ArticleData in brief2016
Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field.
Article in Data in brief, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 18 citations in OpenAlex.
- Immunoinformatics-driven multi-epitope vaccine design targeting PSMA, STEAP1, and B7H3 for prostate cancer.Frontiers in medicine · 2026Article
- Delineating redox cooperativity in water-soluble and membrane multiheme cytochromes through protein design.Protein science : a publication of the Protein Society · 2024Article
- An expandable, modular de novo protein platform for precision redox engineering.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Current Trends and Changes in Use of Membrane Molecular Dynamics Simulations within Academia and the Pharmaceutical Industry.Membranes · 2023Review
- Reaction pathways, proton transfer, and proton pumping in ba3 class cytochrome c oxidase: perspectives from DFT quantum chemistry and molecular dynamics.Frontiers in chemistry · 2023Article
- Data for molecular dynamics simulations ofData in brief · 2021Article
- Subtype-selective mechanisms of negative allosteric modulators binding to group I metabotropic glutamate receptors.Acta pharmacologica Sinica · 2021Article
- Structure-Based Virtual Screening Identifies Multiple Stable Binding Sites at the RecA Domains of SARS-CoV-2 Helicase Enzyme.Molecules (Basel, Switzerland) · 2021Article
- Molecular Determinants of the Promiscuity of MexB and MexY Multidrug Transporters ofFrontiers in microbiology · 2018Article
- Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations.Biochimica et biophysica acta · 2016Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 3 countries.
Funding
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.
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Registered trials
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