Charge parameterization of the metal centers in cytochrome c oxidase

• Published in: Journal of computational chemistry 2008-04, Vol.29 (5), p.753-767
• Main Authors: Johansson, Mikael P, Kaila, Ville R.I, Laakkonen, Liisa
• Format: Article
• Language: English
• Subjects: atomic point charge; Binding Sites; Biochemistry; bioenergetics; Biotechnology; Chemical bonds; Computer Simulation; Copper - chemistry; density functional calculation; Electron Transport Complex IV - chemistry; force field parameter; haem protein; Iron - chemistry; Ligands; metalloprotein; Models, Biological; Molecules; Oxidation-Reduction; Oxygen - chemistry; Proteins; Quantum Theory; RESP; Simulation; Static Electricity
• ISSN: 0192-8651; 1096-987X
• DOI: 10.1002/jcc.20835

Reliable atomic point charges are of key importance for a correct description of the electrostatic interactions when performing classical, force field based simulations. Here, we present a systematic procedure for point charge derivation, based on quantum mechanical methodology suited for the systems at hand. A notable difference to previous procedures is to include an outer region around the actual system of interest. At the cost of increasing the system sizes, here up to 265 atoms, including the surroundings achieves near-neutrality for the systems as well as structural stability, important factors for reliable charge distributions. In addition, the common problem of converting between C---H bonds and C---C bonds at the border vanishes. We apply the procedure to the four redox-active metal centers of cytochrome c oxidase: CuA, haem a, haem a₃, and CuB. Several relevant charge and ligand states are considered. Charges for two different force fields, CHARMM and AMBER, are presented.