Abstract
Cytochrome c oxidase (CcO) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. This article presents parameters for the cofactors of ba3-type CcO that are compatible with the all-atom Amber ff12SB and ff14SB force fields. Specifically, parameters were developed for the CuA pair, heme b, and the dinuclear center that consists of heme a3 and CuB bridged by a hydroperoxo group. The data includes geometries in XYZ coordinate format for cluster models that were employed to compute proton transfer energies and derive bond parameters and point charges for the force field using density functional theory. Also included are the final parameter files that can be employed with the Amber leap program to generate input files for molecular dynamics simulations with the Amber software package. Based on the high resolution (1.8Å) X-ray crystal structure of the ba3-type CcO from Thermus thermophilus (Protein Data Bank ID number PDB: 3S8F), we built a model that is embedded in a POPC lipid bilayer membrane and solvated with TIP3P water molecules and counterions. We provide PDB data files of the initial model and the equilibrated model that can be used for further studies.
Highlights
Cytochrome c oxidase (CcO) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes
Based on the high resolution (1.8 Å) X-ray crystal structure of the ba3-type CcO from Thermus thermophilus (Protein Data Bank ID number PDB: 3S8F), we built a model that is embedded in a POPC lipid
We provide PDB data files of the initial model and the equilibrated model that can be used for further studies
Summary
PDB files, XYZ files and Amber parameter files Density functional theory calculations with ADF; model preparation with the CHARMM-GUI membrane builder, VMD and AmberTools; molecular dynamics simulations with Amber XYZ coordinate files, PDB coordinate files, Amber OFF library files and parameter files Starting geometries based on crystal structure from Protein Data Bank ID number PDB: 3S8F Geometry optimization and ESP charge derivation of cluster models with PW91D3 and OLYP exchange-correlation functionals; 10ns molecular dynamics equilibration with Amber ff12SB, GAFF, Lipid force fields in combination with new parameters and TIP3P water. [1] is based on the high resolution (1.8 Å) X-ray crystal structure of the ba3-type CcO from Thermus thermophilus in the reduced state in lipidic cubic phase (LCP) crystal as obtained from the Protein Data Bank (PDB: 3S8F) [2] This crystal structure contains two oxygen atoms between the Fe and Cu centers of the DNC, which have been proposed to be a bridging hydroperoxide [3]. The build scripts generate files with the Amber Lipid force field [11] in combination with the Amber ff12SB force field [12], TIP3P parameters for water [13], the Joung/Cheatham ion parameters [14], and the parameters for non-standard residues that are provided with this article. Harmonic bond and angle constraints are used between all metal centers and the ligands, with values that are based on the crystal structure for the CuA pair and based on geometries optimized for cluster models with density functional theory (DFT) for the DNC
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