Abstract
NhaA is a secondary active transporter that regulates the cellular concentrations of proton and sodium ions. Sodium binding to two conserved aspartates Asp163 and Asp164 is thought to induce a conformational change from the inward- to the outward-facing state. The dimeric crystal structure of E. coli NhaA in the inward-facing state at acidic pH was recently determined. In contrast to the previous monomeric crystal structure, a salt bridge between the conserved residues Asp163 and Lys300 is formed, while the transmembrane helix that contains Lys300 is disrupted. To delineate the mechanism implicated by the structures, we calculate the pKa values of Asp163, Asp164 and Lys300 using all-atom continuous constant pH molecular dynamics simulations with pH-based replica-exchange sampling protocol. The results provide new insights into the working of the antiporter NhaA.
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