ArticleProceedings of the National Academy of Sciences of the United States of America2005
Computer simulation of explicit proton translocation in cytochrome c oxidase: the D-pathway.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Green Rust: The Simple Organizing 'Seed' of All Life?Life (Basel, Switzerland) · 2018Review
- Multiscale modelization in a small virus: Mechanism of proton channeling and its role in triggering capsid disassembly.PLoS computational biology · 2018Article
- Wide-dynamic-range kinetic investigations of deep proton tunnelling in proteins.Nature chemistry · 2016Article
- Molecular Basis for Differential Anion Binding and Proton Coupling in the Cl(-)/H(+) Exchanger ClC-ec1.Journal of the American Chemical Society · 2016Article
- Microscopic basis for kinetic gating in Cytochrome c oxidase: insights from QM/MM analysis.Chemical science · 2015Article
- Exploring O2 diffusion in A-type cytochrome c oxidases: molecular dynamics simulations uncover two alternative channels towards the binuclear site.PLoS computational biology · 2014Article
- Expanding the view of proton pumping in cytochrome c oxidase through computer simulation.Biochimica et biophysica acta · 2012Article
- Lewis-inspired representation of dissociable water in clusters and Grotthuss chains.Journal of biological physics · 2012Article
- Mechanism of proton transfer in [FeFe]-hydrogenase from Clostridium pasteurianum.The Journal of biological chemistry · 2011Article
- Glu-286 rotation and water wire reorientation are unlikely the gating elements for proton pumping in cytochrome C oxidase.Biophysical journal · 2011Article
- Exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects.Biochimica et biophysica acta · 2011Article
- Intricate role of water in proton transport through cytochrome c oxidase.Journal of the American Chemical Society · 2010Article
- Secondary water pore formation for proton transport in a ClC exchanger revealed by an atomistic molecular-dynamics simulation.Biophysical journal · 2010Article
- A pathogenic mutation in cytochrome c oxidase results in impaired proton pumping while retaining O(2)-reduction activity.Biochimica et biophysica acta · 2010Article
- Partial steps of charge translocation in the nonpumping N139L mutant of Rhodobacter sphaeroides cytochrome c oxidase with a blocked D-channel.Biochemistry · 2010Article
- 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
- Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups.Biophysical journal · 2008Article
- Redox-coupled proton pumping in cytochrome c oxidase: further insights from computer simulation.Biochimica et biophysica acta · 2008Article
- Proton transport behavior through the influenza A M2 channel: insights from molecular simulation.Biophysical journal · 2007Article
- Crystal structure of human arginase I complexed with thiosemicarbazide reveals an unusual thiocarbonyl mu-sulfide ligand in the binuclear manganese cluster.Journal of the American Chemical Society · 2007Article
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2 authors.
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Abstract
Proton translocation in the D-pathway of cytochrome c oxidase has been studied by a combination of classical molecular dynamics and the multistate empirical valence bond methodology. This approach allows for explicit Grotthuss proton hopping between water molecules. According to mutagenesis experiments, the role of proton donor/acceptor along the D-pathway is carried by the highly conserved residue Glu-242. The present multistate empirical valence bond simulations indicate that the protonation/deprotonation state of Glu-242 is strongly coupled to the distance of proton propagation in the D-pathway. The proton was seen to travel the full length of the D-pathway when Glu-242 was deprotonated; however, it was trapped halfway along the path when Glu-242 was protonated. Further investigation in terms of both proton dynamical properties and free energy calculations for the pathway of proton transport provides evidence for a two-step proton transport mechanism in the D-pathway.
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