1
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Rousseau DL, Ishigami I, Yeh SR. Structural and functional mechanisms of cytochrome c oxidase. J Inorg Biochem 2024; 262:112730. [PMID: 39276716 DOI: 10.1016/j.jinorgbio.2024.112730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 08/20/2024] [Accepted: 09/06/2024] [Indexed: 09/17/2024]
Abstract
Cytochrome c oxidase (CcO) is the terminal enzyme in the electron transfer chain in mitochondria. It catalyzes the four-electron reduction of O2 to H2O and harnesses the redox energy to drive unidirectional proton translocation against a proton electrochemical gradient. A great deal of research has been conducted to comprehend the molecular properties of CcO. However, the mechanism by which the oxygen reduction reaction is coupled to proton translocation remains poorly understood. Here, we review the chemical properties of a variety of key oxygen intermediates of bovine CcO (bCcO) revealed by time-resolved resonance Raman spectroscopy and the structural features of the enzyme uncovered by serial femtosecond crystallography, an innovative technique that allows structural determination at room temperature without radiation damage. The implications of these data on the proton translocation mechanism are discussed.
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Affiliation(s)
- Denis L Rousseau
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Izumi Ishigami
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Syun-Ru Yeh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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2
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Ishigami I, Sierra RG, Su Z, Peck A, Wang C, Poitevin F, Lisova S, Hayes B, Moss FR, Boutet S, Sublett RE, Yoon CH, Yeh SR, Rousseau DL. Structural insights into functional properties of the oxidized form of cytochrome c oxidase. Nat Commun 2023; 14:5752. [PMID: 37717031 PMCID: PMC10505203 DOI: 10.1038/s41467-023-41533-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/07/2023] [Indexed: 09/18/2023] Open
Abstract
Cytochrome c oxidase (CcO) is an essential enzyme in mitochondrial and bacterial respiration. It catalyzes the four-electron reduction of molecular oxygen to water and harnesses the chemical energy to translocate four protons across biological membranes. The turnover of the CcO reaction involves an oxidative phase, in which the reduced enzyme (R) is oxidized to the metastable OH state, and a reductive phase, in which OH is reduced back to the R state. During each phase, two protons are translocated across the membrane. However, if OH is allowed to relax to the resting oxidized state (O), a redox equivalent to OH, its subsequent reduction to R is incapable of driving proton translocation. Here, with resonance Raman spectroscopy and serial femtosecond X-ray crystallography (SFX), we show that the heme a3 iron and CuB in the active site of the O state, like those in the OH state, are coordinated by a hydroxide ion and a water molecule, respectively. However, Y244, critical for the oxygen reduction chemistry, is in the neutral protonated form, which distinguishes O from OH, where Y244 is in the deprotonated tyrosinate form. These structural characteristics of O provide insights into the proton translocation mechanism of CcO.
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Affiliation(s)
- Izumi Ishigami
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Zhen Su
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
| | - Ariana Peck
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Cong Wang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Frederic Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Stella Lisova
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Frank R Moss
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
- Altos Labs, Redwood City, CA, 94065, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Robert E Sublett
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Syun-Ru Yeh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| | - Denis L Rousseau
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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3
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Structures of the intermediates in the catalytic cycle of mitochondrial cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148933. [PMID: 36403794 DOI: 10.1016/j.bbabio.2022.148933] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/30/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022]
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4
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Zhang M, Tai H, Yanagisawa S, Yamanaka M, Ogura T, Hirota S. Resonance Raman Studies on Heme Ligand Stretching Modes in Methionine80-Depleted Cytochrome c: Fe-His, Fe-O 2, and O-O Stretching Modes. J Phys Chem B 2023; 127:2441-2449. [PMID: 36919258 PMCID: PMC10041640 DOI: 10.1021/acs.jpcb.3c00514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
The peroxidase activity of cytochrome (cyt) c increases when Met80 dissociates from the heme iron, which is related to the initial cyt c membrane permeation step of apoptosis. Met80-dissociated cyt c can form an oxygenated species. Herein, resonance Raman spectra of Met80-depleted horse cyt c (M80A cyt c) were analyzed to elucidate the heme ligand properties of Met80-dissociated cyt c. The Fe-His stretching (νFe-His) mode of ferrous M80A cyt c was observed at 236 cm-1, and this frequency decreased by 1.5 cm-1 for the 15N-labeled protein. The higher νFe-His frequency of M80A cyt c than of other His-ligated heme proteins indicates strong heme coordination and the imidazolate character of His18. Peaks attributed to the Fe-O2 stretching (νFe-O2) and O-O stretching (νO-O) modes of the oxygenated species of M80A cyt c were observed at 576 and 1148 cm-1, respectively, under an 16O2 atmosphere, whereas the frequencies decreased to 544 and 1077 cm-1, respectively, under an 18O2 atmosphere. The νFe-O2 mode of Hydrogenobacter thermophilus (HT) M59A cyt c552 was observed at 580 cm-1 under an 16O2 atmosphere, whereas the frequency decreased to 553 cm-1 under an 18O2 atmosphere, indicating that relatively high νFe-O2 frequencies are characteristic of c-type cyt proteins. By comparison of the simultaneously observed νFe-O2 and νO-O frequencies of oxygenated cyt c and other oxygenated His-ligated heme proteins, the frequencies tend to have a positive linear relationship; the νFe-O2 frequency increases when the νO-O frequency increases. The imidazolate character of the heme-coordinated His and strong Fe-O and O-O bonds are characteristic of cyt c and apparently related to the peroxidase activity when Met80 dissociates from the heme iron.
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Affiliation(s)
- Mohan Zhang
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Hulin Tai
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Sachiko Yanagisawa
- Graduate School of Life Science, University of Hyogo, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Masaru Yamanaka
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Takashi Ogura
- Graduate School of Life Science, University of Hyogo, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
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Ishigami I, Sierra RG, Su Z, Peck A, Wang C, Poitevin F, Lisova S, Hayes B, Moss FR, Boutet S, Sublett RE, Yoon CH, Yeh SR, Rousseau DL. Structural basis for functional properties of cytochrome c oxidase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.530986. [PMID: 36993562 PMCID: PMC10055264 DOI: 10.1101/2023.03.20.530986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Cytochrome c oxidase (CcO) is an essential enzyme in mitochondrial and bacterial respiration. It catalyzes the four-electron reduction of molecular oxygen to water and harnesses the chemical energy to translocate four protons across biological membranes, thereby establishing the proton gradient required for ATP synthesis1. The full turnover of the CcO reaction involves an oxidative phase, in which the reduced enzyme (R) is oxidized by molecular oxygen to the metastable oxidized OH state, and a reductive phase, in which OH is reduced back to the R state. During each of the two phases, two protons are translocated across the membranes2. However, if OH is allowed to relax to the resting oxidized state (O), a redox equivalent to OH, its subsequent reduction to R is incapable of driving proton translocation2,3. How the O state structurally differs from OH remains an enigma in modern bioenergetics. Here, with resonance Raman spectroscopy and serial femtosecond X-ray crystallography (SFX)4, we show that the heme a3 iron and CuB in the active site of the O state, like those in the OH state5,6, are coordinated by a hydroxide ion and a water molecule, respectively. However, Y244, a residue covalently linked to one of the three CuB ligands and critical for the oxygen reduction chemistry, is in the neutral protonated form, which distinguishes O from OH, where Y244 is in the deprotonated tyrosinate form. These structural characteristics of O provide new insights into the proton translocation mechanism of CcO.
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Affiliation(s)
- Izumi Ishigami
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Raymond G. Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Zhen Su
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305 USA
| | - Ariana Peck
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Cong Wang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Frederic Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Stella Lisova
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Frank R. Moss
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Robert E. Sublett
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Syun-Ru Yeh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Denis L. Rousseau
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 USA
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Noodleman L, Han Du WG, McRee D, Chen Y, Goh T, Götz AW. Coupled transport of electrons and protons in a bacterial cytochrome c oxidase-DFT calculated properties compared to structures and spectroscopies. Phys Chem Chem Phys 2021; 22:26652-26668. [PMID: 33231596 DOI: 10.1039/d0cp04848h] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
After a general introduction to the features and mechanisms of cytochrome c oxidases (CcOs) in mitochondria and aerobic bacteria, we present DFT calculated physical and spectroscopic properties for the catalytic reaction cycle compared with experimental observations in bacterial ba3 type CcO, also with comparisons/contrasts to aa3 type CcOs. The Dinuclear Complex (DNC) is the active catalytic reaction center, containing a heme a3 Fe center and a near lying Cu center (called CuB) where by successive reduction and protonation, molecular O2 is transformed to two H2O molecules, and protons are pumped from an inner region across the membrane to an outer region by transit through the CcO integral membrane protein. Structures, energies and vibrational frequencies for Fe-O and O-O modes are calculated by DFT over the catalytic cycle. The calculated DFT frequencies in the DNC of CcO are compared with measured frequencies from Resonance Raman spectroscopy to clarify the composition, geometry, and electronic structures of different intermediates through the reaction cycle, and to trace reaction pathways. X-ray structures of the resting oxidized state are analyzed with reference to the known experimental reaction chemistry and using DFT calculated structures in fitting observed electron density maps. Our calculations lead to a new proposed reaction pathway for coupling the PR → F → OH (ferryl-oxo → ferric-hydroxo) pathway to proton pumping by a water shift mechanism. Through this arc of the catalytic cycle, major shifts in pKa's of the special tyrosine and a histidine near the upper water pool activate proton transfer. Additional mechanisms for proton pumping are explored, and the role of the CuB+ (cuprous state) in controlling access to the dinuclear reaction site is proposed.
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Affiliation(s)
- Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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7
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Han Du WG, McRee D, Götz AW, Noodleman L. A Water Molecule Residing in the Fe a33+···Cu B2+ Dinuclear Center of the Resting Oxidized as-Isolated Cytochrome c Oxidase: A Density Functional Study. Inorg Chem 2020; 59:8906-8915. [PMID: 32525689 PMCID: PMC8114904 DOI: 10.1021/acs.inorgchem.0c00724] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Indexed: 11/30/2022]
Abstract
Although the dinuclear center (DNC) of the resting oxidized "as-isolated" cytochrome c oxidase (CcO) is not a catalytically active state, its detailed structure, especially the nature of the bridging species between the Fea33+ and CuB2+ metal sites, is still both relevant and unsolved. Recent crystallographic work has shown an extended electron density for a peroxide type dioxygen species (O1-O2) bridging the Fea3 and CuB centers. In this paper, our density functional theory (DFT) calculations show that the observed peroxide type electron density between the two metal centers is most likely a mistaken analysis due to overlap of the electron density of a water molecule located at different positions between apparent O1 and O2 sites in DNCs of different CcO molecules with almost the same energy. Because the diffraction pattern and the resulting electron density map represent the effective long-range order averaged over many molecules and unit cells in the X-ray structure, this averaging can lead to an apparent observed superposition of different water positions between the Fea33+ and CuB2+ metal sites.
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Affiliation(s)
- Wen-Ge Han Du
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Duncan McRee
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Andreas W. Götz
- San
Diego Supercomputer Center, University of
California San Diego, 9500 Gilman Drive MC0505, La Jolla, California 92093, United States
| | - Louis Noodleman
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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8
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Han Du WG, Götz AW, Noodleman L. DFT Fe a3-O/O-O Vibrational Frequency Calculations over Catalytic Reaction Cycle States in the Dinuclear Center of Cytochrome c Oxidase. Inorg Chem 2019; 58:13933-13944. [PMID: 31566371 PMCID: PMC6839913 DOI: 10.1021/acs.inorgchem.9b01840] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Density functional vibrational frequency calculations have been performed on eight geometry optimized cytochrome c oxidase (CcO) dinuclear center (DNC) reaction cycle intermediates and on the oxymyoglobin (oxyMb) active site. The calculated Fe-O and O-O stretching modes and their frequency shifts along the reaction cycle have been compared with the available resonance Raman (rR) measurements. The calculations support the proposal that in state A[Fea33+-O2-•···CuB+] of CcO, O2 binds with Fea32+ in a similar bent end-on geometry to that in oxyMb. The calculations show that the observed 20 cm-1 shift of the Fea3-O stretching mode from the PR to F state is caused by the protonation of the OH- ligand on CuB2+ (PR[Fea34+═O2-···HO--CuB2+] → F[Fea34+═O2-···H2O-CuB2+]), and that the H2O ligand is still on the CuB2+ site in the rR identified F[Fea34+═O2-···H2O-CuB2+] state. Further, the observed rR band at 356 cm-1 between states PR and F is likely an O-Fea3-porphyrin bending mode. The observed 450 cm-1 low Fea3-O frequency mode for the OH active oxidized state has been reproduced by our calculations on a nearly symmetrically bridged Fea33+-OH-CuB2+ structure with a relatively long Fea3-O distance near 2 Å. Based on Badger's rule, the calculated Fea3-O distances correlate well with the calculated νFe-O-2/3 (νFe-O is the Fea3-O stretching frequency) with correlation coefficient R = 0.973.
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Affiliation(s)
- Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
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9
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Kurbah SD, Kumar A, Sanentiba Ozukum O, Syiemlieh I, Lal RA. Synthesis, characterization, crystal structure, and reactivity of heterobimetallic dioxovanadium(V) complexes containing multidentate hydrazone ligands. J COORD CHEM 2017. [DOI: 10.1080/00958972.2017.1380194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Sunshine D. Kurbah
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, Shillong, India
| | - Arvind Kumar
- Faculty of Science and Technology, Department of Chemistry, The University of West-Indies, St. Augustine, Trinidad and Tobago
| | - O. Sanentiba Ozukum
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, Shillong, India
| | - Ibanphylla Syiemlieh
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, Shillong, India
| | - Ram A. Lal
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, Shillong, India
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Schaefer AW, Kieber-Emmons MT, Adam SM, Karlin KD, Solomon EI. Phenol-Induced O-O Bond Cleavage in a Low-Spin Heme-Peroxo-Copper Complex: Implications for O 2 Reduction in Heme-Copper Oxidases. J Am Chem Soc 2017; 139:7958-7973. [PMID: 28521498 PMCID: PMC5605297 DOI: 10.1021/jacs.7b03292] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
This study evaluates the reaction of a biomimetic heme-peroxo-copper complex, {[(DCHIm)(F8)FeIII]-(O22-)-[CuII(AN)]}+ (1), with a phenolic substrate, involving a net H-atom abstraction to cleave the bridging peroxo O-O bond that produces FeIV═O, CuII-OH, and phenoxyl radical moieties, analogous to the chemistry carried out in heme-copper oxidases (HCOs). A 3D potential energy surface generated for this reaction reveals two possible reaction pathways: one involves nearly complete proton transfer (PT) from the phenol to the peroxo ligand before the barrier; the other involves O-O homolysis, where the phenol remains H-bonding to the peroxo OCu in the transition state (TS) and transfers the H+ after the barrier. In both mechanisms, electron transfer (ET) from phenol occurs after the PT (and after the barrier); therefore, only the interaction with the H+ is involved in lowering the O-O cleavage barrier. The relative barriers depend on covalency (which governs ET from Fe), and therefore vary with DFT functional. However, as these mechanisms differ by the amount of PT at the TS, kinetic isotope experiments were conducted to determine which mechanism is active. It is found that the phenolic proton exhibits a secondary kinetic isotope effect, consistent with the calculations for the H-bonded O-O homolysis mechanism. The consequences of these findings are discussed in relation to O-O cleavage in HCOs, supporting a model in which a peroxo intermediate serves as the active H+ acceptor, and both the H+ and e- required for O-O cleavage derive from the cross-linked Tyr residue present at the active site.
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Affiliation(s)
- Andrew W Schaefer
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Matthew T Kieber-Emmons
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
- Department of Chemistry, The University of Utah , Salt Lake City, Utah 84112, United States
| | - Suzanne M Adam
- Department of Chemistry, The Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Kenneth D Karlin
- Department of Chemistry, The Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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11
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Quist DA, Diaz DE, Liu JJ, Karlin KD. Activation of dioxygen by copper metalloproteins and insights from model complexes. J Biol Inorg Chem 2017; 22:253-288. [PMID: 27921179 PMCID: PMC5600896 DOI: 10.1007/s00775-016-1415-2] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/11/2016] [Indexed: 02/08/2023]
Abstract
Nature uses dioxygen as a key oxidant in the transformation of biomolecules. Among the enzymes that are utilized for these reactions are copper-containing metalloenzymes, which are responsible for important biological functions such as the regulation of neurotransmitters, dioxygen transport, and cellular respiration. Enzymatic and model system studies work in tandem in order to gain an understanding of the fundamental reductive activation of dioxygen by copper complexes. This review covers the most recent advancements in the structures, spectroscopy, and reaction mechanisms for dioxygen-activating copper proteins and relevant synthetic models thereof. An emphasis has also been placed on cofactor biogenesis, a fundamentally important process whereby biomolecules are post-translationally modified by the pro-enzyme active site to generate cofactors which are essential for the catalytic enzymatic reaction. Significant questions remaining in copper-ion-mediated O2-activation in copper proteins are addressed.
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Affiliation(s)
- David A Quist
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Daniel E Diaz
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jeffrey J Liu
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kenneth D Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA.
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12
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Spaeth AD, Gagnon NL, Dhar D, Yee GM, Tolman WB. Determination of the Cu(III)-OH Bond Distance by Resonance Raman Spectroscopy Using a Normalized Version of Badger's Rule. J Am Chem Soc 2017; 139:4477-4485. [PMID: 28319386 PMCID: PMC5975256 DOI: 10.1021/jacs.7b00210] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The stretching frequency, ν(Cu-O), of the [CuOH]2+ core in the complexes LCuOH (L = N,N'-bis(2,6-diisopropyl-4-R-phenyl)pyridine-2,6-dicarboxamide, R = H or NO2, or N,N'-bis(2,6-diisopropylphenyl)-1-methylpiperidine-2,6-dicarboxamide) was determined to be ∼630 cm-1 by resonance Raman spectroscopy and verified by isotopic labeling. In efforts to use Badger's rule to estimate the bond distance corresponding to ν(Cu-O), a modified version of the rule was developed through use of stretching frequencies normalized by dividing by the appropriate reduced masses. The modified version was found to yield excellent fits of normalized frequencies to bond distances for >250 data points from theory and experiment for a variety of M-X and X-X bond distances in the range ∼1.1-2.2 Å (root mean squared errors for the predicted bond distances of 0.03 Å). Using the resulting general equation, the Cu-O bond distance was predicted to be ∼1.80 Å for the reactive [CuOH]2+ core. Limitations of the equation and its use in predictions of distances in a variety of moieties for which structural information is not available were explored.
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Affiliation(s)
- Andrew D. Spaeth
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Nicole L. Gagnon
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Debanjan Dhar
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Gereon M. Yee
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - William B. Tolman
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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13
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Sharma V, Wikström M. The role of the K-channel and the active-site tyrosine in the catalytic mechanism of cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1111-1115. [PMID: 26898520 DOI: 10.1016/j.bbabio.2016.02.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/09/2016] [Accepted: 02/15/2016] [Indexed: 02/08/2023]
Abstract
The active site of cytochrome c oxidase (CcO) comprises an oxygen-binding heme, a nearby copper ion (CuB), and a tyrosine residue that is covalently linked to one of the histidine ligands of CuB. Two proton-conducting pathways are observed in CcO, namely the D- and the K-channels, which are used to transfer protons either to the active site of oxygen reduction (substrate protons) or for pumping. Proton transfer through the D-channel is very fast, and its role in efficient transfer of both substrate and pumped protons is well established. However, it has not been fully clear why a separate K-channel is required, apparently for the supply of substrate protons only. In this work, we have analysed the available experimental and computational data, based on which we provide new perspectives on the role of the K-channel. Our analysis suggests that proton transfer in the K-channel may be gated by the protonation state of the active-site tyrosine (Tyr244) and that the neutral radical form of this residue has a more general role in the CcO mechanism than thought previously. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
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Affiliation(s)
- Vivek Sharma
- Department of Physics, Tampere University of Technology, Tampere FI-33101, Finland; Department of Physics, University of Helsinki, Helsinki, Finland.
| | - Mårten Wikström
- Institute of Biotechnology, University of Helsinki, Helsinki, FI-00014, Finland.
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14
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Yoshikawa S, Shimada A, Shinzawa-Itoh K. Respiratory conservation of energy with dioxygen: cytochrome C oxidase. Met Ions Life Sci 2015; 15:89-130. [PMID: 25707467 DOI: 10.1007/978-3-319-12415-5_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Cytochrome c oxidase (CcO) is the terminal oxidase of cell respiration which reduces molecular oxygen (O₂) to H2O coupled with the proton pump. For elucidation of the mechanism of CcO, the three-dimensional location and chemical reactivity of each atom composing the functional sites have been extensively studied by various techniques, such as crystallography, vibrational and time-resolved electronic spectroscopy, since the X-ray structures (2.8 Å resolution) of bovine and bacterial CcO have been published in 1995.X-ray structures of bovine CcO in different oxidation and ligand binding states showed that the O₂reduction site, which is composed of Fe (heme a 3) and Cu (CuB), drives a non-sequential four-electron transfer for reduction of O₂to water without releasing any reactive oxygen species. These data provide the crucial structural basis to solve a long-standing problem, the mechanism of the O₂reduction.Time-resolved resonance Raman and charge translocation analyses revealed the mechanism for coupling between O₂reduction and the proton pump: O₂is received by the O₂reduction site where both metals are in the reduced state (R-intermediate), giving the O₂-bound form (A-intermediate). This is spontaneously converted to the P-intermediate, with the bound O₂fully reduced to 2 O²⁻. Hereafter the P-intermediate receives four electron equivalents from the second Fe site (heme a), one at a time, to form the three intermediates, F, O, and E to regenerate the R-intermediate. Each electron transfer step from heme a to the O₂reduction site is coupled with the proton pump.X-ray structural and mutational analyses of bovine CcO show three possible proton transfer pathways which can transfer pump protons (H) and chemical (water-forming) protons (K and D). The structure of the H-pathway of bovine CcO indicates that the driving force of the proton pump is the electrostatic repulsion between the protons on the H-pathway and positive charges of heme a, created upon oxidation to donate electrons to the O₂reduction site. On the other hand, mutational and time-resolved electrometric findings for the bacterial CcO strongly suggest that the D-pathway transfers both pump and chemical protons. However, the structure for the proton-gating system in the D-pathway has not been experimentally identified. The structural and functional diversities in CcO from various species suggest a basic proton pumping mechanism in which heme a pumps protons while heme a 3 reduces O₂as proposed in 1978.
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Affiliation(s)
- Shinya Yoshikawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Kamigohri Akoh Hyogo, 678-1297, Japan,
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15
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Affiliation(s)
- Shinya Yoshikawa
- Picobiology Institute, Graduate
School of Life Science, University of Hyogo, Kamigohri Akoh Hyogo, 678-1297, Japan
| | - Atsuhiro Shimada
- Picobiology Institute, Graduate
School of Life Science, University of Hyogo, Kamigohri Akoh Hyogo, 678-1297, Japan
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16
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Ishigami I, Hikita M, Egawa T, Yeh SR, Rousseau DL. Proton translocation in cytochrome c oxidase: insights from proton exchange kinetics and vibrational spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:98-108. [PMID: 25268561 DOI: 10.1016/j.bbabio.2014.09.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/11/2014] [Accepted: 09/20/2014] [Indexed: 11/19/2022]
Abstract
Cytochrome c oxidase is the terminal enzyme in the electron transfer chain. It reduces oxygen to water and harnesses the released energy to translocate protons across the inner mitochondrial membrane. The mechanism by which the oxygen chemistry is coupled to proton translocation is not yet resolved owing to the difficulty of monitoring dynamic proton transfer events. Here we summarize several postulated mechanisms for proton translocation, which have been supported by a variety of vibrational spectroscopic studies. We recently proposed a proton translocation model involving proton accessibility to the regions near the propionate groups of the heme a and heme a3 redox centers of the enzyme based by hydrogen/deuterium (H/D) exchange Raman scattering studies (Egawa et al., PLoS ONE 2013). To advance our understanding of this model and to refine the proton accessibility to the hemes, the H/D exchange dependence of the heme propionate group vibrational modes on temperature and pH was measured. The H/D exchange detected at the propionate groups of heme a3 takes place within a few seconds under all conditions. In contrast, that detected at the heme a propionates occurs in the oxidized but not the reduced enzyme and the H/D exchange is pH-dependent with a pKa of ~8.0 (faster at high pH). Analysis of the thermodynamic parameters revealed that, as the pH is varied, entropy/enthalpy compensation held the free energy of activation in a narrow range. The redox dependence of the possible proton pathways to the heme groups is discussed. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Izumi Ishigami
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Masahide Hikita
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Tsuyoshi Egawa
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Denis L Rousseau
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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17
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Weidinger IM. Analysis of structure-function relationships in cytochrome c oxidase and its biomimetic analogs via resonance Raman and surface enhanced resonance Raman spectroscopies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:119-25. [PMID: 25223590 DOI: 10.1016/j.bbabio.2014.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 08/27/2014] [Accepted: 09/05/2014] [Indexed: 01/08/2023]
Abstract
Cytochrome c oxidase (CcO) catalyzes the four electron reduction of molecular oxygen to water while avoiding the formation of toxic peroxide; a quality that is of high relevance for the development of oxygen-reducing catalysts. Resonance Raman spectroscopy has been used since many years as a technique to identify electron transfer pathways in cytochrome c oxidase and to identify the key intermediates in the catalytic cycle. This information can be compared to artificial systems such as modified heme-copper enzymes, molecular heme-copper catalysts or CcO/electrode complexes in order to shed light into the reaction mechanism of these non-natural systems. Understanding the structural commonalities and differences of CcO with its non-natural analogs is of great value for designing efficient oxygen-reducing catalysts. In this review therefore Raman spectroscopic measurements on artificial heme-copper enzymes and model complexes are summarized and compared to the natural enzyme cytochrome c oxidase. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Inez M Weidinger
- Department of Chemistry PC 14, Technische Universitaet Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany.
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18
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Nakashima S, Ogura T, Kitagawa T. Infrared and Raman spectroscopic investigation of the reaction mechanism of cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:86-97. [PMID: 25135480 DOI: 10.1016/j.bbabio.2014.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/07/2014] [Accepted: 08/11/2014] [Indexed: 10/24/2022]
Abstract
Recent progress in studies on the proton-pumping and O₂reduction mechanisms of cytochrome c oxidase (CcO) elucidated by infrared (IR) and resonance Raman (rR) spectroscopy, is reviewed. CcO is the terminal enzyme of the respiratory chain and its O₂reduction reaction is coupled with H⁺ pumping activity across the inner mitochondrial membrane. The former is catalyzed by heme a3 and its mechanism has been determined using a rR technique, while the latter used the protein moiety and has been investigated with an IR technique. The number of H⁺ relative to e⁻ transferred in the reaction is 1:1, and their coupling is presumably performed by heme a and nearby residues. To perform this function, different parts of the protein need to cooperate with each other spontaneously and sequentially. It is the purpose of this article to describe the structural details on the coupling on the basis of the vibrational spectra of certain specified residues and chromophores involved in the reaction. Recent developments in time-resolved IR and Raman technology concomitant with protein manipulation methods have yielded profound insights into such structural changes. In particular, the new IR techniques that yielded the breakthrough are reviewed and assessed in detail. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Satoru Nakashima
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takashi Ogura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan; Department of Life Science, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Teizo Kitagawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
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19
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Solomon EI, Heppner DE, Johnston EM, Ginsbach JW, Cirera J, Qayyum M, Kieber-Emmons MT, Kjaergaard CH, Hadt RG, Tian L. Copper active sites in biology. Chem Rev 2014; 114:3659-853. [PMID: 24588098 PMCID: PMC4040215 DOI: 10.1021/cr400327t] [Citation(s) in RCA: 1147] [Impact Index Per Article: 114.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - David E. Heppner
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | - Jake W. Ginsbach
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Jordi Cirera
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Munzarin Qayyum
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | | | - Ryan G. Hadt
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Li Tian
- Department of Chemistry, Stanford University, Stanford, CA, 94305
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20
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Du WGH, Noodleman L. 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. Inorg Chem 2013; 52:14072-88. [PMID: 24262070 DOI: 10.1021/ic401858s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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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Affiliation(s)
- Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, TPC15, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Paulus A, Rossius SGH, Dijk M, de Vries S. Oxoferryl-porphyrin radical catalytic intermediate in cytochrome bd oxidases protects cells from formation of reactive oxygen species. J Biol Chem 2012; 287:8830-8. [PMID: 22287551 DOI: 10.1074/jbc.m111.333542] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The quinol-linked cytochrome bd oxidases are terminal oxidases in respiration. These oxidases harbor a low spin heme b(558) that donates electrons to a binuclear heme b(595)/heme d center. The reaction with O(2) and subsequent catalytic steps of the Escherichia coli cytochrome bd-I oxidase were investigated by means of ultra-fast freeze-quench trapping followed by EPR and UV-visible spectroscopy. After the initial binding of O(2), the O-O bond is heterolytically cleaved to yield a kinetically competent heme d oxoferryl porphyrin π-cation radical intermediate (compound I) magnetically interacting with heme b(595). Compound I accumulates to 0.75-0.85 per enzyme in agreement with its much higher rate of formation (~20,000 s(-1)) compared with its rate of decay (~1,900 s(-1)). Compound I is next converted to a short lived heme d oxoferryl intermediate (compound II) in a phase kinetically matched to the oxidation of heme b(558) before completion of the reaction. The results indicate that cytochrome bd oxidases like the heme-copper oxidases break the O-O bond in a single four-electron transfer without a peroxide intermediate. However, in cytochrome bd oxidases, the fourth electron is donated by the porphyrin moiety rather than by a nearby amino acid. The production of reactive oxygen species by the cytochrome bd oxidase was below the detection level of 1 per 1000 turnovers. We propose that the two classes of terminal oxidases have mechanistically converged to enzymes in which the O-O bond is broken in a single four-electron transfer reaction to safeguard the cell from the formation of reactive oxygen species.
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Affiliation(s)
- Angela Paulus
- Department of Biotechnology, Section Enzymology, Delft University of Technology, Delft, The Netherlands
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Kieber-Emmons MT, Li Y, Halime Z, Karlin KD, Solomon EI. Electronic structure of a low-spin heme/Cu peroxide complex: spin-state and spin-topology contributions to reactivity. Inorg Chem 2011; 50:11777-86. [PMID: 22007669 PMCID: PMC3226806 DOI: 10.1021/ic2018727] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This study details the electronic structure of the heme–peroxo–copper adduct {[(F8)Fe(DCHIm)]-O2-[Cu(AN)]}+ (LS(AN)) in which O2(2–) bridges the metals in a μ-1,2 or “end-on” configuration. LS(AN) is generated by addition of coordinating base to the parent complex {[(F8)Fe]-O2-[Cu(AN)]}+ (HS(AN)) in which the O2(2–) bridges the metals in an μ-η2:η2 or “side-on” mode. In addition to the structural change of the O2(2–) bridging geometry, coordination of the base changes the spin state of the heme fragment (from S = 5/2 in HS(AN) to S = 1/2 in LS(AN)) that results in an antiferromagnetically coupled diamagnetic ground state in LS(AN). The strong ligand field of the porphyrin modulates the high-spin to low-spin effect on Fe–peroxo bonding relative to nonheme complexes, which is important in the O–O bond cleavage process. On the basis of DFT calculations, the ground state of LS(AN) is dependent on the Fe–O–O–Cu dihedral angle, wherein acute angles (<~150°) yield an antiferromagnetically coupled electronic structure while more obtuse angles yield a ferromagnetic ground state. LS(AN) is diamagnetic and thus has an antiferromagnetically coupled ground state with a calculated Fe–O–O–Cu dihedral angle of 137°. The nature of the bonding in LS(AN) and the frontier molecular orbitals which lead to this magneto-structural correlation provide insight into possible spin topology contributions to O–O bond cleavage by cytochrome c oxidase.
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Affiliation(s)
| | - Yuqi Li
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218
| | - Zakaria Halime
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218
| | - Kenneth D. Karlin
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218
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Kieber-Emmons MT, Qayyum MF, Li Y, Halime Z, Hodgson KO, Hedman B, Karlin KD, Solomon EI. Spectroscopic elucidation of a new heme/copper dioxygen structure type: implications for O···O bond rupture in cytochrome c oxidase. Angew Chem Int Ed Engl 2011; 51:168-72. [PMID: 22095556 DOI: 10.1002/anie.201104080] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 08/24/2011] [Indexed: 11/11/2022]
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24
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Kieber-Emmons MT, Qayyum MF, Li Y, Halime Z, Hodgson KO, Hedman B, Karlin KD, Solomon EI. Spectroscopic Elucidation of a New Heme/Copper Dioxygen Structure Type: Implications for O⋅⋅⋅O Bond Rupture in Cytochrome c Oxidase. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201104080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Active site intermediates in the reduction of O(2) by cytochrome oxidase, and their derivatives. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:468-75. [PMID: 22079200 DOI: 10.1016/j.bbabio.2011.10.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 10/27/2011] [Accepted: 10/29/2011] [Indexed: 11/22/2022]
Abstract
The mechanism of dioxygen activation and reduction in cell respiration, as catalysed by cytochrome c oxidase, has a long history. The work by Otto Warburg, David Keilin and Britton Chance defined the dioxygen-binding heme iron centre, viz. das Atmungsferment, or cytochrome a(3). Chance brought the field further in the mid-1970's by ingenious low-temperature studies that for the first time identified the primary enzyme-substrate (ES) Michaelis complex of cell respiration, the dioxygen adduct of heme a(3), which he termed Compound A. Further work using optical, resonance Raman, EPR, and other sophisticated spectroscopic techniques, some of which with microsecond time resolution, has brought us to the situation today, where major principles of how O(2) reduction occurs in respiration are well understood. Nonetheless, some questions have remained open, for example concerning the precise structures, catalytic roles, and spectroscopic properties of the breakdown products of Compound A that have been called P, F (for peroxy and ferryl), and O (oxidised). This nomenclature has been known to be inadequate for some time already, and an alternative will be suggested here. In addition, the multiple forms of P, F and O states have been confusing, a situation that we endeavour to help clarifying. The P and F states formed artificially by reacting cytochrome oxidase with hydrogen peroxide are especially scrutinised, and some novel interpretations will be given that may account for previously unexplained observations.
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26
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Coordination asymmetry in μ-oxido divanadium complexes: Development of synthetic protocols. Coord Chem Rev 2011. [DOI: 10.1016/j.ccr.2011.02.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Muramoto K, Ohta K, Shinzawa-Itoh K, Kanda K, Taniguchi M, Nabekura H, Yamashita E, Tsukihara T, Yoshikawa S. Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate. Proc Natl Acad Sci U S A 2010; 107:7740-5. [PMID: 20385840 PMCID: PMC2867921 DOI: 10.1073/pnas.0910410107] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The O(2) reduction site of cytochrome c oxidase (CcO), comprising iron (Fe(a3)) and copper (Cu(B)) ions, is probed by x-ray structural analyses of CO, NO, and CN(-) derivatives to investigate the mechanism of the complete reduction of O(2). Formation of the derivative contributes to the trigonal planar coordination of and displaces one of its three coordinated imidazole groups while a water molecule becomes hydrogen bonded to both the CN(-) ligand and the hydroxyl group of Tyr244. When O(2) is bound to Fe2+a3 , it is negatively polarized (O2- ), and expected to induce the same structural change induced by CN(-). This structural change allows to receive three electron equivalents nonsequentially from Cu1B+, Fe3+a3, and Tyr-OH, providing complete reduction of O(2) with minimization of production of active oxygen species. The proton-pumping pathway of bovine CcO comprises a hydrogen-bond network and a water channel which extend to the positive and negative side surfaces, respectively. Protons transferred through the water channel are pumped through the hydrogen-bond network electrostatically with positive charge created at the Fe(a) center by electron donation to the O(2) reduction site. Binding of CO or NO to induces significant narrowing of a section of the water channel near the hydrogen-bond network junction, which prevents access of water molecules to the network. In a similar manner, O(2) binding to is expected to prevent access of water molecules to the hydrogen-bond network. This blocks proton back-leak from the network and provides an efficient gate for proton-pumping.
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Affiliation(s)
- Kazumasa Muramoto
- Department of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigohri, Akoh, Hyogo 678-1297, Japan; and
| | - Kazuhiro Ohta
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Kyoko Shinzawa-Itoh
- Department of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigohri, Akoh, Hyogo 678-1297, Japan; and
| | - Katsumasa Kanda
- Department of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigohri, Akoh, Hyogo 678-1297, Japan; and
| | - Maki Taniguchi
- Department of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigohri, Akoh, Hyogo 678-1297, Japan; and
| | - Hiroyuki Nabekura
- Department of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigohri, Akoh, Hyogo 678-1297, Japan; and
| | - Eiki Yamashita
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Tomitake Tsukihara
- Department of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigohri, Akoh, Hyogo 678-1297, Japan; and
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Shinya Yoshikawa
- Department of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigohri, Akoh, Hyogo 678-1297, Japan; and
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28
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Yoshioka Y, Mitani M. B3LYP study on reduction mechanisms from O2 to H2O at the catalytic sites of fully reduced and mixed-valence bovine cytochrome c oxidases. Bioinorg Chem Appl 2010; 2010:182804. [PMID: 20396396 PMCID: PMC2852611 DOI: 10.1155/2010/182804] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Revised: 11/27/2009] [Accepted: 01/05/2010] [Indexed: 11/26/2022] Open
Abstract
Reduction mechanisms of oxygen molecule to water molecules in the fully reduced (FR) and mixed-valence (MV) bovine cytochrome c oxidases (CcO) have been systematically examined based on the B3LYP calculations. The catalytic cycle using four electrons and four protons has been also shown consistently. The MV CcO catalyses reduction to produce one water molecule, while the FR CcO catalyses to produce two water molecules. One water molecule is added into vacant space between His240 and His290 in the catalytic site. This water molecule constructs the network of hydrogen bonds of Tyr244, farnesyl ethyl, and Thr316 that is a terminal residue of the K-pathway. It plays crucial roles for the proton transfer to the dioxygen to produce the water molecules in both MV and FR CcOs. Tyr244 functions as a relay of the proton transfer from the K-pathway to the added water molecule, not as donors of a proton and an electron to the dioxygen. The reduction mechanisms of MV and FR CcOs are strictly distinguished. In the FR CcO, the Cu atom at the Cu(B) site maintains the reduced state Cu(I) during the process of formation of first water molecule and plays an electron storage. At the final stage of formation of first water molecule, the Cu(I) atom releases an electron to Fe-O. During the process of formation of second water molecule, the Cu atom maintains the oxidized state Cu(II). In contrast with experimental proposals, the K-pathway functions for formation of first water molecule, while the D-pathway functions for second water molecule. The intermediates, P(M), P(R), F, and O, obtained in this work are compared with those proposed experimentally.
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Affiliation(s)
- Yasunori Yoshioka
- Chemistry Department for Materials, Graduate School of Engineering, Mie University, Kurima-machiya 1577, Tsu, Mie 514-8507, Japan.
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Soo HS, Komor AC, Iavarone AT, Chang CJ. A Hydrogen-Bond Facilitated Cycle for Oxygen Reduction by an Acid- and Base-Compatible Iron Platform. Inorg Chem 2009; 48:10024-35. [DOI: 10.1021/ic9006668] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Han Sen Soo
- Department of Chemistry
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | | | | | - Christopher J. Chang
- Department of Chemistry
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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The role of the conserved tryptophan272 of the Paracoccus denitrificans cytochrome c oxidase in proton pumping. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:925-8. [PMID: 18515062 DOI: 10.1016/j.bbabio.2008.05.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2008] [Revised: 04/06/2008] [Accepted: 05/10/2008] [Indexed: 11/20/2022]
Abstract
The catalytic mechanism of heme-copper oxidases - electron transfer coupled to proton pumping - is not yet fully understood. Single turnover experiments in which fully reduced cytochrome aa(3) from Paracoccus denitrificans reacts with O(2) using the microsecond freeze-hyperquenching sampling technique enabled trapping of transient catalytic intermediates and analysis by low temperature UV-Visible, X-band and Q-band EPR spectroscopy. Our recent findings (Wiertz et al. (2007) J. Biol. Chem. 282, 31580-31591), which show that the strictly conserved W272 is a redox active residue are reviewed here. The W272 forms a tryptophan neutral radical in the transition F-->F(W)-->O(H) in which the novel intermediate F(W) harbors the tryptophan radical. The potential role of W272 in proton pumping is highlighted.
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Belevich I, Verkhovsky MI. Molecular mechanism of proton translocation by cytochrome c oxidase. Antioxid Redox Signal 2008; 10:1-29. [PMID: 17949262 DOI: 10.1089/ars.2007.1705] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Cytochrome c oxidase (CcO) is a terminal protein of the respiratory chain in eukaryotes and some bacteria. It catalyzes most of the biologic oxygen consumption on earth done by aerobic organisms. During the catalytic reaction, CcO reduces dioxygen to water and uses the energy released in this process to maintain the electrochemical proton gradient by functioning as a redox-linked proton pump. Even though the structures of several terminal oxidases are known, they are not sufficient in themselves to explain the molecular mechanism of proton pumping. Thus, additional extensive studies of CcO by varieties of biophysical and biochemical approaches are involved to shed light on the mechanism of proton translocation. In this review, we summarize the current level of knowledge about CcO, including the latest model developed to explain the CcO proton-pumping mechanism.
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Affiliation(s)
- Ilya Belevich
- Helsinki Bioenergetics Group, Program for Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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Wiertz FGM, Richter OMH, Ludwig B, de Vries S. Kinetic Resolution of a Tryptophan-radical Intermediate in the Reaction Cycle of Paracoccus denitrificans Cytochrome c Oxidase. J Biol Chem 2007; 282:31580-91. [PMID: 17761680 DOI: 10.1074/jbc.m705520200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The catalytic mechanism, electron transfer coupled to proton pumping, of heme-copper oxidases is not yet fully understood. Microsecond freeze-hyperquenching single turnover experiments were carried out with fully reduced cytochrome aa(3) reacting with O(2) between 83 micros and 6 ms. Trapped intermediates were analyzed by low temperature UV-visible, X-band, and Q-band EPR spectroscopy, enabling determination of the oxidation-reduction kinetics of Cu(A), heme a, heme a(3), and of a recently detected tryptophan radical (Wiertz, F. G. M., Richter, O. M. H., Cherepanov, A. V., MacMillan, F., Ludwig, B., and de Vries, S. (2004) FEBS Lett. 575, 127-130). Cu(B) and heme a(3) were EPR silent during all stages of the reaction. Cu(A) and heme a are in electronic equilibrium acting as a redox pair. The reduction potential of Cu(A) is 4.5 mV lower than that of heme a. Both redox groups are oxidized in two phases with apparent half-lives of 57 micros and 1.2 ms together donating a single electron to the binuclear center in each phase. The formation of the heme a(3) oxoferryl species P(R) (maxima at 430 nm and 606 nm) was completed in approximately 130 micros, similar to the first oxidation phase of Cu(A) and heme a. The intermediate F (absorbance maximum at 571 nm) is formed from P(R) and decays to a hitherto undetected intermediate named F(W)(*). F(W)(*) harbors a tryptophan radical, identified by Q-band EPR spectroscopy as the tryptophan neutral radical of the strictly conserved Trp-272 (Trp-272(*)). The Trp-272(*) populates to 4-5% due to its relatively low rate of formation (t((1/2)) = 1.2 ms) and rapid rate of breakdown (t((1/2)) = 60 micros), which represents electron transfer from Cu(A)/heme a to Trp-272(*). The formation of the Trp-272(*) constitutes the major rate-determining step of the catalytic cycle. Our findings show that Trp-272 is a redox-active residue and is in this respect on an equal par to the metallocenters of the cytochrome c oxidase. Trp-272 is the direct reductant either to the heme a(3) oxoferryl species or to Cu (2+)(B). The potential role of Trp-272 in proton pumping is discussed.
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Affiliation(s)
- Frank G M Wiertz
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands
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Oxygen Activation Mechanism at the Binuclear Site of Heme-Copper Oxidase Superfamily as Revealed by Time-Resolved Resonance Raman Spectroscopy. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/9780470166468.ch6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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Musser SM, Stowell MH, Chan SI. Cytochrome c oxidase: chemistry of a molecular machine. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 71:79-208. [PMID: 8644492 DOI: 10.1002/9780470123171.ch3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The plethora of proposed chemical models attempting to explain the proton pumping reactions catalyzed by the CcO complex, especially the number of recent models, makes it clear that the problem is far from solved. Although we have not discussed all of the models proposed to date, we have described some of the more detailed models in order to illustrate the theoretical concepts introduced at the beginning of this section on proton pumping as well as to illustrate the rich possibilities available for effecting proton pumping. It is clear that proton pumping is effected by conformational changes induced by oxidation/reduction of the various redox centers in the CcO complex. It is for this reason that the CcO complex is called a redox-linked proton pump. The conformational changes of the proton pump cycle are usually envisioned to be some sort of ligand-exchange reaction arising from unstable geometries upon oxidation/reduction of the various redox centers. However, simple geometrical rearrangements, as in the Babcock and Mitchell models are also possible. In any model, however, hydrogen bonds must be broken and reformed due to conformational changes that result from oxidation/reduction of the linkage site during enzyme turnover. Perhaps the most important point emphasized in this discussion, however, is the fact that proton pumping is a directed process and it is electron and proton gating mechanisms that drive the proton pump cycle in the forward direction. Since many of the models discussed above lack effective electron and/or proton gating, it is clear that the major difficulty in developing a viable chemical model is not formulating a cyclic set of protein conformational changes effecting proton pumping (redox linkage) but rather constructing the model with a set of physical constraints so that the proposed cycle proceeds efficiently as postulated. In our discussion of these models, we have not been too concerned about which electron of the catalytic cycle was entering the site of linkage, but merely whether an ET to the binuclear center played a role. However, redox linkage only occurs if ET to the activated binuclear center is coupled to the proton pump. Since all of the models of proton pumping presented here, with the exception of the Rousseau expanded model and the Wikström model, have a maximum stoichiometry of 1 H+/e-, they inadequately explain the 2 H+/e- ratio for the third and fourth electrons of the dioxygen reduction cycle (see Section V.B). One way of interpreting this shortfall of protons is that the remaining protons are pumped by an as yet undefined indirectly coupled mechanism. In this scenario, the site of linkage could be coupled to the pumping of one proton in a direct fashion and one proton in an indirect fashion for a given electron. For a long time, it was assumed that at least some elements of such an indirect mechanism reside in subunit III. While recent evidence argues against the involvement of subunit III in the proton pump, subunit III may still participate in a regulatory and/or structural capacity (Section II.E). Attention has now focused on subunits I and II in the search for residues intimately involved in the proton pump mechanism and/or as part of a proton channel. In particular, the role of some of the highly conserved residues of helix VIII of subunit I are currently being studied by site directed mutagenesis. In our opinion, any model that invokes heme alpha 3 or CuB as the site of linkage must propose a very effective means by which the presumedly fast uncoupling ET to the dioxygen intermediates is prevented. It is difficult to imagine that ET over the short distance from heme alpha 3 or CuB to the dioxygen intermediate requires more than 1 ns. In addition, we expect the conformational changes of the proton pump to require much more than 1 ns (see Section V.B).
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Affiliation(s)
- S M Musser
- Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena 91125, USA
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35
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Affiliation(s)
- Eunsuk Kim
- Department of Chemistry, Johns Hopkins University, Charles and 34th Streets, Baltimore, Maryland 21218, USA
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36
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Einarsdóttir O, Szundi I. Time-resolved optical absorption studies of cytochrome oxidase dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1655:263-73. [PMID: 15100041 DOI: 10.1016/j.bbabio.2003.07.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2003] [Accepted: 07/31/2003] [Indexed: 10/26/2022]
Abstract
Time-resolved spectroscopic studies in our laboratory of bovine heart cytochrome c oxidase dynamics are summarized. Intramolecular electron transfer was investigated upon photolysis of CO from the mixed-valence enzyme, by pulse radiolysis, and upon light-induced electron injection into the cytochrome c/cytochrome oxidase complex from a novel photoactivatable dye. The reduction of dioxygen to water was monitored by a gated multichannel analyzer using the CO flow-flash method or a synthetic caged dioxygen carrier. The pH dependence of the intermediate spectra suggests a mechanism of dioxygen reduction more complex than the conventional unidirectional sequential scheme. A branched model is proposed, in which one branch produces the P form and the other branch the F form. The rate of exchange between the two branches is pH-dependent. A cross-linked histidine-phenol was synthesized and characterized to explore the role of the cross-linked His-Tyr cofactor in the function of the enzyme. Time-resolved optical absorption spectra, EPR and FTIR spectra of the compound generated after UV photolysis indicated the presence of a radical residing primarily on the phenoxyl ring. The relevance of these results to cytochrome oxidase function is discussed.
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Affiliation(s)
- Olöf Einarsdóttir
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA.
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Aono S, Kato T, Matsuki M, Nakajima H, Ohta T, Uchida T, Kitagawa T. Resonance Raman and ligand binding studies of the oxygen-sensing signal transducer protein HemAT from Bacillus subtilis. J Biol Chem 2002; 277:13528-38. [PMID: 11821422 DOI: 10.1074/jbc.m112256200] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
HemAT-Bs is a heme-containing signal transducer protein responsible for aerotaxis of Bacillus subtilis. The recombinant HemAT-Bs expressed in Escherichia coli was purified as the oxy form in which oxygen was bound to the ferrous heme. Oxygen binding and dissociation rate constants were determined to be k(on) = 32 microm(-1) s(-1) and k(off) = 23 s(-1), respectively, revealing that HemAT-Bs has a moderate oxygen affinity similar to that of sperm whale myoglobin (Mb). The rate constant for autoxidation at 37 degrees C was 0.06 h(-1), which is also close to that of Mb. Although the electronic absorption spectra of HemAT-Bs were similar to those of Mb, HemAT-Bs showed some unique characteristics in its resonance Raman spectra. Oxygen-bound HemAT-Bs gave the nu(Fe-O(2)) band at a noticeably low frequency (560 cm(-1)), which suggests a unique hydrogen bonding between a distal amino acid residue and the proximal atom of the bound oxygen molecule. Deoxy HemAT-Bs gave the nu(Fe-His) band at a higher frequency (225 cm(-1)) than those of ordinary His-coordinated deoxy heme proteins. CO-bound HemAT-Bs gave the nu(Fe-CO) and nu(C-O) bands at 494 and 1964 cm(-1), respectively, which fall on the same nu(C-O) versus nu(Fe-CO) correlation line as that of Mb. Based on these results, the structural and functional properties of HemAT-Bs are discussed.
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Affiliation(s)
- Shigetoshi Aono
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Tatsunokuchi, Ishikawa, Japan.
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Schultz BE, Chan SI. Structures and proton-pumping strategies of mitochondrial respiratory enzymes. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2001; 30:23-65. [PMID: 11340051 DOI: 10.1146/annurev.biophys.30.1.23] [Citation(s) in RCA: 192] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Enzymes of the mitochondrial respiratory chain serve as proton pumps, using the energy made available from electron transfer reactions to transport protons across the inner mitochondrial membrane and create an electrochemical gradient used for the production of ATP. The ATP synthase enzyme is reversible and can also serve as a proton pump by coupling ATP hydrolysis to proton translocation. Each of the respiratory enzymes uses a different strategy for performing proton pumping. In this work, the strategies are described and the structural bases for the action of these proteins are discussed in light of recent crystal structures of several respiratory enzymes. The mechanisms and efficiency of proton translocation are also analyzed in terms of the thermodynamics of the substrate transformations catalyzed by these enzymes.
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Affiliation(s)
- B E Schultz
- Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125, USA
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39
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Kitagawa T. Structures of reaction intermediates of bovine cytochrome c oxidase probed by time-resolved vibrational spectroscopy. J Inorg Biochem 2000; 82:9-18. [PMID: 11132644 DOI: 10.1016/s0162-0134(00)00155-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structures of reaction intermediates of bovine cytochrome c oxidase (CcO) in the reactions of its fully reduced form with O2 and fully oxidized form with H2O2 were investigated with time-resolved resonance Raman (RR) and infrared spectroscopy. Six oxygen-associated RR bands were observed for the reaction of CcO with O2. The isotope shifts for an asymmetrically labeled dioxygen, (16)O(18)O, has established that the primary intermediate of cytochrome a3 is an end-on type dioxygen adduct and the subsequent intermediate (P) is an oxoiron species with Fe=O stretch (nu(Fe=O)) at 804/764 cm(-1) for (16)O2/(18)O2 derivatives, although it had been long postulated to be a peroxy species. The P intermediate is converted to the F intermediate with nu(Fe=O) at 785/751 cm(-1) and then to a ferric hydroxy species with nu(Fe-OH) at 450/425 cm(-1) (443/417 cm(-1) in D2O). The rate of reaction from P to F intermediates is significantly slower in D2O than in H2O. The reaction of oxidized CcO with H2O2 yields the same oxygen isotope-sensitive bands as those of P and F, indicating the identity of intermediates. Time-resolved infrared spectroscopy revealed that deprotonation of carboxylic acid side chain takes place upon deligation of a ligand from heme a3. UV RR spectrum gave a prominent band due to cis C=C stretch of phospholipids tightly bound to purified CcO.
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Affiliation(s)
- T Kitagawa
- Center for Integrative Bioscience, Okazaki National Research Institutes, Myodaiji, Japan.
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40
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Yoshikawa S, Shinzawa-Itoh K, Tsukihara T. X-ray structure and the reaction mechanism of bovine heart cytochrome c oxidase. J Inorg Biochem 2000; 82:1-7. [PMID: 11132615 DOI: 10.1016/s0162-0134(00)00137-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
X-ray structure of bovine heart cytochrome c oxidase in the fully oxidized state shows a peroxide bridging between Fe2+ and Cu2+ in the O2 reduction site. The bond distances for Fe-O and Cu-O are 2.52 and 2.16 A, respectively. The structure is consistent with antiferromagnetic coupling between the two metals, which has long been known and to recent redox titration results [J. Biol. Chem. 274 (1999) 33403]. The trigonal planer coordination of Cu1+ in the O2 reduction site is consistent with the very weak interaction between Cu1+ and O2 bound at Fe2+ revealed by time-resolved resonance Raman investigations. One of the three histidine imidazoles coordinated to the Cu ion in the O2 reduction site fixes a tyrosine phenol group near the O2 reduction site with the direct covalent link between the two groups. The structure suggests that the phenol group is the site for donating protons to the bound O2. Redox-coupled conformational change in an extramembrane loop indicates that an aspartate (Asp51) in the loop apart from the O2 reduction site is the site for proton pumping.
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Affiliation(s)
- S Yoshikawa
- Department of Life Science, Himeji Institute of Technology and CREST, Japan Science and Technology Corporation, Kamigohri, Akoh Hyogo.
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41
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Han S, Takahashi S, Rousseau DL. Time dependence of the catalytic intermediates in cytochrome c oxidase. J Biol Chem 2000; 275:1910-9. [PMID: 10636892 DOI: 10.1074/jbc.275.3.1910] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome c oxidase, the terminal enzyme in the electron transfer chain, catalyzes the reduction of oxygen to water in a multiple step process by utilizing four electrons from cytochrome c. To study the reaction mechanism, the resonance Raman spectra of the intermediate states were measured during single turnover of the enzyme after catalytic initiation by photolysis of CO from the fully reduced CO-bound enzyme. By measuring the change in intensity of lines associated with heme a, the electron transfer steps were determined and found to be biphasic with apparent rate constants of approximately 40 x 10(3) s(-1) and approximately 1 x 10(3) s(-1). The time dependence for the oxidation of heme a and for the measured formation and decay of the oxy, the ferryl ("F"), and the hydroxy intermediates could be simulated by a simple reaction scheme. In this scheme, the presence of the "peroxy" ("P") intermediate does not build up a sufficient population to be detected because its decay rate is too fast in buffered H(2)O at neutral pH. A comparison of the change in the spin equilibrium with the formation of the hydroxy intermediate demonstrates that this intermediate is high spin. We also confirm the presence of an oxygen isotope-sensitive line at 355 cm(-1), detectable in the spectrum from 130 to 980 micros, coincident with the presence of the F intermediate.
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Affiliation(s)
- S Han
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Michel H, Behr J, Harrenga A, Kannt A. Cytochrome c oxidase: structure and spectroscopy. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 1998; 27:329-56. [PMID: 9646871 DOI: 10.1146/annurev.biophys.27.1.329] [Citation(s) in RCA: 341] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cytochrome c oxidase, the terminal enzyme of the respiratory chains of mitochondria and aerobic bacteria, catalyzes electron transfer from cytochrome c to molecular oxygen, reducing the latter to water. Electron transfer is coupled to proton translocation across the membrane, resulting in a proton and charge gradient that is then employed by the F0F1-ATPase to synthesize ATP. Over the last years, substantial progress has been made in our understanding of the structure and function of this enzyme. Spectroscopic techniques such as EPR, absorbance and resonance Raman spectroscopy, in combination with site-directed mutagenesis work, have been successfully applied to elucidate the nature of the cofactors and their ligands, to identify key residues involved in proton transfer, and to gain insight into the catalytic cycle and the structures of its intermediates. Recently, the crystal structures of a bacterial and a mitochondrial cytochrome c oxidase have been determined. In this review, we provide an overview of the crystal structures, summarize recent spectroscopic work, and combine structural and spectroscopic data in discussing mechanistic aspects of the enzyme. For the latter, we focus on the structure of the oxygen intermediates, proton-transfer pathways, and the much-debated issue of how electron transfer in the enzyme might be coupled to proton translocation.
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Affiliation(s)
- H Michel
- Max-Planck-Institut für Biophysik, Frankfurt/Main, Germany.
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43
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Brunori M, Giuffré A, Malatesta F, Sarti P. Investigating the mechanism of electron transfer to the binuclear center in Cu-heme oxidases. J Bioenerg Biomembr 1998; 30:41-5. [PMID: 9623804 DOI: 10.1023/a:1020503410377] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Novel experimental evidence is presented further supporting the hypothesis that, starting with resting oxidized cytochrome c oxidase, the internal electron transfer to the oxygen binding site is kinetically controlled. The reduction of the enzyme was followed spectroscopically and in the presence of NO or CO, used as trapping ligands for reduced cytochrome a3; ruthenium hexamine was used as a spectroscopically silent electron donor. Consistent with the high combination rate constant for reduced cytochrome a3, NO proved to be a very efficient trapping ligand, while CO did not. The results are discussed in view of two alternative (thermodynamic and kinetic) hypotheses of control of electron transfer to the binuclear (cyt.a3-CuB) center. Fulfilling the prediction of the kinetic control hypothesis: i) the reduction of cytochrome a3 and ligation are synchronous and proceed at the intrinsic rate of cytochrome a3 reduction, ii) the measured rate of formation of the nitrosyl derivative is independent of the concentration of both the reductant and NO.
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Affiliation(s)
- M Brunori
- Department of Biochemical Sciences A Rossi-Fanelli and CNR Center for Molecular Biology, University of Rome La Sapienza, Italy
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44
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Kitagawa T, Ogura T. Time-resolved resonance Raman investigation of oxygen reduction mechanism of bovine cytochrome c oxidase. J Bioenerg Biomembr 1998; 30:71-9. [PMID: 9623808 DOI: 10.1023/a:1020511612194] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Six oxygen-associated resonance Raman bands were identified for intermediates in the reaction of bovine cytochrome c oxidase with O2 at room temperature. The primary intermediate, corresponding to Compound A of cryogenic measurements, is an O2 adduct of heme a3 and its isotope frequency shifts for 16O18O have established that the binding is of an end-on type. This is followed by two oxoheme intermediates, and the final intermediate appearing around 3 ms is the Fe-OH heme. The reaction rate between the two oxoheme intermediates is significantly slower in D2O than in H2O, suggesting that the electron transfer is regulated by proton translocations at this step. It is noted that the reaction intermediates of oxidized enzyme with hydrogen peroxide yield the same three sets of oxygen isotope-sensitive bands as those of oxoheme intermediates seen for O2 reduction and that the O-O bond has already been cleaved in the so-called peroxy form (or 607 nm form).
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Affiliation(s)
- T Kitagawa
- Institute for Molecular Science, Okazaki National Research Institutes, Myodaiji, Japan
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45
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Konstantinov AA, Siletsky S, Mitchell D, Kaulen A, Gennis RB. The roles of the two proton input channels in cytochrome c oxidase from Rhodobacter sphaeroides probed by the effects of site-directed mutations on time-resolved electrogenic intraprotein proton transfer. Proc Natl Acad Sci U S A 1997; 94:9085-90. [PMID: 9256439 PMCID: PMC23042 DOI: 10.1073/pnas.94.17.9085] [Citation(s) in RCA: 265] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/1996] [Accepted: 05/28/1997] [Indexed: 02/05/2023] Open
Abstract
The crystal structures of cytochrome c oxidase from both bovine and Paracoccus denitrificans reveal two putative proton input channels that connect the heme-copper center, where dioxygen is reduced, to the internal aqueous phase. In this work we have examined the role of these two channels, looking at the effects of site-directed mutations of residues observed in each of the channels of the cytochrome c oxidase from Rhodobacter sphaeroides. A photoelectric technique was used to monitor the time-resolved electrogenic proton transfer steps associated with the photo-induced reduction of the ferryl-oxo form of heme a3 (Fe4+ = O2-) to the oxidized form (Fe3+OH-). This redox step requires the delivery of a "chemical" H+ to protonate the reduced oxygen atom and is also coupled to proton pumping. It is found that mutations in the K channel (K362M and T359A) have virtually no effect on the ferryl-oxo-to-oxidized (F-to-Ox) transition, although steady-state turnover is severely limited. In contrast, electrogenic proton transfer at this step is strongly suppressed by mutations in the D channel. The results strongly suggest that the functional roles of the two channels are not the separate delivery of chemical or pumped protons, as proposed recently [Iwata, S., Ostermeier, C., Ludwig, B. & Michel, H. (1995) Nature (London) 376, 660-669]. The D channel is likely to be involved in the uptake of both "chemical" and "pumped" protons in the F-to-Ox transition, whereas the K channel is probably idle at this partial reaction and is likely to be used for loading the enzyme with protons at some earlier steps of the catalytic cycle. This conclusion agrees with different redox states of heme a3 in the K362M and E286Q mutants under aerobic steady-state turnover conditions.
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Affiliation(s)
- A A Konstantinov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
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Brunori M, Giuffrè A, D'Itri E, Sarti P. Internal electron transfer in Cu-heme oxidases. Thermodynamic or kinetic control? J Biol Chem 1997; 272:19870-4. [PMID: 9242650 DOI: 10.1074/jbc.272.32.19870] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We present novel experimental evidence that, starting with the oxidized enzyme, the internal electron transfer in cytochrome c oxidase is kinetically controlled. The anaerobic reduction of the oxidized enzyme by ruthenium hexamine has been followed in the absence and presence of CO or NO, used as trapping ligands for reduced cytochrome a3. In the presence of NO, the rate of formation of the cytochrome a32+-NO adduct is independent of the concentration of ruthenium hexamine and of NO, indicating that in the oxidized enzyme cytochrome a and a3 are not in very rapid redox equilibrium; on the other hand, CO proved to be a poor "trapping" ligand. We conclude that the intrinsic rate constant for a --> a3 electron transfer in the oxidized enzyme is 25 s-1. These data are discussed with reference to a model (Verkhovsky, M. I., Morgan, J. E., and Wikström, M. (1995) Biochemistry 34, 7483-7491) in which H+ diffusion and/or binding at the binuclear site is the rate-limiting step in the reduction of cytochrome a3 in the oxidized enzyme.
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Affiliation(s)
- M Brunori
- Department of Biochemical Sciences A. Rossi-Fanelli and CNR Center of Molecular Biology, University of Rome La Sapienza, I-00185 Rome, Italy
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Proton and electrical charge translocation by cytochrome-c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1997. [DOI: 10.1016/s0005-2728(96)00152-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Verkhovsky MI, Morgan JE, Wikström M. Redox transitions between oxygen intermediates in cytochrome-c oxidase. Proc Natl Acad Sci U S A 1996; 93:12235-9. [PMID: 8901563 PMCID: PMC37973 DOI: 10.1073/pnas.93.22.12235] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Some intermediates in the reduction of O2 to water by cytochrome-c oxidase have been characterized by optical, Raman, and magnetic circular dichroism spectroscopy. The so-called "peroxy" (P) and "ferryl" (F) forms of the enzyme, which have been considered to be intermediates of the oxygen reaction, can be generated when the oxidized enzyme reacts with H2O2, or when the two-electron reduced ("CO mixed-valence") enzyme reacts with O2. The structures as well as the overall redox states of P and F have recently been controversial. We show here, using tris(2,2'-bipyridyl)ruthenium(II) as a photoinducible reductant, that one-electron reduction of P yields F, and that one-electron reduction of F yields the oxidized enzyme. This confirms that the overall redox states of P and F differ from the oxidized enzyme by two and one electron equivalents, respectively. The structures of the P and F states are discussed.
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Affiliation(s)
- M I Verkhovsky
- Department of Medical Chemistry, University of Helsinki, Finland
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Takahashi S, Ching YC, Wang J, Rousseau DL. Microsecond generation of oxygen-bound cytochrome c oxidase by rapid solution mixing. J Biol Chem 1995; 270:8405-7. [PMID: 7721733 DOI: 10.1074/jbc.270.15.8405] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Current understanding of the oxygen reduction and proton translocation processes in cytochrome c oxidase is largely derived from the data obtained by a nonphysiological method for initiating the catalytic reaction: photolyzing carbon monoxide (CO) from the CO-inhibited enzyme in the presence of oxygen (O2). However, considerable evidence suggests that the use of CO introduces artifacts into the reaction mechanism. We have therefore developed a rapid solution mixer with a mixing time of 20 microseconds to study the catalytic reaction by directly mixing the enzyme with O2 without using CO. Unexpectedly, the resonance Raman scattering detected for the first 120 microseconds after the mixing show that the CO influences neither the structure of the primary oxy-intermediate, its rate of decay, nor the rate of oxidation of cytochrome a. This implies that CO has an effect on the later stages of the catalytic process, which may involve the proton translocation steps, and calls for the re-examination of the catalytic process by using the direct mixing method. In addition, these results demonstrate the feasibility of using the rapid mixing device for the study of biological reactions in the microsecond time domain.
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Affiliation(s)
- S Takahashi
- AT&T Bell Laboratories, Murray Hill, New Jersey 07974, USA
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Hirota S, Mogi T, Ogura T, Hirano T, Anraku Y, Kitagawa T. Observation of the Fe-O2 and FeIV=O stretching Raman bands for dioxygen reduction intermediates of cytochrome bo isolated from Escherichia coli. FEBS Lett 1994; 352:67-70. [PMID: 7925945 DOI: 10.1016/0014-5793(94)00919-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Reaction intermediates in dioxygen reduction by the E. coli cytochrome bo-type ubiquinol oxidase were studied by time-resolved resonance Raman spectroscopy using the artificial cardiovascular system. At 0-20 microseconds following photolysis of the enzyme-CO adduct in the presence of O2, we observed the Fe-O2 stretching Raman band at 568 cm-1 which shifted to 535 cm-1 with the 18O2 derivative. These frequencies are remarkably close to those of other oxyhemoproteins including dioxygen-bound hemoglobin and aa3-type cytochrome c oxidase. In the later time range (20-40 microseconds), other oxygen-isotope-sensitive Raman bands were observed at 788 and 361 cm-1. Since the 781 cm-1 band exhibited a downshift by 37 cm-1 upon 18O2 substitution, we assigned it to the FeIV=O stretching mode. This band is considered to arise from the ferryl intermediate, but its appearance was much earlier than the corresponding intermediate of bovine cytochrome c oxidase (> 100 microseconds). The 361 cm-1 band showed the 16O/18O isotopic frequency shift of 14 cm-1 similar to the case of bovine cytochrome c oxidase reaction.
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Affiliation(s)
- S Hirota
- Graduate University for Advanced Studies, Okazaki National Research Institutes, Japan
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