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

Gal Masrati, Ramakanta Mondal, Abraham Rimon, Amit Kessel, Etana Padan, Erik Lindahl, Nir Ben-Tal*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


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.

Original languageEnglish
Pages (from-to)31850-31860
Number of pages11
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number50
StatePublished - 15 Dec 2020


FundersFunder number
Abraham E. Kazan Chair
EU BioExcel Center of Excellence823830
German-Israeli Project Cooperation
German–Israeli Project CooperationLA3655
Lady Davies Fellowship
USA-Israel Binational Science Foundation
United States - Israel Binational Science Foundation
Hebrew University of Jerusalem
Tel Aviv University


    • Cation/proton antiporters
    • Elevator mechanism
    • Molecular dynamics
    • NhaA
    • Rocking bundle mechanism


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