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SAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein
Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. Here, we present an elastic network, SAHBNET (Surface Accessibility Hydrogen-Bonds elastic NETwork), that will main...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Molecular Diversity Preservation International (MDPI)
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3709745/ https://www.ncbi.nlm.nih.gov/pubmed/23722660 http://dx.doi.org/10.3390/ijms140611510 |
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author | Dony, Nicolas Crowet, Jean Marc Joris, Bernard Brasseur, Robert Lins, Laurence |
author_facet | Dony, Nicolas Crowet, Jean Marc Joris, Bernard Brasseur, Robert Lins, Laurence |
author_sort | Dony, Nicolas |
collection | PubMed |
description | Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. Here, we present an elastic network, SAHBNET (Surface Accessibility Hydrogen-Bonds elastic NETwork), that will maintain the structure of soluble or membrane proteins based on the hydrogen bonds present in the atomistic structure and the proximity between buried residues. This network is applied on the coarse-grained beads defined by the MARTINI model, and was designed to be more physics-based than a simple elastic network. The SAHBNET model is evaluated against atomistic simulations, and compared with ELNEDYN models. The SAHBNET is then used to simulate two membrane proteins inserted in complex lipid bilayers. These bilayers are formed by self-assembly and the use of a modified version of the GROMACS tool genbox (which is accessible through the gcgs.gembloux.ulg.ac.be website). The results show that SAHBNET keeps the structure close to the atomistic one and is successfully used for the simulation of membrane proteins. |
format | Online Article Text |
id | pubmed-3709745 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Molecular Diversity Preservation International (MDPI) |
record_format | MEDLINE/PubMed |
spelling | pubmed-37097452013-07-12 SAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein Dony, Nicolas Crowet, Jean Marc Joris, Bernard Brasseur, Robert Lins, Laurence Int J Mol Sci Article Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. Here, we present an elastic network, SAHBNET (Surface Accessibility Hydrogen-Bonds elastic NETwork), that will maintain the structure of soluble or membrane proteins based on the hydrogen bonds present in the atomistic structure and the proximity between buried residues. This network is applied on the coarse-grained beads defined by the MARTINI model, and was designed to be more physics-based than a simple elastic network. The SAHBNET model is evaluated against atomistic simulations, and compared with ELNEDYN models. The SAHBNET is then used to simulate two membrane proteins inserted in complex lipid bilayers. These bilayers are formed by self-assembly and the use of a modified version of the GROMACS tool genbox (which is accessible through the gcgs.gembloux.ulg.ac.be website). The results show that SAHBNET keeps the structure close to the atomistic one and is successfully used for the simulation of membrane proteins. Molecular Diversity Preservation International (MDPI) 2013-05-30 /pmc/articles/PMC3709745/ /pubmed/23722660 http://dx.doi.org/10.3390/ijms140611510 Text en © 2013 by the authors; licensee MDPI, Basel, Switzerland This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/). |
spellingShingle | Article Dony, Nicolas Crowet, Jean Marc Joris, Bernard Brasseur, Robert Lins, Laurence SAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein |
title | SAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein |
title_full | SAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein |
title_fullStr | SAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein |
title_full_unstemmed | SAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein |
title_short | SAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein |
title_sort | sahbnet, an accessible surface-based elastic network: an application to membrane protein |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3709745/ https://www.ncbi.nlm.nih.gov/pubmed/23722660 http://dx.doi.org/10.3390/ijms140611510 |
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