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An Efficient Algorithm to Perform Local Concerted Movements of a Chain Molecule
The devising of efficient concerted rotation moves that modify only selected local portions of chain molecules is a long studied problem. Possible applications range from speeding the uncorrelated sampling of polymeric dense systems to loop reconstruction and structure refinement in protein modeling...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380501/ https://www.ncbi.nlm.nih.gov/pubmed/25825903 http://dx.doi.org/10.1371/journal.pone.0118342 |
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author | Zamuner, Stefano Rodriguez, Alex Seno, Flavio Trovato, Antonio |
author_facet | Zamuner, Stefano Rodriguez, Alex Seno, Flavio Trovato, Antonio |
author_sort | Zamuner, Stefano |
collection | PubMed |
description | The devising of efficient concerted rotation moves that modify only selected local portions of chain molecules is a long studied problem. Possible applications range from speeding the uncorrelated sampling of polymeric dense systems to loop reconstruction and structure refinement in protein modeling. Here, we propose and validate, on a few pedagogical examples, a novel numerical strategy that generalizes the notion of concerted rotation. The usage of the Denavit-Hartenberg parameters for chain description allows all possible choices for the subset of degrees of freedom to be modified in the move. They can be arbitrarily distributed along the chain and can be distanced between consecutive monomers as well. The efficiency of the methodology capitalizes on the inherent geometrical structure of the manifold defined by all chain configurations compatible with the fixed degrees of freedom. The chain portion to be moved is first opened along a direction chosen in the tangent space to the manifold, and then closed in the orthogonal space. As a consequence, in Monte Carlo simulations detailed balance is easily enforced without the need of using Jacobian reweighting. Moreover, the relative fluctuations of the degrees of freedom involved in the move can be easily tuned. We show different applications: the manifold of possible configurations is explored in a very efficient way for a protein fragment and for a cyclic molecule; the “local backbone volume”, related to the volume spanned by the manifold, reproduces the mobility profile of all-α helical proteins; the refinement of small protein fragments with different secondary structures is addressed. The presented results suggest our methodology as a valuable exploration and sampling tool in the context of bio-molecular simulations. |
format | Online Article Text |
id | pubmed-4380501 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-43805012015-04-09 An Efficient Algorithm to Perform Local Concerted Movements of a Chain Molecule Zamuner, Stefano Rodriguez, Alex Seno, Flavio Trovato, Antonio PLoS One Research Article The devising of efficient concerted rotation moves that modify only selected local portions of chain molecules is a long studied problem. Possible applications range from speeding the uncorrelated sampling of polymeric dense systems to loop reconstruction and structure refinement in protein modeling. Here, we propose and validate, on a few pedagogical examples, a novel numerical strategy that generalizes the notion of concerted rotation. The usage of the Denavit-Hartenberg parameters for chain description allows all possible choices for the subset of degrees of freedom to be modified in the move. They can be arbitrarily distributed along the chain and can be distanced between consecutive monomers as well. The efficiency of the methodology capitalizes on the inherent geometrical structure of the manifold defined by all chain configurations compatible with the fixed degrees of freedom. The chain portion to be moved is first opened along a direction chosen in the tangent space to the manifold, and then closed in the orthogonal space. As a consequence, in Monte Carlo simulations detailed balance is easily enforced without the need of using Jacobian reweighting. Moreover, the relative fluctuations of the degrees of freedom involved in the move can be easily tuned. We show different applications: the manifold of possible configurations is explored in a very efficient way for a protein fragment and for a cyclic molecule; the “local backbone volume”, related to the volume spanned by the manifold, reproduces the mobility profile of all-α helical proteins; the refinement of small protein fragments with different secondary structures is addressed. The presented results suggest our methodology as a valuable exploration and sampling tool in the context of bio-molecular simulations. Public Library of Science 2015-03-31 /pmc/articles/PMC4380501/ /pubmed/25825903 http://dx.doi.org/10.1371/journal.pone.0118342 Text en © 2015 Zamuner 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. |
spellingShingle | Research Article Zamuner, Stefano Rodriguez, Alex Seno, Flavio Trovato, Antonio An Efficient Algorithm to Perform Local Concerted Movements of a Chain Molecule |
title | An Efficient Algorithm to Perform Local Concerted Movements of a Chain Molecule |
title_full | An Efficient Algorithm to Perform Local Concerted Movements of a Chain Molecule |
title_fullStr | An Efficient Algorithm to Perform Local Concerted Movements of a Chain Molecule |
title_full_unstemmed | An Efficient Algorithm to Perform Local Concerted Movements of a Chain Molecule |
title_short | An Efficient Algorithm to Perform Local Concerted Movements of a Chain Molecule |
title_sort | efficient algorithm to perform local concerted movements of a chain molecule |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380501/ https://www.ncbi.nlm.nih.gov/pubmed/25825903 http://dx.doi.org/10.1371/journal.pone.0118342 |
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