Docking of calcium ions in proteins with flexible side chains and deformable backbones.
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.
Cheng
Ricky C K
RC
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
Zhorov
Boris S
BS
D001665:Binding Sites; D002118:Calcium / Q000737:chemistry*; D002135:Calcium-Binding Proteins / Q000737:chemistry*; D003198:Computer Simulation; D055119:Elastic Modulus; D007477:Ions; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding
D002135:Calcium-Binding Proteins; D007477:Ions; D002118:Calcium