Screening for mechanical responses of proteins using coarse-grained elastic network models

Abstract

Owing to recent progress in structural biology, the structures of a number of proteins have been resolved and deposited into databases such as the Protein Data Bank (PDB). Many proteins function as molecular machines or show allosteric effects, which require integrated communication between different parts of the protein structure;however, the general principles underlying such communication are not yet clear. All-atom molecular dynamics simulation is a powerful tool for tracking molecular motion, but is still far too computationally costly to be applied widely. In this paper, we present a simple method for assessing the properties of mechanical communications using coarse-grained steered molecular dynamics simulations with elastic network models. The method was tested by screening for a certain mechanical property among protein structures in the PDB.