title: Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger.
abstract: Na(+)/Ca(2+) exchangers use the Na(+) electrochemical gradient across the plasma membrane to extrude intracellular Ca(2+) and play a central role in Ca(2+) homeostasis. Here, we elucidate their mechanisms of extracellular ion recognition and exchange through a structural analysis of the exchanger from Methanococcus jannaschii (NCX_Mj) bound to Na(+), Ca(2+) or Sr(2+) in various occupancies and in an apo state. This analysis defines the binding mode and relative affinity of these ions, establishes the structural basis for the anticipated 3:1 Na(+)/Ca(2+)-exchange stoichiometry and reveals the conformational changes at the onset of the alternating-access transport mechanism. An independent analysis of the dynamics and conformational free-energy landscape of NCX_Mj in different ion-occupancy states, based on enhanced-sampling molecular dynamics simulations, demonstrates that the crystal structures reflect mechanistically relevant, interconverting conformations. These calculations also reveal the mechanism by which the outward-to-inward transition is controlled by the ion occupancy, thereby explaining the emergence of strictly coupled Na(+)/Ca(2+) antiport.
authors.affiliation: School of Life Science and Technology, ShanghaiTech University, Shanghai, P.R. China.
authors.forename: Jun
authors.initials: J
authors.lastname: Liao
authors.affiliation: Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
authors.forename: Fabrizio
authors.initials: F
authors.lastname: Marinelli
authors.affiliation: Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.|Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
authors.forename: ChangKeun
authors.initials: C
authors.lastname: Lee
authors.affiliation: Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
authors.forename: Yihe
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
authors.forename: José D
authors.initials: JD
authors.lastname: Faraldo-Gómez
authors.affiliation: Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.|Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
authors.forename: Youxing
authors.initials: Y
authors.lastname: Jiang
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry / Q000378:metabolism*; D001665:Binding Sites; D002118:Calcium / Q000378:metabolism; D018360:Crystallography, X-Ray; D007474:Ion Exchange; D063747:Methanocaldococcus / Q000737:chemistry / Q000378:metabolism*; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D012964:Sodium / Q000378:metabolism; D019831:Sodium-Calcium Exchanger / Q000737:chemistry / Q000378:metabolism*; D013324:Strontium / Q000378:metabolism
chemical_list: D019843:Archaeal Proteins; D019831:Sodium-Calcium Exchanger; D012964:Sodium; D002118:Calcium; D013324:Strontium