Parametrization of calcium binding site in proteins and molecular dynamics simulation on phospholipase A2

The empirical energy parameters for a calcium ion and its ligands in proteins were determined within a pairwise additive framework. The interaction energies of Ca²⁺-water, Ca²⁺-peptide group and Ca²⁺-carboxyl group systems were calculated using the ab initio molecular orbital method with basis sets of double zeta quality including polarization or diffuse functions. The resulting potential energy surfaces served as references for the determination of the nonbonded parameters in the empirical energy function. The nonadditive corrections for the Ca²⁺-ligand pair potentials are incorporated implicitly in the nonbonded paremeters by treating three-body (1:2 complex) or seven-body (1:6 complex) systems in reference calculations. Ligand polarizations induced by Ca²⁺ are estimated from the partial atomic charges of two-body (1:1 complex) systems. The charge sets were determined by scaling so as to reproduce the reference potential energy surfaces. The newly determined parameter set was used in a stochastic boundary molecular dynamics simulation of phospholipase A₂. The solvated structure of the Ca²⁺-binding site obtained from an X-ray crystallographic study is well reproduced by the parameter set.