Premium
Classical force field parameters for the heme prosthetic group of cytochrome c
Author(s) -
Autenrieth Felix,
Tajkhorshid Emad,
Baudry Jerome,
LutheySchulten Zaida
Publication year - 2004
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.20079
Subject(s) - heme , chemistry , redox , molecular dynamics , docking (animal) , basis set , cytochrome , force field (fiction) , hemeprotein , computational chemistry , density functional theory , cytochrome c , ab initio , energy minimization , chemical physics , physics , quantum mechanics , organic chemistry , enzyme , medicine , biochemistry , nursing , mitochondrion
Accurate force fields are essential for describing biological systems in a molecular dynamics simulation. To analyze the docking of the small redox protein cytochrome c (cyt c ) requires simulation parameters for the heme in both the reduced and oxidized states. This work presents parameters for the partial charges and geometries for the heme in both redox states with ligands appropriate to cyt c . The parameters are based on both protein X‐ray structures and ab initio density functional theory (DFT) geometry optimizations at the B3LYP/6‐31G* level. The simulations with the new parameter set reproduce the geometries of the X‐ray structures and the interaction energies between water and heme prosthetic group obtained from B3LYP/6‐31G* calculations. The parameter set developed here will provide new insights into docking processes of heme containing redox proteins. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1613–1622, 2004