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

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


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.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Archaeal Proteins / chemistry
  • Archaeal Proteins / metabolism*
  • Binding Sites
  • Calcium / metabolism
  • Crystallography, X-Ray
  • Ion Exchange
  • Methanocaldococcus / chemistry
  • Methanocaldococcus / metabolism*
  • Molecular Docking Simulation
  • Molecular Dynamics Simulation
  • Protein Conformation
  • Sodium / metabolism
  • Sodium-Calcium Exchanger / chemistry
  • Sodium-Calcium Exchanger / metabolism*
  • Strontium / metabolism


  • Archaeal Proteins
  • Sodium-Calcium Exchanger
  • Sodium
  • Calcium
  • Strontium