ArticleEuropean biophysics journal : EBJ2010
Docking of calcium ions in proteins with flexible side chains and deformable backbones.
Article in European biophysics journal : EBJ, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed, 7 citations in OpenAlex.
- Trends for isolated amino acids and dipeptides: Conformation, divalent ion binding, and remarkable similarity of binding to calcium and lead.Scientific reports · 2016Article
- First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids.Scientific data · 2016Article
- Possible roles of exceptionally conserved residues around the selectivity filters of sodium and calcium channels.The Journal of biological chemistry · 2011Article
- Potassium channel block by a tripartite complex of two cationophilic ligands and a potassium ion.Molecular pharmacology · 2010Article
- Structural modeling of calcium binding in the selectivity filter of the L-type calcium channel.European biophysics journal : EBJ · 2010Article
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Authors and funding
2 authors at 1 institution in 1 country.
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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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