ArticlePLoS computational biology2012
Molecular dynamics simulations reveal proton transfer pathways in cytochrome C-dependent nitric oxide reductase.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 30 citations in OpenAlex.
- Molecular understanding of heteronuclear active sites in heme-copper oxidases, nitric oxide reductases, and sulfite reductases through biomimetic modelling.Chemical Society reviews · 2021Review
- Biological and Bioinspired Inorganic N-N Bond-Forming Reactions.Chemical reviews · 2020Review
- Rapid Decay of the Native Intermediate in the Metallooxidase Fet3p Enables Controlled FeJournal of the American Chemical Society · 2020Article
- Visualizing the protons in a metalloenzyme electron proton transfer pathway.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Bacterial denitrifying nitric oxide reductases and aerobic respiratory terminal oxidases use similar delivery pathways for their molecular substrates.Biochimica et biophysica acta. Bioenergetics · 2018Article
- Article
- The nitric-oxide reductase from Paracoccus denitrificans uses a single specific proton pathway.The Journal of biological chemistry · 2013Article
- Characterization of the nitric oxide reductase from Thermus thermophilus.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Detection of an intermediary, protonated water cluster in photosynthetic oxygen evolution.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nitric oxide reductases (NORs) are membrane proteins that catalyze the reduction of nitric oxide (NO) to nitrous oxide (N(2)O), which is a critical step of the nitrate respiration process in denitrifying bacteria. Using the recently determined first crystal structure of the cytochrome c-dependent NOR (cNOR) [Hino T, Matsumoto Y, Nagano S, Sugimoto H, Fukumori Y, et al. (2010) Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 330: 1666-70.], we performed extensive all-atom molecular dynamics (MD) simulations of cNOR within an explicit membrane/solvent environment to fully characterize water distribution and dynamics as well as hydrogen-bonded networks inside the protein, yielding the atomic details of functionally important proton channels. Simulations reveal two possible proton transfer pathways leading from the periplasm to the active site, while no pathways from the cytoplasmic side were found, consistently with the experimental observations that cNOR is not a proton pump. One of the pathways, which was newly identified in the MD simulation, is blocked in the crystal structure and requires small structural rearrangements to allow for water channel formation. That pathway is equivalent to the functional periplasmic cavity postulated in cbb(3) oxidase, which illustrates that the two enzymes share some elements of the proton transfer mechanisms and confirms a close evolutionary relation between NORs and C-type oxidases. Several mechanisms of the critical proton transfer steps near the catalytic center are proposed.
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