ArticleBiochimica et biophysica acta2009
Molecular dynamics simulation of water in cytochrome c oxidase reveals two water exit pathways and the mechanism of transport.
Article in Biochimica et biophysica acta, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 50 citations in OpenAlex.
- Structural and functional mechanisms of cytochrome c oxidase.Journal of inorganic biochemistry · 2025Review
- Phosphorylations and Acetylations of CytochromeCells · 2024Review
- 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
- Targeting N-Terminal Human Maltase-Glucoamylase to Unravel Possible Inhibitors Using Molecular Docking, Molecular Dynamics Simulations, and Adaptive Steered Molecular Dynamics Simulations.Frontiers in chemistry · 2021Article
- A common coupling mechanism for A-type heme-copper oxidases from bacteria to mitochondria.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Cytochrome c phosphorylation: Control of mitochondrial electron transport chain flux and apoptosis.The international journal of biochemistry & cell biology · 2020Article
- Snapshot of an oxygen intermediate in the catalytic reaction of cytochromeProceedings of the National Academy of Sciences of the United States of America · 2019Article
- DEPC modification of the CuJournal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2019Article
- Structure-Related Differences between Cytochrome Oxidase I Proteins in a Stable Heteroplasmic Mitochondrial System.Genome biology and evolution · 2017Article
- Reactive oxygen species leave a damage trail that reveals water channels in Photosystem II.Science advances · 2017Article
- Phosphorylation of Cytochrome c Threonine 28 Regulates Electron Transport Chain Activity in Kidney: IMPLICATIONS FOR AMP KINASE.The Journal of biological chemistry · 2017Article
- Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations.Biochimica et biophysica acta · 2016Article
- Proton translocation in cytochrome c oxidase: insights from proton exchange kinetics and vibrational spectroscopy.Biochimica et biophysica acta · 2015Review
- Exploring O2 diffusion in A-type cytochrome c oxidases: molecular dynamics simulations uncover two alternative channels towards the binuclear site.PLoS computational biology · 2014Article
- Functions of the hydrophilic channels in protonmotive cytochrome c oxidase.Journal of the Royal Society, Interface · 2013Review
- Direct regulation of cytochrome c oxidase by calcium ions.PloS one · 2013Article
- Article
- From static structure to living protein: computational analysis of cytochrome c oxidase main-chain flexibility.Biophysical journal · 2012Article
- Gating and regulation of the cytochrome c oxidase proton pump.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
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
We have examined the network of connected internal cavities in cytochrome c oxidase along which water produced at the catalytic center is removed from the enzyme. Using combination of structural analysis, molecular dynamics simulations, and free energy calculations we have identified two exit pathways that connect the Mg2+ ion cavity to the outside of the enzyme. Each pathway has a well-defined bottleneck, which determines the overall rate of water traffic along the exit pathway, and a specific cooperative mechanism of passing it. One of the pathways is going via Arg438/439 (in bovine numbering) toward the CuA center, approaching closely its His204B ligand and Lys171B residue; and the other is going toward Asp364 and Thr294. Comparison of the pathways among different aa3-type enzymes shows that they are well conserved. Possible connections of the finding to redox-coupled proton pumping mechanism are discussed. We propose specific mutations near the bottlenecks of the exit pathways that can test some of our hypotheses.
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