Docking of calcium ions in proteins with flexible side chains and deformable backbones

Eur Biophys J. 2010 Apr;39(5):825-38. doi: 10.1007/s00249-009-0561-7. Epub 2009 Nov 25.


A method of docking Ca(2+) ions in proteins with flexible side chains and deformable backbones is proposed. The energy was calculated with the AMBER force field, implicit solvent, and solvent exposure-dependent and distance-dependent dielectric function. Starting structures were generated with Ca(2+) coordinates and side-chain torsions sampled in 1000 A(3) cubes centered at the experimental Ca(2+) positions. The energy was Monte Carlo-minimized. The method was tested on fourteen Ca(2+)-binding sites. For twelve Ca(2+)-binding sites the root mean square (RMS) deviation of the apparent global minimum from the experimental structure was below 1.3 and 1.7 A for Ca(2+) ions and side-chain heavy atoms, respectively. Energies of multiple local minima correlate with the RMS deviations from the X-ray structures. Two Ca(2+)-binding sites at the surface of proteinase K were not predicted, because of underestimation of Ca(2+) hydration energy by the implicit-solvent method.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Calcium / chemistry*
  • Calcium-Binding Proteins / chemistry*
  • Computer Simulation
  • Elastic Modulus
  • Ions
  • Models, Chemical*
  • Models, Molecular*
  • Protein Binding


  • Calcium-Binding Proteins
  • Ions
  • Calcium