Simulating the Function of the MjNhaP1 Transporter

The structures of transport proteins have been steadily revealed in the last few decades, and yet the conversion of this information into molecular-level understanding of their function is still lagging behind. In this study, we try to elucidate how the action of the archaeal sodium/proton antiporter MjNhaP1 depends on its structure-energy relationship. To this end, we calculate the binding energies of its substrates and evaluate the conformational change barrier, focusing on the rotation of the catalytic residue D161. We find that sodium ions and protons compete against a common binding site and that the accessibility of this binding site is restricted to either the inside or outside of the cell. We suggest that the rotation of D161 chi 1 angle correlates with the conformational change and is energetically unfavorable when D161 does not bind any substrate. This restriction ensures coupling between the sodium ions and the protons, allowing MjNhaP1 and probably other similar transporters to exchange substrates with minimal leak. Using Monte Carlo simulations we demonstrate the feasibility of our model. Overall we present a complete picture that reproduces the electroneutral (at 1:1 substrate ratio) and coupled transport activity of MjNhaP1 including the energetic basis for the criteria provided by Jardetzky half a century ago.