Coarse-grained molecular dynamics simulation of protein conformational change coupled to ligand binding

Abstract

In this paper, we present a new coarse-grained molecular dynamics simulation method that enables the conformational change of a protein between two conformations. In this method, the intramolecular interactions within a protein are described by a potential energy function that has minima near two given reference structures. Other intramolecular interactions and all the intermolecular interactions are described by the MARTINI force field. This method was applied to a protein–ligand system to investigate the processes of ligand binding and the accompanying protein conformational changes. It has been demonstrated that our method can appropriately reproduce the coupling mechanisms in these processes.