title: Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA.
abstract: 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. The second proton carrier Lys300 forms a salt bridge with Asp163 in the inactive state, and releases a proton when a sodium ion binds Asp163. These data reconcile current models and illustrate the power of state-of-the-art molecular dynamics simulations in providing atomic details of proton-coupled transport across membrane which is challenging to elucidate by experimental techniques.
authors.affiliation: Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA.
authors.forename: Yandong
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.affiliation: Department of Physics, Arizona State University, Tempe, Arizona 85287, USA.
authors.forename: David L
authors.identifier: 0000-0001-5879-2942
authors.initials: DL
authors.lastname: Dotson
authors.affiliation: Department of Physics, Arizona State University, Tempe, Arizona 85287, USA.|Center for Biological Physics, Arizona State University, Tempe, Arizona 85287, USA.
authors.forename: Oliver
authors.identifier: 0000-0003-1340-0831
authors.initials: O
authors.lastname: Beckstein
authors.affiliation: Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA.
authors.forename: Jana
authors.identifier: 0000-0002-3234-0769
authors.initials: J
authors.lastname: Shen
mesh_terms: D001224:Aspartic Acid / Q000737:chemistry; D020134:Catalytic Domain; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D003593:Cytoplasm / Q000378:metabolism; D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D057927:Hydrophobic and Hydrophilic Interactions; D007477:Ions; D008239:Lysine / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D000072417:Protein Domains; D011522:Protons; D012964:Sodium / Q000737:chemistry; D017923:Sodium-Hydrogen Exchangers / Q000737:chemistry* / Q000378:metabolism
chemical_list: D029968:Escherichia coli Proteins; D007477:Ions; C102839:NhaA protein, E coli; D011522:Protons; D017923:Sodium-Hydrogen Exchangers; D001224:Aspartic Acid; D012964:Sodium; D008239:Lysine