Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations

It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a ‘tube model’ approach, we present here a s...

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Main Authors:	Kukic, Predrag, Kannan, Arvind, Dijkstra, Maurits J. J., Abeln, Sanne, Camilloni, Carlo, Vendruscolo, Michele
Format:	Online
Language:	English
Published:	Public Library of Science 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4624779/

id	pubmed-4624779
recordtype	oai_dc
spelling	pubmed-46247792015-11-06 Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations Kukic, Predrag Kannan, Arvind Dijkstra, Maurits J. J. Abeln, Sanne Camilloni, Carlo Vendruscolo, Michele Research Article It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a ‘tube model’ approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the ‘CamTube’ force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost. Public Library of Science 2015-10-27 /pmc/articles/PMC4624779/ /pubmed/26505754 http://dx.doi.org/10.1371/journal.pcbi.1004435 Text en © 2015 Kukic et al http://creativecommons.org/licenses/by/4.0/ 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 properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Kukic, Predrag Kannan, Arvind Dijkstra, Maurits J. J. Abeln, Sanne Camilloni, Carlo Vendruscolo, Michele
spellingShingle	Kukic, Predrag Kannan, Arvind Dijkstra, Maurits J. J. Abeln, Sanne Camilloni, Carlo Vendruscolo, Michele Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations
author_facet	Kukic, Predrag Kannan, Arvind Dijkstra, Maurits J. J. Abeln, Sanne Camilloni, Carlo Vendruscolo, Michele
author_sort	Kukic, Predrag
title	Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations
title_short	Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations
title_full	Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations
title_fullStr	Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations
title_full_unstemmed	Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations
title_sort	mapping the protein fold universe using the camtube force field in molecular dynamics simulations
description	It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a ‘tube model’ approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the ‘CamTube’ force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost.
publisher	Public Library of Science
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4624779/
_version_	1613494373190729728

Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations

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