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

• DOI: 10.1073/pnas.2002710117
• Publication Date: 2020-12-01T01:31:49Z
• Authors: Gal Masrati; Ramakanta Mondal; Abraham Rimon; Amit Kessel; Etana Padan; Erik Lindahl; Nir Ben-Tal
• Keywords: Protein Conformation, alpha-Helical; 0301 basic medicine; 0303 health sciences; Sodium-Hydrogen Exchangers; Escherichia coli Proteins; Thermus thermophilus; Cell Membrane; Sodium; Biological Sciences; Molecular Dynamics Simulation; Crystallography, X-Ray; 03 medical and health sciences; Protein Domains; Protons

Significance Membrane-embedded cation/proton antiporters (CPAs) exchange monovalent cations with protons by alternating between two extreme states: inward- and outward-facing. Although atomic-resolution structures are available, there is still an ongoing debate regarding these antiporters’ transport mechanism. Here, we use computer simulations to explore the dynamics of two bacterial antiporters along two axes of motion: a tilting movement and a vertical translation of the antiporters’ two functional domains. By analyzing these dynamic changes, rather than comparing the two extreme states that CPAs adopt, we determine that it is the tilting movement of the antiporters’ mobile domain that drives the relevant conformational changes. Finally, by applying the knowledge gained from these simulations, we predict an unknown outward-facing conformation and verify it experimentally.