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      Dynamic Scenario of Membrane Binding Process of Kalata B1

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          Abstract

          Kalata B1 (kB1), a cyclotide that has been used in medical applications, displays cytotoxicity related to membrane binding and oligomerization. Our molecular dynamics simulation results demonstrate that Trp19 in loop 5 of both monomeric and tetrameric kB1 is a key residue for initial anchoring in the membrane binding process. This residue also facilitates the formation of kB1 tetramers. Additionally, we elucidate that kB1 preferentially binds to the membrane interfacial zone and is unable to penetrate into the membrane. In particular, significant roles of amino acid residues in loop 5 and loop 6 on the localization of kB1 to this membrane-water interface zone are found. This study reveals the roles of amino acid residues in the bioactivity of kB1, which is information that can be useful for designing new therapeutic cyclotides with less toxicity.

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          Most cited references 46

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          GROMACS: fast, flexible, and free.

          This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org. (c) 2005 Wiley Periodicals, Inc.
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            The MARTINI force field: coarse grained model for biomolecular simulations.

            We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To reproduce the free energies of these chemical building blocks, the number of possible interaction levels of the coarse-grained sites has increased compared to those of the previous model. Application of the new model to lipid bilayers shows an improved behavior in terms of the stress profile across the bilayer and the tendency to form pores. An extension of the force field now also allows the simulation of planar (ring) compounds, including sterols. Application to a bilayer/cholesterol system at various concentrations shows the typical cholesterol condensation effect similar to that observed in all atom representations.
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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: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2014
                4 December 2014
                : 9
                : 12
                Affiliations
                [1 ]Biological Engineering Program, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, Thung Khru, Bangkok, Thailand
                [2 ]Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
                [3 ]Bioinformatics and Systems Biology program, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bang Khun Thian, Bangkok, Thailand
                [4 ]Biotechnology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bang Khun Thian, Bangkok, Thailand
                University of Queensland, Australia
                Author notes

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

                Conceived and designed the experiments: WN SH MR. Performed the experiments: WN. Analyzed the data: WN. Contributed reagents/materials/analysis tools: WN. Contributed to the writing of the manuscript: WN MR.

                Article
                PONE-D-14-38337
                10.1371/journal.pone.0114473
                4256454
                25473840

                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.

                Counts
                Pages: 20
                Funding
                This work was partly supported by a research grant (NRMJ: 2557A30602295#57000139) from the National Research Council of Thailand ( http://en.nrct.go.th) and a grant (P-11-01089) from the National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Thailand ( http://www.biotec.or.th). 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
                Computational Biology
                Molecular Biology
                Computer and Information Sciences
                Computer Modeling
                Computerized Simulations
                Custom metadata
                The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files.

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