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

TL;DR

This paper introduces a method to derive coarse-grained elastic parameters and dynamics of large protein assemblies from all-atom simulations, enabling better modeling of structures like virus capsids.

Contribution

The authors develop a novel approach to extract elastic and dynamic properties of protein domains from all-atom simulations, facilitating coarse-grained modeling of large assemblies.

Findings

Predicted stiffness of HIV capsid layer.

Estimated relaxation time for capsid breathing mode.

Validated the method with consistency checks.

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.