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Nat Struct Mol Biol. 2016 Jun;23(6):590-599. doi: 10.1038/nsmb.3230. Epub 2016 May 16.

Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger.

Author information

1
School of Life Science and Technology, ShanghaiTech University, Shanghai, P.R. China.
2
Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
3
Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
4
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
#
Contributed equally

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.

PMID:
27183196
PMCID:
PMC4918766
DOI:
10.1038/nsmb.3230
[Indexed for MEDLINE]
Free PMC Article

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