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Proteins. 2012 Feb;80(2):616-25. doi: 10.1002/prot.23225. Epub 2011 Nov 22.

Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion.

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  • 1Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213; Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213.

Abstract

Recent studies suggest that protein motions observed in molecular simulations are related to biochemical activities, although the computed time scales do not necessarily match those of the experimentally observed processes. The molecular origin of this conflicting observation is explored here for a test protein, cyanovirin-N (CV-N), through a series of molecular dynamics simulations that span a time range of three orders of magnitude up to 0.4 μs. Strikingly, increasing the simulation time leads to an approximately uniform amplification of the motional sizes, while maintaining the same conformational mechanics. Residue fluctuations exhibit amplitudes of 1-2 Å in the nanosecond simulations, whereas their average sizes increase by a factor of 4-5 in the microsecond regime. The mean-square displacements averaged over all residues (y) exhibit a power law dependence of the form y ∝ x(0.26) on the simulation time (x). Essential dynamics analysis of the trajectories, on the other hand, demonstrates that CV-N has robust preferences to undergo specific types of motions that already can be detected at short simulation times, provided that multiple runs are performed and carefully analyzed.

Copyright © 2011 Wiley Periodicals, Inc.

KEYWORDS:

equilibrium fluctuations of cyanovirin-N; global motions; molecular dynamics simulations; power law; structure-encoded dynamics

PMID:
22105881
[PubMed - in process]
PMCID:
PMC3290687
Free PMC Article
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