ArticleBiochimica et biophysica acta2008
Redox-coupled proton pumping in cytochrome c oxidase: further insights from computer simulation.
Article in Biochimica et biophysica acta, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Exploring O2 diffusion in A-type cytochrome c oxidases: molecular dynamics simulations uncover two alternative channels towards the binuclear site.PLoS computational biology · 2014Article
- Copper active sites in biology.Chemical reviews · 2014Review
- Structure-phenotype correlations of human CYP21A2 mutations in congenital adrenal hyperplasia.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Proton-pumping mechanism of cytochrome c oxidase: a kinetic master-equation approach.Biochimica et biophysica acta · 2012Review
- Coupled electron and proton transfer reactions during the O→E transition in bovine cytochrome c oxidase.Biochimica et biophysica acta · 2012Review
- Expanding the view of proton pumping in cytochrome c oxidase through computer simulation.Biochimica et biophysica acta · 2012Article
- Insights into the mechanism of proton transport in cytochrome c oxidase.Journal of the American Chemical Society · 2012Article
- Energetics and dynamics of proton transfer reactions along short water wires.Physical chemistry chemical physics : PCCP · 2011Article
- Exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects.Biochimica et biophysica acta · 2011Article
- Multiconformation continuum electrostatics analysis of the effects of a buried Asp introduced near heme a in Rhodobacter sphaeroides cytochrome c oxidase.Biochemistry · 2010Article
- Proton transport pathway in the ClC Cl-/H+ antiporter.Biophysical journal · 2009Article
- Proton-coupled electron transfer in solution, proteins, and electrochemistry.The journal of physical chemistry. B · 2008Review
- Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Proton-coupled electron transfer.Chemical reviews · 2007Review
- Uncovering channels in photosystem II by computer modelling: current progress, future prospects, and lessons from analogous systems.Photosynthesis researchReview
- Molecular mechanisms for generating transmembrane proton gradients.Biochimica et biophysica actaReview
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The membrane-bound enzyme cytochrome c oxidase, the terminal member in the respiratory chain, converts oxygen into water and generates an electrochemical gradient by coupling the electron transfer to proton pumping across the membrane. Here we have investigated the dynamics of an excess proton and the surrounding protein environment near the active sites. The multi-state empirical valence bond (MS-EVB) molecular dynamics method was used to simulate the explicit dynamics of proton transfer through the critically important hydrophobic channel between Glu242 (bovine notation) and the D-propionate of heme a3 (PRDa3) for the first time. The results from these molecular dynamics simulations indicate that the PRDa3 can indeed re-orientate and dissociate from Arg438, despite the high stability of such an ion pair, and has the ability to accept protons via bound water molecules. Any large conformational change of the adjacent heme a D-propionate group is, however, sterically blocked directly by the protein. Free energy calculations of the PRDa3 side chain isomerization and the proton translocation between Glu242 and the PRDa3 site have also been performed. The results exhibit a redox state-dependent dynamical behavior and indicate that reduction of the low-spin heme a may initiate internal transfer of the pumped proton from Glu242 to the PRDa3 site.
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