ArticleJournal of the American Chemical Society2008
Toward a chemical mechanism of proton pumping by the B-type cytochrome c oxidases: application of density functional theory to cytochrome ba3 of Thermus thermophilus.
Article in Journal of the American Chemical Society, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 65 citations in OpenAlex.
- Coupled transport of electrons and protons in a bacterial cytochromePhysical chemistry chemical physics : PCCP · 2020Article
- A Water Molecule Residing in the FeInorganic chemistry · 2020Article
- DFT FeInorganic chemistry · 2019Article
- Geometric and Electronic Structure Contributions to O-O Cleavage and the Resultant Intermediate Generated in Heme-Copper Oxidases.Journal of the American Chemical Society · 2019Article
- A Water Dimer Shift Activates a Proton Pumping Pathway in the PInorganic chemistry · 2018Article
- ns-μs Time-Resolved Step-Scan FTIR of ba₃ Oxidoreductase from Thermus thermophilus: Protonic Connectivity of w941-w946-w927.International journal of molecular sciences · 2016Article
- Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field.Data in brief · 2016Article
- Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations.Biochimica et biophysica acta · 2016Article
- A broken-symmetry density functional study of structures, energies, and protonation states along the catalytic O-O bond cleavage pathway in ba3 cytochrome c oxidase from Thermus thermophilus.Physical chemistry chemical physics : PCCP · 2016Article
- Synthetic heme/copper assemblies: toward an understanding of cytochrome c oxidase interactions with dioxygen and nitrogen oxides.Accounts of chemical research · 2015Article
- Broken Symmetry DFT Calculations/Analysis for Oxidized and Reduced Dinuclear Center in Cytochrome c Oxidase: Relating Structures, Protonation States, Energies, and Mössbauer Properties in ba3 Thermus thermophilus.Inorganic chemistry · 2015Article
- Broken-Symmetry DFT Computations for the Reaction Pathway of IspH, an Iron-Sulfur Enzyme in Pathogenic Bacteria.Inorganic chemistry · 2015Article
- Mutation of a single residue in the ba3 oxidase specifically impairs protonation of the pump site.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- A "naked" Fe(III)-(O₂²⁻)-Cu(II) species allows for structural and spectroscopic tuning of low-spin heme-peroxo-Cu complexes.Journal of the American Chemical Society · 2015Article
- Proton transfer in the K-channel analog of B-type Cytochrome c oxidase from Thermus thermophilus.Biophysical journal · 2014Article
- Use of Broken-Symmetry Density Functional Theory To Characterize the IspH Oxidized State: Implications for IspH Mechanism and Inhibition.Journal of chemical theory and computation · 2014Article
- Linking chemical electron-proton transfer to proton pumping in cytochrome c oxidase: broken-symmetry DFT exploration of intermediates along the catalytic reaction pathway of the iron-copper dinuclear complex.Inorganic chemistry · 2014Article
- Density functional study for the bridged dinuclear center based on a high-resolution X-ray crystal structure of ba3 cytochrome c oxidase from Thermus thermophilus.Inorganic chemistry · 2013Article
- Single mutations that redirect internal proton transfer in the ba3 oxidase from Thermus thermophilus.Biochemistry · 2013Article
- Spectroscopic and kinetic investigation of the fully reduced and mixed valence states of ba3-cytochrome c oxidase from Thermus thermophilus: a Fourier transform infrared (FTIR) and time-resolved step-scan FTIR study.The Journal of biological chemistry · 2012Article
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3 authors at 1 institution in 1 country.
Funding
Abstract
A mechanism for proton pumping by the B-type cytochrome c oxidases is presented in which one proton is pumped in conjunction with the weakly exergonic, two-electron reduction of Fe-bound O 2 to the Fe-Cu bridging peroxodianion and three protons are pumped in conjunction with the highly exergonic, two-electron reduction of Fe(III)- (-)O-O (-)-Cu(II) to form water and the active oxidized enzyme, Fe(III)- (-)OH,Cu(II). The scheme is based on the active-site structure of cytochrome ba 3 from Thermus thermophilus, which is considered to be both necessary and sufficient for coupled O 2 reduction and proton pumping when appropriate gates are in place (not included in the model). Fourteen detailed structures obtained from density functional theory (DFT) geometry optimization are presented that are reasonably thought to occur during the four-electron reduction of O 2. Each proton-pumping step takes place when a proton resides on the imidazole ring of I-His376 and the large active-site cluster has a net charge of +1 due to an uncompensated, positive charge formally associated with Cu B. Four types of DFT were applied to determine the energy of each intermediate, and standard thermochemical approaches were used to obtain the reaction free energies for each step in the catalytic cycle. This application of DFT generally conforms with previously suggested criteria for a valid model (Siegbahn, P. E. M.; Blomberg, M. A. R. Chem. Rev. 2000, 100, 421-437) and shows how the chemistry of O 2 reduction in the heme a 3 -Cu B dinuclear center can be harnessed to generate an electrochemical proton gradient across the lipid bilayer.
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