Proton-Coupled Ion and Substrate Transport Across Biological Membrane

The extension of the hybrid-solvent CpHMD for transmembrane proteins has opened a door for obtaining previously unattainable insights into biological proton/ion transport. To pave the way, we demonstrated that CpHMD can directly reveal the atomic details of the pH-dependent conformational transitions of a proton channel, an antiporter, and a multi-drug efflux pump.


Shen J*, 

Zooming in on a small multidrug transporter reveals details of asymmetric protonation. 

Proc Natl Acad Sci USA 115: 8060-8062, 2018.

Yue Z, Chen W, Zgurskaya, H, and Shen J*,

Constant pH molecular dynamics reveals how proton release drives the conformational transition of a transmembrane efflux pump.

J Chem Theory Comput 13: 6405-6414, 2017.


Chen W, Huang YD, and Shen J*,

Conformational activation of a transmembrane proton channel from constant pH molecular dynamics.

J Phys Chem Lett 7: 3961-3966, 2016.

Huang YD, Chen W, Dotson DL, Beckstein O, and Shen J*,

Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA.

Nat Commun 7: 12940, 2016.