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An angular motion of a conserved four-helix bundle facilitates alternating access transport in the TtNapA and EcNhaA transporters
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Number of Authors: 72020 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 117, no 50, p. 31850-31860Article in journal (Refereed) Published
Abstract [en]

There is ongoing debate regarding the mechanism through which cation/proton antiporters (CPAs), like Thermus thermophilus NapA (TtNapA) and Escherichia coli NapA (EcNhaA), alternate between their outward- and inward-facing conformations in the membrane. CPAs comprise two domains, and it is unclear whether the transition is driven by their rocking-bundle or elevator motion with respect to each other. Here we address this question using metadynamics simulations of TtNapA, where we bias conformational sampling along two axes characterizing the two proposed mechanisms: angular and translational motions, respectively. By applying the bias potential for the two axes simultaneously, as well as to the angular, but not the translational, axis alone, we manage to reproduce each of the two known states of TtNapA when starting from the opposite state, in support of the rocking-bundle mechanism as the driver of conformational change. Next, starting from the inward-facing conformation of EcNhaA, we sample what could be its long-sought-after outward-facing conformation and verify it using cross-linking experiments.

Place, publisher, year, edition, pages
2020. Vol. 117, no 50, p. 31850-31860
Keywords [en]
cation/proton antiporters, rocking bundle mechanism, elevator mechanism, molecular dynamics, NhaA
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URN: urn:nbn:se:su:diva-190656DOI: 10.1073/pnas.2002710117ISI: 000600608300043PubMedID: 33257549Scopus ID: 2-s2.0-85098468257OAI: oai:DiVA.org:su-190656DiVA, id: diva2:1533105
Available from: 2021-03-03 Created: 2021-03-03 Last updated: 2023-10-27Bibliographically approved

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Mondal, RamakantaKessel, AmitLindahl, Erik

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