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      Peptidoglycan potentiates the membrane disrupting effect of the carboxyamidated form of DMS-DA6, a Gram-positive selective antimicrobial peptide isolated from Pachymedusa dacnicolor skin

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          Abstract

          The occurrence of nosocomial infections has been on the rise for the past twenty years. Notably, infections caused by the Gram-positive bacteria Staphylococcus aureus represent a major clinical problem, as an increase in antibiotic multi-resistant strains has accompanied this rise. There is thus a crucial need to find and characterize new antibiotics against Gram-positive bacteria, and against antibiotic-resistant strains in general. We identified a new dermaseptin, DMS-DA6, produced by the skin of the Mexican frog Pachymedusa dacnicolor, with specific antibacterial activity against Gram-positive bacteria. This peptide is particularly effective against two multiple drug-resistant strains Enterococcus faecium BM4147 and Staphylococcus aureus DAR5829, and has no hemolytic activity. DMS-DA6 is naturally produced with the C-terminal carboxyl group in either the free or amide forms. By using Gram-positive model membranes and different experimental approaches, we showed that both forms of the peptide adopt an α-helical fold and have the same ability to insert into, and to disorganize a membrane composed of anionic lipids. However, the bactericidal capacity of DMS-DA6-NH 2 was consistently more potent than that of DMS-DA6-OH. Remarkably, rather than resulting from the interaction with the negatively charged lipids of the membrane, or from a more stable conformation towards proteolysis, the increased capacity to permeabilize the membrane of Gram-positive bacteria of the carboxyamidated form of DMS-DA6 was found to result from its enhanced ability to interact with peptidoglycan.

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          Most cited references41

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          The expanding scope of antimicrobial peptide structures and their modes of action.

          Antimicrobial peptides (AMPs) are an integral part of the innate immune system that protect a host from invading pathogenic bacteria. To help overcome the problem of antimicrobial resistance, cationic AMPs are currently being considered as potential alternatives for antibiotics. Although extremely variable in length, amino acid composition and secondary structure, all peptides can adopt a distinct membrane-bound amphipathic conformation. Recent studies demonstrate that they achieve their antimicrobial activity by disrupting various key cellular processes. Some peptides can even use multiple mechanisms. Moreover, several intact proteins or protein fragments are now being shown to have inherent antimicrobial activity. A better understanding of the structure-activity relationships of AMPs is required to facilitate the rational design of novel antimicrobial agents. Copyright © 2011 Elsevier Ltd. All rights reserved.
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            Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.

            A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, ≥90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed (ϕ, ψ) torsion angles of ca 12º. TALOS-N also reports sidechain χ(1) rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts.
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              Describing the mechanism of antimicrobial peptide action with the interfacial activity model.

              Antimicrobial peptides (AMPs) have been studied for three decades, and yet a molecular understanding of their mechanism of action is still lacking. Here we summarize current knowledge for both synthetic vesicle experiments and microbe experiments, with a focus on comparisons between the two. Microbial experiments are done at peptide to lipid ratios that are at least 4 orders of magnitude higher than vesicle-based experiments. To close the gap between the two concentration regimes, we propose an "interfacial activity model", which is based on an experimentally testable molecular image of AMP-membrane interactions. The interfacial activity model may be useful in driving engineering and design of novel AMPs.
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                Author and article information

                Contributors
                Role: Data curationRole: Formal analysisRole: Investigation
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: InvestigationRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: Investigation
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: Formal analysis
                Role: Data curationRole: Formal analysis
                Role: ConceptualizationRole: Writing – review & editing
                Role: Writing – review & editing
                Role: Data curationRole: Formal analysis
                Role: Data curationRole: Formal analysis
                Role: Data curationRole: Formal analysis
                Role: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: Project administrationRole: SupervisionRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                16 October 2018
                2018
                : 13
                : 10
                : e0205727
                Affiliations
                [1 ] Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, Paris, France
                [2 ] Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Plate-forme Spectrométrie de Masse et Protéomique, Paris, France
                [3 ] Instituto de Biotecnologia, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
                [4 ] Université de Bretagne Occidentale, LUBEM EA, IUT Quimper, Quimper, France
                [5 ] Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Plate-forme de Synthèse Peptidique, Paris, France
                [6 ] Faculté des Sciences et Technologie, Université Paris Est-Créteil Val de Marne, Créteil, France
                VIT University, INDIA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-9036-6561
                http://orcid.org/0000-0001-9428-8145
                Article
                PONE-D-18-16077
                10.1371/journal.pone.0205727
                6191125
                30325956
                0e95e12b-f0da-4061-b556-99629bd26f24
                © 2018 Cardon et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 29 May 2018
                : 1 October 2018
                Page count
                Figures: 8, Tables: 5, Pages: 24
                Funding
                Funded by: CONACYT
                Award ID: 2015-02-853
                Award Recipient :
                This work was supported by Grant number: 2015-02-853, Fronteras de la Ciencia 2015-2 issued by CONACYT (Consejo Nacional de Ciencia y tecnologia), Mexico, https://www.conacyt.gob.mx/, to YR. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Biochemistry
                Lipids
                Biology and Life Sciences
                Microbiology
                Bacteriology
                Gram Positive Bacteria
                Physical Sciences
                Chemistry
                Polymer Chemistry
                Macromolecules
                Polymers
                Peptidoglycans
                Physical Sciences
                Materials Science
                Materials
                Polymers
                Peptidoglycans
                Physical Sciences
                Chemistry
                Polymer Chemistry
                Polymers
                Peptidoglycans
                Biology and Life Sciences
                Organisms
                Bacteria
                Staphylococcus
                Staphylococcus Aureus
                Biology and Life Sciences
                Microbiology
                Medical Microbiology
                Microbial Pathogens
                Bacterial Pathogens
                Staphylococcus
                Staphylococcus Aureus
                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Pathogens
                Microbial Pathogens
                Bacterial Pathogens
                Staphylococcus
                Staphylococcus Aureus
                Biology and Life Sciences
                Cell Biology
                Cellular Structures and Organelles
                Vesicles
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Vertebrates
                Amphibians
                Frogs
                Medicine and Health Sciences
                Pharmacology
                Drugs
                Antimicrobials
                Antibacterials
                Biology and Life Sciences
                Microbiology
                Microbial Control
                Antimicrobials
                Antibacterials
                Biology and Life Sciences
                Biochemistry
                Lipids
                Phospholipids
                Custom metadata
                All relevant data are within the paper and its Supporting Information files.

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