Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange.

ABSTRACT: A computational tool that offers accurate pKa values and atomically detailed knowledge of protonation-coupled conformational dynamics is valuable for elucidating mechanisms of energy transduction processes in biology, such as enzyme catalysis and electron transfer as well as proton and drug transport. Toward this goal we present a new technique of embedding continuous constant pH molecular dynamics within an explicit-solvent representation. In this technique we make use of the efficiency of the generalized-Born (GB) implicit-solvent model for estimating the free energy of protein solvation while propagating conformational dynamics using the more accurate explicit-solvent model. Also, we employ a pH-based replica exchange scheme to significantly enhance both protonation and conformational s

SUBMITTER: Wallace JA 

PROVIDER: S-EPMC6425487 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature