Continuous Constant pH Molecular Dynamics Simulations of Transmembrane Proteins.
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ABSTRACT:
SUBMITTER: Huang Y
PROVIDER: S-EPMC8062021 | biostudies-literature | 2021
REPOSITORIES: biostudies-literature
Publications
Continuous Constant pH Molecular Dynamics Simulations of Transmembrane Proteins.
Huang Yandong Y Henderson Jack A JA Shen Jana J
Methods in molecular biology (Clifton, N.J.) 20210101
Many membrane channels, transporters, and receptors utilize a pH gradient or proton coupling to drive functionally relevant conformational transitions. Conventional molecular dynamics simulations employ fixed protonation states, thus neglecting the coupling between protonation and conformational equilibria. Here we describe the membrane-enabled hybrid-solvent continuous constant pH molecular dynamics method for capturing atomic details of proton-coupled conformational dynamics of transmembrane p ...[more]
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