Format

Send to

Choose Destination
See comment in PubMed Commons below
Data Brief. 2016 Jul 26;8:1209-14. doi: 10.1016/j.dib.2016.07.043. eCollection 2016.

Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field.

Author information

  • 1Department of Chemistry, Nanchang University, 999 Xuefudadao, Nanchang, Jiangxi 330031, China; San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
  • 2San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway.
  • 3Department of Integrative Structural and Computational Biology, GAC1118, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA.
  • 4San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
  • 5San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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 (1.8 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 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.

PMID:
27547799
PMCID:
PMC4979044
DOI:
10.1016/j.dib.2016.07.043
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Elsevier Science Icon for PubMed Central
    Loading ...
    Support Center