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

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Title Docking of calcium ions in proteins with flexible side chains and deformable backbones
Authors/Editors* Cheng RC, Zhorov BS.
Where published* Eur Biophys J.
How published* Journal
Year* 2010
Volume 39
Number 5
Pages 525-538
Publisher
Keywords
Link http://www.ncbi.nlm.nih.gov/pubmed/19937325
Abstract
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.
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