ArticleInorganic chemistry2013
Density functional study for the bridged dinuclear center based on a high-resolution X-ray crystal structure of ba3 cytochrome c oxidase from Thermus thermophilus.
Article in Inorganic chemistry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 21 citations in OpenAlex.
- DFT Calculations for Mössbauer Properties on Dinuclear Center Models of the Resting Oxidized Cytochrome c Oxidase.Chemphyschem : a European journal of chemical physics and physical chemistry · 2022Article
- Coupled transport of electrons and protons in a bacterial cytochromePhysical chemistry chemical physics : PCCP · 2020Article
- A Water Molecule Residing in the FeInorganic chemistry · 2020Article
- Heme-Cu Binucleating Ligand Supports Heme/OInorganic chemistry · 2019Article
- Geometric and Electronic Structure Contributions to O-O Cleavage and the Resultant Intermediate Generated in Heme-Copper Oxidases.Journal of the American Chemical Society · 2019Article
- Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function.Chemical reviews · 2018Review
- A Water Dimer Shift Activates a Proton Pumping Pathway in the PInorganic chemistry · 2018Article
- Critical Aspects of Heme-Peroxo-Cu Complex Structure and Nature of Proton Source Dictate Metal-O(peroxo) Breakage versus Reductive O-O Cleavage Chemistry.Journal of the American Chemical Society · 2017Article
- Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations.Biochimica et biophysica acta · 2016Article
- Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field.Data in brief · 2016Article
- A broken-symmetry density functional study of structures, energies, and protonation states along the catalytic O-O bond cleavage pathway in ba3 cytochrome c oxidase from Thermus thermophilus.Physical chemistry chemical physics : PCCP · 2016Article
- Electrocatalytic O2-Reduction by Synthetic Cytochrome c Oxidase Mimics: Identification of a "Bridging Peroxo" Intermediate Involved in Facile 4e(-)/4H(+) O2-Reduction.Journal of the American Chemical Society · 2015Article
- Broken Symmetry DFT Calculations/Analysis for Oxidized and Reduced Dinuclear Center in Cytochrome c Oxidase: Relating Structures, Protonation States, Energies, and Mössbauer Properties in ba3 Thermus thermophilus.Inorganic chemistry · 2015Article
- A "naked" Fe(III)-(O₂²⁻)-Cu(II) species allows for structural and spectroscopic tuning of low-spin heme-peroxo-Cu complexes.Journal of the American Chemical Society · 2015Article
- Linking chemical electron-proton transfer to proton pumping in cytochrome c oxidase: broken-symmetry DFT exploration of intermediates along the catalytic reaction pathway of the iron-copper dinuclear complex.Inorganic chemistry · 2014Article
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2 authors at 1 institution in 1 country.
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Abstract
Strong electron density for a peroxide type dioxygen species bridging the Fea3 and CuB dinuclear center (DNC) was observed in the high-resolution (1.8 Å) X-ray crystal structures (PDB entries 3S8G and 3S8F) of ba3 cytochrome c oxidase (CcO) from Thermus thermophilus. The crystals represent the as-isolated X-ray photoreduced CcO structures. The bridging peroxide was proposed to arise from the recombination of two radiation-produced HO(•) radicals formed either very near to or even in the space between the two metals of the DNC. It is unclear whether this peroxide species is in the O2(2-), O2(•)(-), HO2(-), or the H2O2 form and what is the detailed electronic structure and binding geometry including the DNC. In order to answer what form of this dioxygen species was observed in the DNC of the 1.8 Å X-ray CcO crystal structure (3S8G), we have applied broken-symmetry density functional theory (BS-DFT) geometric and energetic calculations (using OLYP potential) on large DNC cluster models with different Fea3-CuB oxidation and spin states and with O2(2-), O2(•)(-), HO2(-), or H2O2 in the bridging position. By comparing the DFT optimized geometries with the X-ray crystal structure (3S8G), we propose that the bridging peroxide is HO2(-). The X-ray crystal structure is likely to represent the superposition of the Fea3(2+)-(HO2(-))-CuB(+) DNC's in different states (Fe(2+) in low spin (LS), intermediate spin (IS), or high spin (HS)) with the majority species having the proton of the HO2(-) residing on the oxygen atom (O1) which is closer to the Fea3(2+) site in the Fea3(2+)-(HO-O)(-)-CuB(+) conformation. Our calculations show that the side chain of Tyr237 is likely trapped in the deprotonated Tyr237(-) anion form in the 3S8G X-ray crystal structure.
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