ArticleJournal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry2009
Dioxygen and nitric oxide pathways and affinity to the catalytic site of rubredoxin:oxygen oxidoreductase from Desulfovibrio gigas.
Article in Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed, 21 citations in OpenAlex.
- Structures of variants of Escherichia coli flavodiiron-type nitric oxide reductase reveal changes in the di-iron site.Acta crystallographica. Section D, Structural biology · 2026Article
- Validation of a Coarse-Grained Martini 3 Model for Molecular Oxygen.Journal of chemical theory and computation · 2025Article
- When anaerobes encounter oxygen: mechanisms of oxygen toxicity, tolerance and defence.Nature reviews. Microbiology · 2021Review
- Exploring O2 diffusion in A-type cytochrome c oxidases: molecular dynamics simulations uncover two alternative channels towards the binuclear site.PLoS computational biology · 2014Article
- Histidine ligand variants of a flavo-diiron protein: effects on structure and activities.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2012Article
- Insights into the nitric oxide reductase mechanism of flavodiiron proteins from a flavin-free enzyme.Biochemistry · 2010Article
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3 authors at 1 institution in 1 country.
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Abstract
Rubredoxin:oxygen oxidoreductase (ROO) is the terminal oxidase of a soluble electron transfer chain found in Desulfovibrio gigas. This protein belongs to the flavodiiron family and was initially described as an oxygen reductase, converting this substrate to water and acting as an oxygen-detoxifying system. However, more recent studies evidenced also the ability for this protein to act as a nitric oxide reductase, suggesting an alternative physiological role. To clarify the apparent bifunctional nature of this protein, we performed molecular dynamics simulations of the protein, in different redox states, together with O(2) and NO molecules in aqueous solution. The two small molecules were parameterized using free-energy calculations of the hydration process. With these simulations we were able to identify specific protein paths that allow the diffusion of both these molecules through the protein towards the catalytic centers. Also, we have tried to characterize the preference of ROO towards the presence of O(2) and/or NO at the active site. By using free-energy simulations, we did not find any significant preference for ROO to accommodate both O(2) and NO. Also, from our molecular dynamics simulations we were able to identify similar diffusion profiles for both O(2) and NO molecules. These two conclusions are in good agreement with previous experimental works stating that ROO is able to catalyze both O(2) and NO.
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