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bioRxiv · 10.1101/2024.11.23.624977

Molecular mechanism of Na+/H+ antiporting in NhaA

Xie, T.·He, J.·Sun, S.·Chen, Y.·Huang, J.·Huang, Y.
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Abstract

Sodium-proton antiporter NhaA of Escherichia coli is a paradigm to investigate the mechanistic basis of the fundamental Na+/H+ exchange in cells. However, all existing crystal structures of NhaA are inward-facing (IF) and the putative outward-facing (OF) structures are still unsolved by experiment, limiting a complete understanding of the transport cycle where Lys300 plays a key role in both structural stability and transport function. Here, we report a set of regular molecular dynamics (MD) simulations that start from the structure predicted by an artificial intelligence method that generates function-relevant alternative conformations. It is found that NhaA rapidly relaxes into either the IF or OF conformation. Further-more, neutralization of Lys300 allows two sodium ions bound to the reaction cavity, which is associated with enhanced conformational sampling. Based on these observations, we propose a sodium-coupled mechanism of Na+/H+ antiporting.

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Xie, T., He, J., Sun, S., Chen, Y., Huang, J., Huang, Y.. 2024-11-25. Molecular mechanism of Na+/H+ antiporting in NhaA. https://doi.org/10.1101/2024.11.23.624977

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