Continuous Constant pH Molecular Dynamics of Transmembrane Proteins [article]

Yandong Huang, Jack A. Henderson, Jana Shen
2020 bioRxiv   pre-print
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
more » ... s of transmembrane proteins. Example protocols from our recent application studies of proton channels and ion/substrate transporters are discussed.
doi:10.1101/2020.08.06.239772 fatcat:aq2wcngo3ba6xfnfb4y2elxa6a