Charge parameterization of the metal centers in cytochrome c oxidase.
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: Cu(A), haem a, haem a(3), and Cu(B). Several relevant charge and ligand states are considered. Charges for two different force fields, CHARMM and AMBER, are presented.
Johansson
Mikael P
MP
Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland. mikael.johansson@iki.fi
Kaila
Ville R I
VR
Laakkonen
Liisa
L
D001665:Binding Sites; D003198:Computer Simulation; D003300:Copper / Q000737:chemistry*; D003576:Electron Transport Complex IV / Q000737:chemistry*; D007501:Iron / Q000737:chemistry*; D008024:Ligands; D008954:Models, Biological; D010084:Oxidation-Reduction; D010100:Oxygen / Q000737:chemistry; D011789:Quantum Theory; D055672:Static Electricity
D008024:Ligands; D003300:Copper; D007501:Iron; D003576:Electron Transport Complex IV; D010100:Oxygen