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Conformational modes in biomolecules: dynamics and approximate invariance

Par Conseil national de recherches du Canada

DOITrouver le DOI : https://doi.org/10.1103/PhysRevE.85.020901
AuteurRechercher : ; Rechercher : 1
Affiliation
  1. Conseil national de recherches du Canada. Institut national de nanotechnologie
FormatTexte, Article
Sujetbiomolecular dynamics; coarse-grained structure; conformational change; conformational dynamics; dimensionality reduction; dynamical properties; human prion protein; invariant properties; molecular dynamics simulations; molecular dynamics trajectories; multi-scale approaches; perturbation theory; physical mechanism; soft matter; subnanosecond; theoretical framework; time-dependent; biomolecules; molecular dynamics; statistical mechanics; dynamics
Résumé
Understanding the physical mechanisms behind the folding and conformational dynamics of biomolecules is one of the major unsolved challenges of soft matter theory. In this contribution, a theoretical framework for biomolecular dynamics is introduced, employing selected aspects of statistical mechanics, dimensionality reduction, the perturbation theory, and the theory of matrices. Biomolecular dynamics is represented by time-dependent orthogonal conformational modes, the dynamics of the modes is investigated, and invariant properties that persist are identified. As an example, the dynamics of a human prion protein is considered. The theory provides a rigorous background for assessing the stable dynamical properties of biomolecules, such as their coarse-grained structure, through a multiscale approach using short subnanosecond segments of molecular dynamics trajectories. Furthermore, the paper offers a theoretical platform for models of conformational changes in macromolecules, which may allow complementing molecular dynamics simulations. ©2012 American Physical Society.
Date de publication
Dans
  • Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics 85, nº 2, 20901.
Langueanglais
Publications évaluées par des pairsOui
Numéro NPARC21269199
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Identificateur de l’enregistrementd23b9364-1662-45b9-8b52-89ed3009a399
Enregistrement créé2013-12-12
Enregistrement modifié2020-04-21
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