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arXiv · 0903.2082

Coarse-grained protein-protein stiffnesses and dynamics from all-atom simulations

Stephen D. Hicks·C. L. Henley
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Abstract

Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid domains linked by generalized (rotational and stretching) harmonic springs. We present a method to obtain the elastic parameters and overdamped dynamics for these springs from all-atom molecular dynamics simulations of one pair of domains at a time. The computed relaxation times of this pair give a consistency check for the simulation, and (using a fluctuation-dissipation relationship) we find the corrective force needed to null systematic drifts. As a first application we predict the stiffness of an HIV capsid layer and the relaxation time for its breathing mode.

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Stephen D. Hicks, C. L. Henley. 2009-03-12. Coarse-grained protein-protein stiffnesses and dynamics from all-atom simulations. https://doi.org/10.1103/physreve.81.030903

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