Parameterization of Ca+2-protein interactions for molecular dynamics simulations.
Molecular dynamics simulations of Ca+2 ions near protein were performed with three force fields: GROMOS96, OPLS-AA, and CHARMM22. The simulations reveal major, force-field dependent, inconsistencies in the interaction between the Ca+2 ions with the protein. The variations are attributed to the nonbonded parameterizations of the Ca+2-carboxylates interactions. The simulations results were compared to experimental data, using the Ca+2-HCOO- equilibrium as a model. The OPLS-AA force field grossly overestimates the binding affinity of the Ca+2 ions to the carboxylate whereas the GROMOS96 and CHARMM22 force fields underestimate the stability of the complex. Optimization of the Lennard-Jones parameters for the Ca+2-carboxylate interactions were carried out, yielding new parameters which reproduce experimental data.
Project
Elad
E
Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel 69978.
Nachliel
Esther
E
Gutman
Menachem
M
D002118:Calcium / Q000737:chemistry*; D002264:Carboxylic Acids / Q000737:chemistry; D003198:Computer Simulation; D005561:Formates / Q000737:chemistry; D007477:Ions / Q000737:chemistry; D008956:Models, Chemical; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D013997:Time Factors
D002264:Carboxylic Acids; D005561:Formates; D007477:Ions; D011506:Proteins; C030544:formic acid; D002118:Calcium