Modeling and simulation of ion-coupled and ATP-driven membrane proteins

Curr Opin Struct Biol. 2011 Apr;21(2):173-9. doi: 10.1016/ Epub 2011 Feb 16.


The molecular mechanisms of membrane proteins that are activated either by ions or by ATP are just beginning to come into focus, as long-awaited structural data are revealed. This information is being leveraged and supplemented to great effect by molecular modeling and computer simulation studies. Important examples include the homology modeling of eukaryotic protein structures based on distantly related templates, as well as the use of internal structural symmetry for modeling different states in conformational cycles. Molecular simulation studies have elucidated the location and coordination structure of ion binding sites, and explained their selectivity, while also providing tantalizing insights into the mechanisms that couple conformational change to ion translocation or ATP hydrolysis.

Publication types

  • Review

MeSH terms

  • ATP Synthetase Complexes / chemistry
  • ATP Synthetase Complexes / metabolism
  • Adenosine Triphosphate / metabolism*
  • Binding Sites
  • Computer Simulation*
  • Ions / metabolism*
  • Membrane Proteins / chemistry*
  • Membrane Proteins / metabolism*
  • Models, Molecular*
  • Protein Binding
  • Protein Conformation
  • Substrate Specificity


  • Ions
  • Membrane Proteins
  • Adenosine Triphosphate
  • ATP Synthetase Complexes