Simulating the Function of the MjNhaP1 Transporter

Abstract

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 χ1 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.

An angular motion of a conserved four-helix bundle facilitates alternating access transport in the TtNapA and EcNhaA transporters

“…It follows that this analysis is a qualitative approximation of the conformational sampling associated with the IF-OF transition in both antiporters. Indeed, the calculated height of the free energy barrier between the IF and OF states, ∼10 to ∼16 kcal/mol, might slightly underestimate experimentally derived values, which range between 14 and 18 kcal/mol (21,24). It is noteworthy that our aim was to determine the mode of motion underlying the conformational changes in TtNapA and EcNhaA, rather than to accurately estimate the heights of the respective energy barriers.…”

ZnT2 is an electroneutral proton-coupled vesicular antiporter displaying an apparent stoichiometry of two protons per zinc ion

“…two binding sites for protons compared to only one binding site for zinc). The entropic contributions were very small (<1 kcal/mol) and were subtracted from the input potential; this process was successfully applied in previous studies [31,32]. The simulations were run for 10 10 steps, except for the temperatures of 400K and 425K which were run for 2.2×10 10 steps.…”

On the control of the proton current in the voltage-gated proton channel Hv1

“…The PMF calculations for the rotation of the Asp residue were done following a protocol similar to that described previously (46). In brief, a harmonic constraint on the D112 χ 1 torsion angle was imposed at different reference points, using a modified aspartic acid residue with no torsional interactions along the χ 1 angle.…”