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Conformational modes in biomolecules: Dynamics and approximate invariance

Alex Potapov and Maria Stepanova
Phys. Rev. E 85, 020901(R) – Published 13 February 2012
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Abstract

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.

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  • Received 27 December 2010

DOI:https://doi.org/10.1103/PhysRevE.85.020901

©2012 American Physical Society

Authors & Affiliations

Alex Potapov

  • Centre for Mathematical Biology, University of Alberta, Edmonton, Alberta, Canada

Maria Stepanova

  • National Institute for Nanotechnology, National Research Council (NRC), Edmonton, Alberta, Canada

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Issue

Vol. 85, Iss. 2 — February 2012

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Physical Review E Scope Description to Include Biological Physics
January 14, 2016

The editors of Physical Review E are pleased to announce that the journal’s stated scope has been expanded to explicitly include the term “Biological Physics.”

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