Abstract
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 proteins. Example protocols from our recent application studies of proton channels and ion/substrate transporters are discussed.
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Acknowledgments
The authors acknowledge the National Institutes of Health (R01GM098818 and R01GM118772) for funding. Yandong Huang and Jack A. Henderson contributed equally to this work.
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Huang, Y., Henderson, J.A., Shen, J. (2021). Continuous Constant pH Molecular Dynamics Simulations of Transmembrane Proteins. In: Schmidt-Krey, I., Gumbart, J.C. (eds) Structure and Function of Membrane Proteins. Methods in Molecular Biology, vol 2302. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1394-8_15
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DOI: https://doi.org/10.1007/978-1-0716-1394-8_15
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