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Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics
Exploring the landscape of large scale conformational changes such as protein folding at atomistic detail poses a considerable computational challenge. Coarse-grained representations of the peptide chain have therefore been developed and over the last decade have proved extremely valuable. These inc...
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Formato: | Texto |
Lenguaje: | English |
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Molecular Diversity Preservation International (MDPI)
2009
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2672008/ https://www.ncbi.nlm.nih.gov/pubmed/19399227 http://dx.doi.org/10.3390/ijms10030889 |
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author | Hills, Ronald D. Brooks, Charles L. |
author_facet | Hills, Ronald D. Brooks, Charles L. |
author_sort | Hills, Ronald D. |
collection | PubMed |
description | Exploring the landscape of large scale conformational changes such as protein folding at atomistic detail poses a considerable computational challenge. Coarse-grained representations of the peptide chain have therefore been developed and over the last decade have proved extremely valuable. These include topology-based Gō models, which constitute a smooth and funnel-like approximation to the folding landscape. We review the many variations of the Gō model that have been employed to yield insight into folding mechanisms. Their success has been interpreted as a consequence of the dominant role of the native topology in folding. The role of local contact density in determining protein dynamics is also discussed and is used to explain the ability of Gō-like models to capture sequence effects in folding and elucidate conformational transitions. |
format | Text |
id | pubmed-2672008 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Molecular Diversity Preservation International (MDPI) |
record_format | MEDLINE/PubMed |
spelling | pubmed-26720082009-04-27 Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics Hills, Ronald D. Brooks, Charles L. Int J Mol Sci Review Exploring the landscape of large scale conformational changes such as protein folding at atomistic detail poses a considerable computational challenge. Coarse-grained representations of the peptide chain have therefore been developed and over the last decade have proved extremely valuable. These include topology-based Gō models, which constitute a smooth and funnel-like approximation to the folding landscape. We review the many variations of the Gō model that have been employed to yield insight into folding mechanisms. Their success has been interpreted as a consequence of the dominant role of the native topology in folding. The role of local contact density in determining protein dynamics is also discussed and is used to explain the ability of Gō-like models to capture sequence effects in folding and elucidate conformational transitions. Molecular Diversity Preservation International (MDPI) 2009-03-02 /pmc/articles/PMC2672008/ /pubmed/19399227 http://dx.doi.org/10.3390/ijms10030889 Text en © 2009 by the authors; licensee Molecular Diversity Preservation International, 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/). 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 | Review Hills, Ronald D. Brooks, Charles L. Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics |
title | Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics |
title_full | Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics |
title_fullStr | Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics |
title_full_unstemmed | Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics |
title_short | Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics |
title_sort | insights from coarse-grained gō models for protein folding and dynamics |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2672008/ https://www.ncbi.nlm.nih.gov/pubmed/19399227 http://dx.doi.org/10.3390/ijms10030889 |
work_keys_str_mv | AT hillsronaldd insightsfromcoarsegrainedgomodelsforproteinfoldinganddynamics AT brookscharlesl insightsfromcoarsegrainedgomodelsforproteinfoldinganddynamics |