𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Charge parameterization of the metal centers in cytochrome c oxidase

✍ Scribed by Mikael P. Johansson; Ville R. I. Kaila; Liisa Laakkonen

Publisher
John Wiley and Sons
Year
2008
Tongue
English
Weight
302 KB
Volume
29
Category
Article
ISSN
0192-8651

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

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. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008

📜 SIMILAR VOLUMES

Thermotropic behavior of dimyristoylphos
Thermotropic behavior of dimyristoylphosphatidylcholine in the presence of cytochrome c oxidase
✍ Chang-Hwei Chen; Deborah Guard-Friar; Chang-An Yu 📂 Article 📅 1985 🏛 Wiley (John Wiley & Sons) 🌐 English ⚖ 803 KB

The thermotropic behavior of lipid vesicles prepared from dimyristoylphosphatidylcholine in the presence of cytochrome c oxidase has been studied by highly sensitive differential scanning microcalorimetry. This protein has a remarkable effect on the gel-liquid crystalline transition of dimyristoylph

Electronic structures of heme a of cytoc
Electronic structures of heme a of cytochrome c oxidase in the redox states—Charge density migration to the propionate groups of heme a
✍ Yu Takano; Haruki Nakamura 📂 Article 📅 2009 🏛 John Wiley and Sons 🌐 English ⚖ 903 KB

## Abstract The electronic structures of heme __a__ of cytochrome __c__ oxidase in the redox states were studied, using hybrid density functional theory with a polarizable continuum model and a point charge model. We found that the most stable electronic configurations of the d electrons of the Fe

Quantum chemistry applied to the mechani
Quantum chemistry applied to the mechanisms of transition metal containing enzymes—Cytochrome c oxidase, a particularly challenging case
✍ Margareta R. A. Blomberg; Per E. M. Siegbahn 📂 Article 📅 2006 🏛 John Wiley and Sons 🌐 English ⚖ 645 KB

## Abstract The Density functional theory (B3LYP) has been used to study the mechanisms of OO bond cleavage and proton pumping in cytochrome __c__ oxidase. To understand how the energy from the exergonic reduction of molecular oxygen is used to pump protons across the mitochondrial membrane, the e