Targeting electrostatic interactions in accelerated molecular dynamics with application to protein partial unfolding.

ABSTRACT: Accelerated molecular dynamics (aMD) is a promising sampling method to generate an ensemble of conformations and to explore the free energy landscape of proteins in explicit solvent. Its success resides in its ability to reduce barriers in the dihedral and the total potential energy space. However, aMD simulations of large proteins can generate large fluctuations of the dihedral and total potential energy with little conformational changes in the protein structure. To facilitate wider conformational sampling of large proteins in explicit solvent, we developed a direct intrasolute electrostatic interactions accelerated MD (DISEI-aMD) approach. This method aims to reduce energy barriers within rapidly changing electrostatic interactions between solute atoms at short-range distances. It also

SUBMITTER: Flores-Canales JC 

PROVIDER: S-EPMC4925148 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature