Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.

ABSTRACT: pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH m

SUBMITTER: Goh GB 

PROVIDER: S-EPMC4394622 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature