Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics.

The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or on their ability to perform wider and sometimes highly elaborated motions. Hence, there is considerable interest in the definition of accurate coarse-grained des...

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Autores principales:	Yves Dehouck, Alexander S Mikhailov
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/b4cbcc2304174a7fbe5366cdf5ee1115
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spelling	oai:doaj.org-article:b4cbcc2304174a7fbe5366cdf5ee11152021-11-18T05:53:37ZEffective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics.1553-734X1553-735810.1371/journal.pcbi.1003209https://doaj.org/article/b4cbcc2304174a7fbe5366cdf5ee11152013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24009495/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or on their ability to perform wider and sometimes highly elaborated motions. Hence, there is considerable interest in the definition of accurate coarse-grained descriptions of protein dynamics, as an alternative to more computationally expensive approaches. In particular, the elastic network model, in which residue motions are subjected to pairwise harmonic potentials, is known to capture essential aspects of conformational dynamics in proteins, but has so far remained mostly phenomenological, and unable to account for the chemical specificities of amino acids. We propose, for the first time, a method to derive residue- and distance-specific effective harmonic potentials from the statistical analysis of an extensive dataset of NMR conformational ensembles. These potentials constitute dynamical counterparts to the mean-force statistical potentials commonly used for static analyses of protein structures. In the context of the elastic network model, they yield a strongly improved description of the cooperative aspects of residue motions, and give the opportunity to systematically explore the influence of sequence details on protein dynamics.Yves DehouckAlexander S MikhailovPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 9, Iss 8, p e1003209 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Yves Dehouck Alexander S Mikhailov Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics.
description	The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or on their ability to perform wider and sometimes highly elaborated motions. Hence, there is considerable interest in the definition of accurate coarse-grained descriptions of protein dynamics, as an alternative to more computationally expensive approaches. In particular, the elastic network model, in which residue motions are subjected to pairwise harmonic potentials, is known to capture essential aspects of conformational dynamics in proteins, but has so far remained mostly phenomenological, and unable to account for the chemical specificities of amino acids. We propose, for the first time, a method to derive residue- and distance-specific effective harmonic potentials from the statistical analysis of an extensive dataset of NMR conformational ensembles. These potentials constitute dynamical counterparts to the mean-force statistical potentials commonly used for static analyses of protein structures. In the context of the elastic network model, they yield a strongly improved description of the cooperative aspects of residue motions, and give the opportunity to systematically explore the influence of sequence details on protein dynamics.
format	article
author	Yves Dehouck Alexander S Mikhailov
author_facet	Yves Dehouck Alexander S Mikhailov
author_sort	Yves Dehouck
title	Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics.
title_short	Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics.
title_full	Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics.
title_fullStr	Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics.
title_full_unstemmed	Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics.
title_sort	effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/b4cbcc2304174a7fbe5366cdf5ee1115
work_keys_str_mv	AT yvesdehouck effectiveharmonicpotentialsinsightsintotheinternalcooperativityandsequencespecificityofproteindynamics AT alexandersmikhailov effectiveharmonicpotentialsinsightsintotheinternalcooperativityandsequencespecificityofproteindynamics
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Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics.

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