A Sodium-Sensitive Salt Bridge in the Na+/H+ Antiporter NhaA

The transmembrane protein NhaA from Escherichia coli is a prototypical sodium/proton antiporter. It enables the bacterium to grow under high salt conditions while homologous proteins in eukaryotes are involved in pH and cell volume regulation. A number of acidic and basic residues have been shown to be essential for the transport of one sodium ion for two protons but the mechanistic details of their involvement have not been fully determined. In particular, a highly conserved lysine residue (Lys300) near the center of the membrane had so far been only given a possible indirect role in the transport mechanism. We present a new atomic resolution structure of the inward facing conformation that shows a novel salt bridge between Lys300 and the conserved Asp163. Microsecond molecular dynamics simulations indicate that the salt bridge is sensitive to the presence of a sodium ion that spontaneously binds to the conserved aspartate residue 164. The simulations show how binding of sodium ion can be coupled to a structural change which might trigger a conformational change to an outward facing conformation. Taken together, the structural and simulation data generate a new hypothesis for how Lys300 could be directly involved in proton transport.