Conformational modes in biomolecules: Dynamics and approximate invariance

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Journal titlePhysical Review E - Statistical, Nonlinear, and Soft Matter Physics
Article number20901
SubjectBiomolecular 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
AbstractUnderstanding 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.
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AffiliationNational Research Council Canada (NRC-CNRC); National Institute for Nanotechnology (NINT-INNT)
Peer reviewedYes
NPARC number21269199
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Record identifierd23b9364-1662-45b9-8b52-89ed3009a399
Record created2013-12-12
Record modified2016-05-09
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