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

Abstract

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.

Coarse-Grained Protein Dynamics Studies Using Elastic Network Models

“…Furthermore, this method can be applied theoretically to any kind of protein structure. The low computational cost makes it feasible to exhaustively analyze communication patterns inside the molecule for a variety of protein structures deposited in the Protein Data Bank, which may enable us to systematically study the structural basis of allosteric regulation [74].…”

Theoretical framework for analyzing structural compliance properties of proteins

“…Related to the NMA by using ENM, it is know that we can analyze ENM behavior when an external force is applied by adding external force terms to the formulation of NMA. By using the methods, the structural mechanisms that enable the allosteric effect were investigated [ 21 ], and roles of forces were investigated from the view point of mechanobiology [ 25 ]. In contrast to the methods, we directly analyze the structural compliance properties of ENMs and extract information about motion properties without calculating the normal modes.…”