antibodies A novel neutralization epitope on the -thumb‖ subdomain of human immunodeficiency virus type 1 reverse transcriptase revealed by a monoclonal antibody Recombinant human antibodies against the reverse transcriptase of human immunodeficiency virus type-1 HIV-1 Rev nuclear export signal binding peptides isolated by phage display Measuring cooperative Rev protein-protein interactions on rev responsive RNA by fluorescence resonance energy transfer An intrabody based on a llama single-domain antibody targeting the N-terminal α-helical multimerization domain of HIV-1 Rev prevents viral production Generation and characterization of a chimeric rabbit/human fab for co-crystallization of HIV-1 Rev A peptide inhibitor of HIV-1 assembly in vitro Potential drug targets on the HIV-1 envelope glycoproteins, gp120 and gp41 Small-molecule HIV-1 gp120 inhibitors to prevent HIV-1 entry: An emerging opportunity for drug development Molecular characterization of the circulating anti-HIV-1 gp120-specific b cell repertoire using antibody phage display libraries generated from pre-selected HIV-1 gp120 binding PBLs Relevance of the antibody response against human immunodeficiency virus type 1 envelope to vaccine design Binding of glycoprotein 120 and peptides from the HIV-1 envelope by autoantibodies in mice with experimentally induced systemic lupus erythematosus and in patients with the disease Prospects for immunotherapeutic proteolytic antibodies Phosphonate ester probes for proteolytic antibodies Naturally occurring proteolytic antibodies: Selective immunoglobulin m-catalyzed hydrolysis of HIV gp120 Theory of proteolytic antibody occurrence Site-directed mutagenesis of proteolytic antibody light chain Naturally occurring antibodies devoid of light chains Nanobodies(r): New ammunition to battle viruses Mode of action for linear peptide inhibitors of HIV-1 gp120 interactions Cutting edge: CD4 is the receptor for the tick saliva immunosuppressor, Salp15 The ixodes scapularis salivary protein, Salp15, prevents the association of HIV-1 gp120 and CD4 Natural human antibodies retrieved by phage display libraries from healthy donors: Polyreactivity and recognition of human immunodeficiency virus type 1gp120 epitopes A VH clonal deficit in human immunodeficiency virus-positive individuals reflects a B-cell maturational arrest Selective variations in vivo of VH3 and VH1 gene family expression in peripheral B cell igM, igD and igG during HIV infection Molecular analysis of HIV-1 gp120 antibody response using isotype igM and igG phage display libraries from a long-term non-progressor HIV-1-infected individual Improvement in affinity and HIV-1 neutralization by somatic mutation in the heavy chain first complementarity-determining region of antibodies triggered by HIV-1 infection Cross-reactive human igm-derived monoclonal antibodies that bind to HIV-1 envelope glycoproteins Characterization of germline antibody libraries from human umbilical cord blood and selection of monoclonal antibodies to viral envelope glycoproteins: Implications for mechanisms of immune evasion and design of vaccine immunogens Cross-reactive HIV-1-neutralizing human monoclonal antibodies identified from a patient with 2F5-like antibodies Enfuvirtide: The first therapy to inhibit the entry of HIV-1 into host CD4 lymphocytes Identification of D-peptide ligands through mirror-image phage display Protein design of an HIV-1 entry inhibitor Molecular recognition by a binary code Structural basis for HIV-1 neutralization by a gp41 fusion intermediate-directed antibody Subdomain folding and biological activity of the core structure from human immunodeficiency virus type 1 gp41: A representative sequence from the first group (268.1, HLGPGR), corresponded to the crown of the V3 loop, a linear epitope, while two sequences of the second group (268.2, KAIHRI and 268.3, KSLHRH), showed no homology to linear HIV-1 epitopes.


id: cord-022955-vy0qgtll
title: Proteases
date: 2005-06-20
extension: .txt
mime: text/plain
words: 36483
sentence: 1524
flesch: 40
cache: cache/cord-022955-vy0qgtll.txt
txt: txt/cord-022955-vy0qgtll.txt
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.


id: cord-333262-xvfl7ycj
author: Robson, B.
date: 2020-04-11
extension: .txt
mime: text/plain
words: 21686
sentence: 798
flesch: 45
cache: cache/cord-333262-xvfl7ycj.txt
txt: txt/cord-333262-xvfl7ycj.txt
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

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).


id: cord-023225-5quigar4
title: Posters
date: 2012-08-21
extension: .txt
mime: text/plain
words: 70555
sentence: 3043
flesch: 41
cache: cache/cord-023225-5quigar4.txt
txt: txt/cord-023225-5quigar4.txt
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.


id: cord-023208-w99gc5nx
title: Poster Presentation Abstracts
date: 2006-09-01
extension: .txt
mime: text/plain
words: 71178
sentence: 3089
flesch: 41
cache: cache/cord-023208-w99gc5nx.txt
txt: txt/cord-023208-w99gc5nx.txt
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.


id: cord-023209-un2ysc2v
title: Poster Presentations
date: 2008-10-07
extension: .txt
mime: text/plain
words: 112272
sentence: 4699
flesch: 42
cache: cache/cord-023209-un2ysc2v.txt
txt: txt/cord-023209-un2ysc2v.txt
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.


id: cord-001835-0s7ok4uw
title: Abstracts of the 29th Annual Symposium of The Protein Society
date: 2015-10-01
extension: .txt
mime: text/plain
words: 138771
sentence: 5463
flesch: 38
cache: cache/cord-001835-0s7ok4uw.txt
txt: txt/cord-001835-0s7ok4uw.txt
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.


