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. Most recently, we have begun to explore the molecular mechanisms of ligand-receptor recognition and activation.
Nature is efficient; why would it require two protons if one is enough to do the job? This commentary article discusses a recent computational work in the context of our current understanding of how proton translocation mediates the active transport of drugs and substrates across the biological membrane.
AcrB is the inner-membrane transporter of the AcrAB-TolC efflux complex in E. coli which confers resistance to antibiotics. Crystal structures have revealed three distinct states in the drug transport cycle; however, detailed mechanism remains unknown. Our study offered convincing support for the 1:1 drug:proton stoichiometry by depicting how proton release triggers the conformational transition, in agreement with the crystal structure.
Proton-coupled transmembrane proteins play important roles in human health and diseases. We performed the first computer simulation that 1) directly describes the proton-coupled conformational activation of a transmembrane channel with fully atomic detail; 2) accurately determines the stepwise acid-base constants of a transmembrane channel; 3) provides the proton-coupled free energy of channel activation. The presented methodologies and major findings are generalizable for studies of proton-coupled channels and transporters.
Escherichia coli NhaA is a prototype sodium-proton antiporter, which has been extensively characterized by X-ray crystallography, biochemical and biophysical experiments. However, the identities of proton carriers and details of pH-regulated mechanism remain controversial. Here we report constant pH molecular dynamics data, which reveal that NhaA activation involves a net charge switch of a pH sensor at the entrance of the cytoplasmic funnel and opening of a hydrophobic gate at the end of the funnel. The latter is triggered by charging of Asp164, the first proton carrier.