Abstract
The molecular basis of the function of transporters is a problem of significant importance, and the emerging structural information has not yet been converted to a full understanding of the corresponding function. This work explores the molecular origin of the function of the bacterial Na+/H+ antiporter NhaA by evaluating the energetics of the Na+ and H+ movement and then using the resulting landscape in Monte Carlo simulations that examine two transport models and explore which model can reproduce the relevant experimental results. The simulations reproduce the observed transport features by a relatively simple model that relates the protein structure to its transporting function. Focusing on the two key aspartic acid residues of NhaA, D163 and D164, shows that the fully charged state acts as an Na+ trap and that the fully protonated one poses an energetic barrier that blocks the transport of Na+. By alternating between the former and latter states, mediated by the partially protonated protein, protons, and Na+ can be exchanged across the membrane at 2:1 stoichiometry. Our study provides a numerical validation of the need of large conformational changes for effective transport. Furthermore, we also yield a reasonable explanation for the observation that some mammalian transporters have 1:1 stoichiometry. The present coarse-grained model can provide a general way for exploring the function of transporters on a molecular level.
Highlights
The molecular basis of the function of transporters is a problem of significant importance, and the emerging structural information has not yet been converted to a full understanding of the corresponding function
We note that our calculated pKa values result in a shift to an acidic optimal pH, compared with the experimental results, when we calculated pKa values using a microscopic adiabatic charging approach, we obtained pKas of around 10–12. This fully microscopic approach tends to overestimate the pKa of internal groups [33], the results indicate that the actual pKa values should be somewhat higher than the ones we used in the Monte Carlo (MC) models, resulting in better agreement with the pH profile
Our study provides an interesting hint regarding the stoichiometry of mammalian Na+/H+ exchangers, which, in contrast to bacterial NhaA, is 1:1
Summary
The molecular basis of the function of transporters is a problem of significant importance, and the emerging structural information has not yet been converted to a full understanding of the corresponding function. Focusing on the two key aspartic acid residues of NhaA, D163 and D164, shows that the fully charged state acts as an Na+ trap and that the fully protonated one poses an energetic barrier that blocks the transport of Na+. By alternating between the former and latter states, mediated by the partially protonated protein, protons, and Na+ can be exchanged across the membrane at 2:1 stoichiometry. The stoichiometry of NhaA has been determined to be 2:1, so two protons are consumed in the pumping of one sodium ion against its electrochemical gradient [12]. The transporter has been shown to function in reverse, allowing a sodium gradient to pump protons actively, if needed [13]
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