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Parametrization of calcium binding site in proteins and molecular dynamics simulation on phospholipase A 2
Author(s) -
Shiratori Yasuhiko,
Nakagawa Setsuko
Publication year - 1991
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540120609
Subject(s) - molecular dynamics , chemistry , parametrization (atmospheric modeling) , scaling , binding energy , computational chemistry , interaction energy , partial charge , chemical physics , molecular physics , atomic physics , thermodynamics , molecule , physics , quantum mechanics , geometry , mathematics , organic chemistry , radiative transfer
The empirical energy parameters for a calcium ion and its ligands in proteins were determined within a pairwise additive framework. The interaction energies of Ca 2+ ‐water, Ca 2+ ‐peptide group and Ca 2+ ‐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 Ca 2+ ‐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 Ca 2+ 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 A 2 . The solvated structure of the Ca 2+ ‐binding site obtained from an X‐ray crystallographic study is well reproduced by the parameter set.