Docking of calcium ions in proteins with flexible side chains and deformable backbones.
Eur Biophys J
; 39(5): 825-38, 2010 Apr.
Article
en En
| MEDLINE
| ID: mdl-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.
Texto completo:
1
Base de datos:
MEDLINE
Asunto principal:
Proteínas de Unión al Calcio
/
Modelos Moleculares
/
Calcio
/
Modelos Químicos
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
Eur Biophys J
Asunto de la revista:
BIOFISICA
Año:
2010
Tipo del documento:
Article
País de afiliación:
Canadá