Titr-DMD-A Rapid, Coarse-Grained Quasi-All-Atom Constant pH Molecular Dynamics Framework.

ABSTRACT: The pH-dependence of enzyme fold stability and catalytic activity is a fundamentally dynamic, structural property which is difficult to study. The challenges and expense of investigating dynamic, atomic scale behavior experimentally means that computational methods, particularly constant pH molecular dynamics (CpHMD), are well situated tools for this. However, these methods often struggle with affordable sampling of sufficiently long time scales while also obtaining accurate pK_a prediction and verifying the structures they generate. We introduce Titr-DMD, an affordable CpHMD method that combines the quasi-all-atom coarse-grained discrete molecular dynamics (DMD) method for conformational sampling with Propka for pK_a prediction, to circumvent these issues

SUBMITTER: Reilley DJ 

PROVIDER: S-EPMC10662685 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature