1
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Safari C, Ghosh S, Andersson R, Johannesson J, Båth P, Uwangue O, Dahl P, Zoric D, Sandelin E, Vallejos A, Nango E, Tanaka R, Bosman R, Börjesson P, Dunevall E, Hammarin G, Ortolani G, Panman M, Tanaka T, Yamashita A, Arima T, Sugahara M, Suzuki M, Masuda T, Takeda H, Yamagiwa R, Oda K, Fukuda M, Tosha T, Naitow H, Owada S, Tono K, Nureki O, Iwata S, Neutze R, Brändén G. Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase. SCIENCE ADVANCES 2023; 9:eadh4179. [PMID: 38064560 PMCID: PMC10708180 DOI: 10.1126/sciadv.adh4179] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023]
Abstract
Cytochrome c oxidase (CcO) is part of the respiratory chain and contributes to the electrochemical membrane gradient in mitochondria as well as in many bacteria, as it uses the energy released in the reduction of oxygen to pump protons across an energy-transducing biological membrane. Here, we use time-resolved serial femtosecond crystallography to study the structural response of the active site upon flash photolysis of carbon monoxide (CO) from the reduced heme a3 of ba3-type CcO. In contrast with the aa3-type enzyme, our data show how CO is stabilized on CuB through interactions with a transiently ordered water molecule. These results offer a structural explanation for the extended lifetime of the CuB-CO complex in ba3-type CcO and, by extension, the extremely high oxygen affinity of the enzyme.
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Affiliation(s)
- Cecilia Safari
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Swagatha Ghosh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Rebecka Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Jonatan Johannesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Owens Uwangue
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Peter Dahl
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Doris Zoric
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Emil Sandelin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Adams Vallejos
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Robert Bosman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Per Börjesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Elin Dunevall
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Greger Hammarin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Giorgia Ortolani
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Matthijs Panman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Ayumi Yamashita
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Toshi Arima
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Michihiro Sugahara
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Mamoru Suzuki
- Laboratory of Supramolecular Crystallography, Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Tetsuya Masuda
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Japan
| | - Hanae Takeda
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Raika Yamagiwa
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Kazumasa Oda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Masahiro Fukuda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takehiko Tosha
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hisashi Naitow
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
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2
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Panda S, Phan H, Karlin KD. Heme-copper and Heme O 2-derived synthetic (bioinorganic) chemistry toward an understanding of cytochrome c oxidase dioxygen chemistry. J Inorg Biochem 2023; 249:112367. [PMID: 37742491 PMCID: PMC10615892 DOI: 10.1016/j.jinorgbio.2023.112367] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/22/2023] [Accepted: 09/07/2023] [Indexed: 09/26/2023]
Abstract
Cytochrome c oxidase (CcO), also widely known as mitochondrial electron-transport-chain complex IV, is a multi-subunit transmembrane protein responsible for catalyzing the last step of the electron transport chain, dioxygen reduction to water, which is essential to the establishment and maintenance of the membrane proton gradient that drives ATP synthesis. Although many intermediates in the CcO catalytic cycle have been spectroscopically and/or computationally authenticated, the specifics regarding the IP intermediate, hypothesized to be a heme-Cu (hydro)peroxo species whose O-O bond homolysis is supported by a hydrogen-bonding network of water molecules, are largely obscured by the fast kinetics of the A (FeIII-O2•-/CuI/Tyr) → PM (FeIV=O/CuII-OH/Tyr•) step. In this review, we have focused on the recent advancements in the design, development, and characterization of synthetic heme-peroxo‑copper model complexes, which can circumvent the abovementioned limitation, for the investigation of the formation of IP and its O-O cleavage chemistry. Novel findings regarding (a) proton and electron transfer (PT/ET) processes, together with their contributions to exogenous phenol induced O-O cleavage, (b) the stereo-electronic tunability of the secondary coordination sphere (especially hydrogen-bonding) on the geometric and spin state alteration of the heme-peroxo‑copper unit, and (c) a plausible mechanism for the Tyr-His cofactor biogenesis, are discussed in great detail. Additionally, since the ferric-superoxide and the ferryl-oxo (Compound II) species are critically involved in the CcO catalytic cycle, this review also highlights a few fundamental aspects of these heme-only (i.e., without copper) species, including the structural and reactivity influences of electron-donating trans-axial ligands and Lewis acid-promoted H-bonding.
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Affiliation(s)
- Sanjib Panda
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Hai Phan
- 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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3
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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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Chowdhury SN, Biswas S, Das S, Biswas AN. Kinetic and mechanistic investigations of dioxygen reduction by a molecular Cu(II) catalyst bearing a pentadentate amidate ligand. Dalton Trans 2023; 52:11581-11590. [PMID: 37548356 DOI: 10.1039/d3dt02194g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
A pentadentate Cu(II) complex, [CuII(dpaq)](ClO4) (1), featuring a redox active ligand, H-dpaq (H-dpaq = 2-[bis(pyridine-2-ylmethyl)]amino-N-quinolin-8-yl-acetamidate), catalyses four-electron reduction of dioxygen by decamethylferrocene (Fc*) in the presence of trifluoroacetic acid (CF3COOH) in acetone at 298 K. No catalytic oxygen reduction was observed in the presence of stronger Brønsted acids than CF3COOH, such as perchloric acid (HClO4) or trifluoromethanesulphonic acid (HOTf). In contrast, facile catalytic reduction of O2 occurs by Fc* with 1 and HClO4 or HOTf in dimethylformamide (DMF). The use of CF3COOH as the proton source in DMF results in the suppression of O2 reduction under otherwise identical reaction conditions. While the O2 reduction reactions in DMF are linearly dependent on the pKa of Brønsted acids, the acid dependence on catalytic O2-reduction reactivity by 1 in acetone showed complete reversal. Cyclic voltammetry studies using p-chloranil as the probe substrates in the presence of acids in the solvents reveal that the strengths of the protonic acids increase significantly in acetone compared to that in DMF. The amidate-N in [CuII(dpaq)](ClO4) (1) undergoes protonation in the presence of HClO4 or HOTf in DMF to form [CuII(H-dpaq)]2+ (1-H+), but not in the presence of CF3COOH. Enhanced acid strength of CF3COOH in acetone, however, effectively protonates 1 and triggers O2 reduction. Protonation of 1 with HClO4 or HOTf in acetone results in the change of its coordination environment, and this protonated species does not trigger O2 reduction. Detailed kinetic studies indicate that 1-H+ undergoes reduction by two-electrons and the reduced species binds O2 to form a Cu(II)-superoxo intermediate. This is followed by a rate-determining proton-coupled electron-transfer (PCET) reduction to generate the Cu(II)-hydroperoxo intermediate. While catalytic O2 reduction in acetone occurs predominantly via a 4e-/4H+ pathway, product selectivity (H2O vs. H2O2) in DMF depends upon the concentration of the reductant (Fc*). While dioxygen reduction to H2O2 is favoured at low [Fc*], mechanistic studies suggest that O2 reduction with high [Fc*] proceeds via a [2e- + 2e-] mechanism, where the released H2O2 during catalysis is further reduced to water.
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Affiliation(s)
- Srijan Narayan Chowdhury
- Department of Chemistry, National Institute of Technology Sikkim, Ravangla, South Sikkim 737139, India.
| | - Sachidulal Biswas
- Department of Chemistry, National Institute of Technology Sikkim, Ravangla, South Sikkim 737139, India.
| | - Saikat Das
- Department of Chemistry, National Institute of Technology Sikkim, Ravangla, South Sikkim 737139, India.
| | - Achintesh N Biswas
- Department of Chemistry, National Institute of Technology Sikkim, Ravangla, South Sikkim 737139, India.
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5
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Sadri S, Tomar N, Yang C, Audi SH, Cowley AW, Dash RK. Effects of ROS pathway inhibitors and NADH and FADH 2 linked substrates on mitochondrial bioenergetics and ROS emission in the heart and kidney cortex and outer medulla. Arch Biochem Biophys 2023; 744:109690. [PMID: 37429534 PMCID: PMC10528392 DOI: 10.1016/j.abb.2023.109690] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023]
Abstract
Mitochondria are major sources of reactive oxygen species (ROS), which play important roles in both physiological and pathological processes. However, the specific contributions of different ROS production and scavenging components in the mitochondria of metabolically active tissues such as heart and kidney cortex and outer medulla (OM) are not well understood. Therefore, the goal of this study was to determine contributions of different ROS production and scavenging components and provide detailed comparisons of mitochondrial respiration, bioenergetics, ROS emission between the heart and kidney cortex and OM using tissues obtained from the same Sprague-Dawley rat under identical conditions and perturbations. Specifically, data were obtained using both NADH-linked substrate pyruvate + malate and FADH2-linked substrate succinate followed by additions of inhibitors of different components of the electron transport chain (ETC) and oxidative phosphorylation (OxPhos) and other ROS production and scavenging systems. Currently, there is limited data available for the mitochondria of kidney cortex and OM, the two major energy-consuming tissues in the body only next to the heart, and scarce quantitative information on the interplay between mitochondrial ROS production and scavenging systems in the three tissues. The findings from this study demonstrate significant differences in mitochondrial respiratory and bioenergetic functions and ROS emission among the three tissues. The results quantify the rates of ROS production from different complexes of the ETC, identify the complexes responsible for variations in mitochondrial membrane depolarization and regulations of ROS production, and quantify the contributions of ROS scavenging enzymes towards overall mitochondrial ROS emission. These findings advance our fundamental knowledge of tissue-specific and substrate-dependent mitochondrial respiratory and bioenergetic functions and ROS emission. This is important given the critical role that excess ROS production, oxidative stress, and mitochondrial dysfunction in the heart and kidney cortex and OM play in the pathogenesis of cardiovascular and renal diseases, including salt-sensitive hypertension.
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Affiliation(s)
- Shima Sadri
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Namrata Tomar
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Chun Yang
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Said H Audi
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI, 53226, USA; Department of Biomedical Engineering, Marquette University, Milwaukee, WI, 53223, USA
| | - Allen W Cowley
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA; Cardiovascular Research Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Ranjan K Dash
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI, 53226, USA; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA; Cardiovascular Research Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA; Department of Biomedical Engineering, Marquette University, Milwaukee, WI, 53223, USA.
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6
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Abstract
We present a brief review of the mitochondrial respiratory chain with emphasis on complexes I, III and IV, which contribute to the generation of protonmotive force across the inner mitochondrial membrane, and drive the synthesis of ATP by the process called oxidative phosphorylation. The basic structural and functional details of these complexes are discussed. In addition, we briefly review the information on the so-called supercomplexes, aggregates of complexes I-IV, and summarize basic physiological aspects of cell respiration.
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Affiliation(s)
- Mårten Wikström
- HiLife Institute of Biotechnology, University of Helsinki, Biocenter, Viikinkaari, Helsinki, Finland.
| | - Cristina Pecorilla
- Department of Physics, University of Helsinki, Gustaf Hällströmin katu, Helsinki, Finland
| | - Vivek Sharma
- HiLife Institute of Biotechnology, University of Helsinki, Biocenter, Viikinkaari, Helsinki, Finland; Department of Physics, University of Helsinki, Gustaf Hällströmin katu, Helsinki, Finland
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7
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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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8
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Kielb PJ, Teutloff C, Bittl R, Gray HB, Winkler JR. Does Tyrosine Protect S. coelicolor Laccase from Oxidative Degradation or Act as an Extended Catalytic Site? J Phys Chem B 2022; 126:7943-7949. [PMID: 36191240 PMCID: PMC10231039 DOI: 10.1021/acs.jpcb.2c04835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have investigated the roles of tyrosine (Tyr) and tryptophan (Trp) residues in the four-electron reduction of oxygen catalyzed by Streptomyces coelicolor laccase (SLAC). During normal enzymatic turnover in laccases, reducing equivalents are delivered to a type 1 Cu center (CuT1) and then are transferred over 13 Å to a trinuclear Cu site (TNC: (CuT3)2CuT2) where O2 reduction occurs. The TNC in SLAC is surrounded by a large cluster of Tyr and Trp residues that can provide reducing equivalents when the normal flow of electrons is disrupted. Prior studies by Canters and co-workers [J. Am. Chem. Soc. 2009, 131 (33), 11680-11682] have shown that when O2 reacts with a reduced SLAC variant lacking the CuT1 center, a Tyr108• radical near the TNC forms rapidly. We have found that the Tyr108• radical is reduced 10 times faster than CuT12+ by excess ascorbate, possibly because of radical transfer along Tyr/Trp chains.
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Affiliation(s)
- Patrycja J. Kielb
- Beckman Institute, California Institute of Technology, Pasadena CA 91125, United States
| | | | - Robert Bittl
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena CA 91125, United States
| | - Jay R. Winkler
- Beckman Institute, California Institute of Technology, Pasadena CA 91125, United States
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9
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Electric fields control water-gated proton transfer in cytochrome c oxidase. Proc Natl Acad Sci U S A 2022; 119:e2207761119. [PMID: 36095184 PMCID: PMC9499568 DOI: 10.1073/pnas.2207761119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aerobic life is powered by membrane-bound enzymes that catalyze the transfer of electrons to oxygen and protons across a biological membrane. Cytochrome c oxidase (CcO) functions as a terminal electron acceptor in mitochondrial and bacterial respiratory chains, driving cellular respiration and transducing the free energy from O2 reduction into proton pumping. Here we show that CcO creates orientated electric fields around a nonpolar cavity next to the active site, establishing a molecular switch that directs the protons along distinct pathways. By combining large-scale quantum chemical density functional theory (DFT) calculations with hybrid quantum mechanics/molecular mechanics (QM/MM) simulations and atomistic molecular dynamics (MD) explorations, we find that reduction of the electron donor, heme a, leads to dissociation of an arginine (Arg438)-heme a3 D-propionate ion-pair. This ion-pair dissociation creates a strong electric field of up to 1 V Å-1 along a water-mediated proton array leading to a transient proton loading site (PLS) near the active site. Protonation of the PLS triggers the reduction of the active site, which in turn aligns the electric field vectors along a second, "chemical," proton pathway. We find a linear energy relationship of the proton transfer barrier with the electric field strength that explains the effectivity of the gating process. Our mechanism shows distinct similarities to principles also found in other energy-converting enzymes, suggesting that orientated electric fields generally control enzyme catalysis.
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10
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Haslem L, Hays JM, Hays FA. p66Shc in Cardiovascular Pathology. Cells 2022; 11:cells11111855. [PMID: 35681549 PMCID: PMC9180016 DOI: 10.3390/cells11111855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 02/06/2023] Open
Abstract
p66Shc is a widely expressed protein that governs a variety of cardiovascular pathologies by generating, and exacerbating, pro-apoptotic ROS signals. Here, we review p66Shc’s connections to reactive oxygen species, expression, localization, and discuss p66Shc signaling and mitochondrial functions. Emphasis is placed on recent p66Shc mitochondrial function discoveries including structure/function relationships, ROS identity and regulation, mechanistic insights, and how p66Shc-cyt c interactions can influence p66Shc mitochondrial function. Based on recent findings, a new p66Shc mitochondrial function model is also put forth wherein p66Shc acts as a rheostat that can promote or antagonize apoptosis. A discussion of how the revised p66Shc model fits previous findings in p66Shc-mediated cardiovascular pathology follows.
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Affiliation(s)
- Landon Haslem
- Biochemistry and Molecular Biology Department, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (L.H.); (J.M.H.)
| | - Jennifer M. Hays
- Biochemistry and Molecular Biology Department, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (L.H.); (J.M.H.)
| | - Franklin A. Hays
- Biochemistry and Molecular Biology Department, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (L.H.); (J.M.H.)
- Stephenson Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Correspondence:
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11
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Roy M, Nath AK, Pal I, Dey SG. Second Sphere Interactions in Amyloidogenic Diseases. Chem Rev 2022; 122:12132-12206. [PMID: 35471949 DOI: 10.1021/acs.chemrev.1c00941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloids are protein aggregates bearing a highly ordered cross β structural motif, which may be functional but are mostly pathogenic. Their formation, deposition in tissues and consequent organ dysfunction is the central event in amyloidogenic diseases. Such protein aggregation may be brought about by conformational changes, and much attention has been directed toward factors like metal binding, post-translational modifications, mutations of protein etc., which eventually affect the reactivity and cytotoxicity of the associated proteins. Over the past decade, a global effort from different groups working on these misfolded/unfolded proteins/peptides has revealed that the amino acid residues in the second coordination sphere of the active sites of amyloidogenic proteins/peptides cause changes in H-bonding pattern or protein-protein interactions, which dramatically alter the structure and reactivity of these proteins/peptides. These second sphere effects not only determine the binding of transition metals and cofactors, which define the pathology of some of these diseases, but also change the mechanism of redox reactions catalyzed by these proteins/peptides and form the basis of oxidative damage associated with these amyloidogenic diseases. The present review seeks to discuss such second sphere modifications and their ramifications in the etiopathology of some representative amyloidogenic diseases like Alzheimer's disease (AD), type 2 diabetes mellitus (T2Dm), Parkinson's disease (PD), Huntington's disease (HD), and prion diseases.
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Affiliation(s)
- Madhuparna Roy
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Arnab Kumar Nath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Ishita Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
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12
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Barolet AC, Litvinov IV, Barolet D. Light-induced nitric oxide release in the skin beyond UVA and blue light: Red & near-infrared wavelengths. Nitric Oxide 2021; 117:16-25. [PMID: 34536586 DOI: 10.1016/j.niox.2021.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/03/2021] [Accepted: 09/13/2021] [Indexed: 12/16/2022]
Abstract
Nitric oxide (NO) is omnipresent in the body and synthesized by 3 isoenzymes (nNOS, eNOS and iNOS), all detected in human skin. NO can be stored in a pool of compounds readily converted to NO following skin irradiation by UVR and blue light. This non-enzymatic (without NOS involvement) photolytic reaction mobilizes cutaneous stores of NO derivatives to the bloodstream, lowering blood pressure. However, with the likelihood of skin deleterious effects caused by UVR/blue light, safer wavelengths in the red/near-infrared (NIR) spectrum are becoming potential contenders to release cutaneous NO, possibly via NOS temperature-dependent effects. The use of red/NIR light to mobilize NO stores from the body's largest organ (the skin) is auspicious. This review focuses on UVR, blue, red, and NIR spectra and their capacity to release NO in human skin. PubMed and Google Scholar were used as article databases to find relevant publications related to this particular field.
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Affiliation(s)
- A C Barolet
- Deptartment of Surgery, Experimental Surgery Graduate Training Program, McGill University, Montreal, Quebec, Canada; Division of Dermatology, McGill University Health Centre, Montreal, Quebec, Canada.
| | - I V Litvinov
- Deptartment of Surgery, Experimental Surgery Graduate Training Program, McGill University, Montreal, Quebec, Canada; Division of Dermatology, McGill University Health Centre, Montreal, Quebec, Canada; Deptartment of Medicine, Experimental Medicine Graduate Training Program, McGill University, Montreal, Quebec, Canada
| | - D Barolet
- Division of Dermatology, McGill University Health Centre, Montreal, Quebec, Canada; RoseLab Skin Optics Research Laboratory, Laval, Quebec, Canada
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13
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Vilbert AC, Liu Y, Dai H, Lu Y. Recent advances in tuning redox properties of electron transfer centers in metalloenzymes catalyzing oxygen reduction reaction and H 2 oxidation important for fuel cells design. CURRENT OPINION IN ELECTROCHEMISTRY 2021; 30:100780. [PMID: 34435160 PMCID: PMC8382256 DOI: 10.1016/j.coelec.2021.100780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Current fuel-cell catalysts for oxygen reduction reaction (ORR) and H2 oxidation use precious metals and, for ORR, require high overpotentials. In contrast, metalloenzymes perform their respective reaction at low overpotentials using earth-abundant metals, making metalloenzymes ideal candidates for inspiring electrocatalytic design. Critical to the success of these enzymes are redox-active metal centers surrounding the enzyme active sites that ensure fast electron transfer (ET) to or away from the active site, by tuning the catalytic potential of the reaction as observed in multicopper oxidases but also in dictating the catalytic bias of the reaction as realized in hydrogenases. This review summarizes recent advances in studying these ET centers in multicopper oxidases and heme-copper oxidases that perform ORR and hydrogenases in carrying out H2 oxidation. Insights gained from understanding how the reduction potential of the ET centers effects reactivity at the active site in both the enzymes and their models are provided.
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Affiliation(s)
| | - Yiwei Liu
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huiguang Dai
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yi Lu
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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14
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Cook EN, Machan CW. Bioinspired mononuclear Mn complexes for O 2 activation and biologically relevant reactions. Dalton Trans 2021; 50:16871-16886. [PMID: 34730590 DOI: 10.1039/d1dt03178c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A general interest in harnessing the oxidizing power of dioxygen (O2) continues to motivate research efforts on bioinspired and biomimetic complexes to better understand how metalloenzymes mediate these reactions. The ubiquity of Fe- and Cu-based enzymes attracts significant attention and has resulted in many noteworthy developments for abiotic systems interested in direct O2 reduction and small molecule activation. However, despite the existence of Mn-based metalloenzymes with important O2-dependent activity, there has been comparatively less focus on the development of these analogues relative to Fe- and Cu-systems. In this Perspective, we summarize important contributions to the development of bioinspired mononuclear Mn complexes for O2 activation and studies on their reactivity, emphasizing important design parameters in the primary and secondary coordination spheres and outlining mechanistic trends.
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Affiliation(s)
- Emma N Cook
- Department of Chemistry, University of Virginia, PO Box 400319, Charlottesville, VA 22904-4319, USA.
| | - Charles W Machan
- Department of Chemistry, University of Virginia, PO Box 400319, Charlottesville, VA 22904-4319, USA.
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15
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Siletsky SA, Borisov VB. Proton Pumping and Non-Pumping Terminal Respiratory Oxidases: Active Sites Intermediates of These Molecular Machines and Their Derivatives. Int J Mol Sci 2021; 22:10852. [PMID: 34639193 PMCID: PMC8509429 DOI: 10.3390/ijms221910852] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022] Open
Abstract
Terminal respiratory oxidases are highly efficient molecular machines. These most important bioenergetic membrane enzymes transform the energy of chemical bonds released during the transfer of electrons along the respiratory chains of eukaryotes and prokaryotes from cytochromes or quinols to molecular oxygen into a transmembrane proton gradient. They participate in regulatory cascades and physiological anti-stress reactions in multicellular organisms. They also allow microorganisms to adapt to low-oxygen conditions, survive in chemically aggressive environments and acquire antibiotic resistance. To date, three-dimensional structures with atomic resolution of members of all major groups of terminal respiratory oxidases, heme-copper oxidases, and bd-type cytochromes, have been obtained. These groups of enzymes have different origins and a wide range of functional significance in cells. At the same time, all of them are united by a catalytic reaction of four-electron reduction in oxygen into water which proceeds without the formation and release of potentially dangerous ROS from active sites. The review analyzes recent structural and functional studies of oxygen reduction intermediates in the active sites of terminal respiratory oxidases, the features of catalytic cycles, and the properties of the active sites of these enzymes.
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Affiliation(s)
- Sergey A. Siletsky
- Department of Bioenergetics, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - Vitaliy B. Borisov
- Department of Molecular Energetics of Microorganisms, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia;
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16
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Jose A, Schaefer AW, Roveda AC, Transue WJ, Choi SK, Ding Z, Gennis RB, Solomon EI. The three-spin intermediate at the O-O cleavage and proton-pumping junction in heme-Cu oxidases. Science 2021; 373:1225-1229. [PMID: 34516790 DOI: 10.1126/science.abh3209] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Anex Jose
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Andrew W Schaefer
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Antonio C Roveda
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Wesley J Transue
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Sylvia K Choi
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
| | - Ziqiao Ding
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
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17
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Brzezinski P, Moe A, Ädelroth P. Structure and Mechanism of Respiratory III-IV Supercomplexes in Bioenergetic Membranes. Chem Rev 2021; 121:9644-9673. [PMID: 34184881 PMCID: PMC8361435 DOI: 10.1021/acs.chemrev.1c00140] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Indexed: 12/12/2022]
Abstract
In the final steps of energy conservation in aerobic organisms, free energy from electron transfer through the respiratory chain is transduced into a proton electrochemical gradient across a membrane. In mitochondria and many bacteria, reduction of the dioxygen electron acceptor is catalyzed by cytochrome c oxidase (complex IV), which receives electrons from cytochrome bc1 (complex III), via membrane-bound or water-soluble cytochrome c. These complexes function independently, but in many organisms they associate to form supercomplexes. Here, we review the structural features and the functional significance of the nonobligate III2IV1/2 Saccharomyces cerevisiae mitochondrial supercomplex as well as the obligate III2IV2 supercomplex from actinobacteria. The analysis is centered around the Q-cycle of complex III, proton uptake by CytcO, as well as mechanistic and structural solutions to the electronic link between complexes III and IV.
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Affiliation(s)
- Peter Brzezinski
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Agnes Moe
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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18
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Blomberg MRA. Activation of O 2 and NO in heme-copper oxidases - mechanistic insights from computational modelling. Chem Soc Rev 2021; 49:7301-7330. [PMID: 33006348 DOI: 10.1039/d0cs00877j] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Heme-copper oxidases are transmembrane enzymes involved in aerobic and anaerobic respiration. The largest subgroup contains the cytochrome c oxidases (CcO), which reduce molecular oxygen to water. A significant part of the free energy released in this exergonic process is conserved as an electrochemical gradient across the membrane, via two processes, electrogenic chemistry and proton pumping. A deviant subgroup is the cytochrome c dependent NO reductases (cNOR), which reduce nitric oxide to nitrous oxide and water. This is also an exergonic reaction, but in this case none of the released free energy is conserved. Computational studies applying hybrid density functional theory to cluster models of the bimetallic active sites in the heme-copper oxidases are reviewed. To obtain a reliable description of the reaction mechanisms, energy profiles of the entire catalytic cycles, including the reduction steps have to be constructed. This requires a careful combination of computational results with certain experimental data. Computational studies have elucidated mechanistic details of the chemical parts of the reactions, involving cleavage and formation of covalent bonds, which have not been obtainable from pure experimental investigations. Important insights regarding the mechanisms of energy conservation have also been gained. The computational studies show that the reduction potentials of the active site cofactors in the CcOs are large enough to afford electrogenic chemistry and proton pumping, i.e. efficient energy conservation. These results solve a conflict between different types of experimental data. A mechanism for the proton pumping, involving a specific and crucial role for the active site tyrosine, conserved in all CcOs, is suggested. For the cNORs, the calculations show that the low reduction potentials of the active site cofactors are optimized for fast elimination of the toxic NO molecules. At the same time, the low reduction potentials lead to endergonic reduction steps with high barriers. To prevent even higher barriers, which would lead to a too slow reaction, when the electrochemical gradient across the membrane is present, the chemistry must occur in a non-electrogenic manner. This explains why there is no energy conservation in cNOR.
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Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden.
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19
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Blomberg MRA. The Redox-Active Tyrosine Is Essential for Proton Pumping in Cytochrome c Oxidase. Front Chem 2021; 9:640155. [PMID: 33937193 PMCID: PMC8079940 DOI: 10.3389/fchem.2021.640155] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/05/2021] [Indexed: 11/13/2022] Open
Abstract
Cellular respiration involves electron transport via a number of enzyme complexes to the terminal Cytochrome c oxidase (CcO), in which molecular oxygen is reduced to water. The free energy released in the reduction process is used to establish a transmembrane electrochemical gradient, via two processes, both corresponding to charge transport across the membrane in which the enzymes are embedded. First, the reduction chemistry occurring in the active site of CcO is electrogenic, which means that the electrons and protons are delivered from opposite sides of the membrane. Second, the exergonic chemistry is coupled to translocation of protons across the entire membrane, referred to as proton pumping. In the largest subfamily of the CcO enzymes, the A-family, one proton is pumped for every electron needed for the chemistry, making the energy conservation particularly efficient. In the present study, hybrid density functional calculations are performed on a model of the A-family CcOs. The calculations show that the redox-active tyrosine, conserved in all types of CcOs, plays an essential role for the energy conservation. Based on the calculations a reaction mechanism is suggested involving a tyrosyl radical (possibly mixed with tyrosinate character) in all reduction steps. The result is that the free energy released in each reduction step is large enough to allow proton pumping in all reduction steps without prohibitively high barriers when the gradient is present. Furthermore, the unprotonated tyrosine provides a mechanism for coupling the uptake of two protons per electron in every reduction step, i.e. for a secure proton pumping.
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Affiliation(s)
- Margareta R A Blomberg
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm, Sweden
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20
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Reed CJ, Lam QN, Mirts EN, Lu Y. Molecular understanding of heteronuclear active sites in heme-copper oxidases, nitric oxide reductases, and sulfite reductases through biomimetic modelling. Chem Soc Rev 2021; 50:2486-2539. [PMID: 33475096 PMCID: PMC7920998 DOI: 10.1039/d0cs01297a] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Heme-copper oxidases (HCO), nitric oxide reductases (NOR), and sulfite reductases (SiR) catalyze the multi-electron and multi-proton reductions of O2, NO, and SO32-, respectively. Each of these reactions is important to drive cellular energy production through respiratory metabolism and HCO, NOR, and SiR evolved to contain heteronuclear active sites containing heme/copper, heme/nonheme iron, and heme-[4Fe-4S] centers, respectively. The complexity of the structures and reactions of these native enzymes, along with their large sizes and/or membrane associations, make it challenging to fully understand the crucial structural features responsible for the catalytic properties of these active sites. In this review, we summarize progress that has been made to better understand these heteronuclear metalloenzymes at the molecular level though study of the native enzymes along with insights gained from biomimetic models comprising either small molecules or proteins. Further understanding the reaction selectivity of these enzymes is discussed through comparisons of their similar heteronuclear active sites, and we offer outlook for further investigations.
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Affiliation(s)
- Christopher J Reed
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA.
| | - Quan N Lam
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA
| | - Evan N Mirts
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA. and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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21
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Marquardt M, Cula B, Budhija V, Dallmann A, Schwalbe M. Structural Determination of an Unusual Cu I -Porphyrin-π-Bond in a Hetero-Pacman Cu-Zn-Complex. Chemistry 2021; 27:3991-3996. [PMID: 33405305 PMCID: PMC7986761 DOI: 10.1002/chem.202004945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/17/2020] [Indexed: 12/02/2022]
Abstract
The synthesis and characterization of a hetero‐dinuclear compound is presented, in which a copper(I) trishistidine type coordination unit is positioned directly above a zinc porphyrin unit. The close distance between the two coordination fragments is secured by a rigid xanthene backbone, and a unique (intramolecular) copper porphyrin‐π‐bond was determined for the first time in the molecular structure. This structural motif was further analyzed by temperature‐dependent NMR studies: In solution at room temperature the coordinative bond fluctuates, while it can be frozen at low temperatures. Preliminary reactivity studies revealed a reduced reactivity of the copper(I) moiety towards dioxygen. The results adumbrate why nature is avoiding metal porphyrin‐π‐bonds by fixing reactive metal centers in a predetermined distance to each other within multimetallic enzymatic reaction centers.
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Affiliation(s)
- Michael Marquardt
- Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
| | - Beatrice Cula
- Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
| | - Vishal Budhija
- Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
| | - André Dallmann
- Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
| | - Matthias Schwalbe
- Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
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22
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Computing Proton-Coupled Redox Potentials of Fluorotyrosines in a Protein Environment. J Phys Chem B 2020; 125:128-136. [PMID: 33378205 DOI: 10.1021/acs.jpcb.0c09974] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oxidation of tyrosine to form the neutral tyrosine radical via proton-coupled electron transfer is essential for a wide range of biological processes. The precise measurement of the proton-coupled redox potentials of tyrosine (Y) in complex protein environments is challenging mainly because of the highly oxidizing and reactive nature of the radical state. Herein, a computational strategy is presented for predicting proton-coupled redox potentials in a protein environment. In this strategy, both the reduced Y-OH and oxidized Y-O• forms of tyrosine are sampled with molecular dynamics using a molecular mechanical force field. For a large number of conformations, a quantum mechanical/molecular mechanical (QM/MM) electrostatic embedding scheme is used to compute the free-energy differences between the reduced and oxidized forms, including the zero-point energy and entropic contributions as well as the impact of the protein electrostatic environment. This strategy is applied to a series of fluorinated tyrosine derivatives embedded in a de novo α-helical protein denoted as α3Y. The force fields for both the reduced and oxidized forms of these noncanonical fluorinated tyrosine residues are parameterized for general use. The calculated relative proton-coupled redox potentials agree with experimentally measured values with a mean unsigned error of 24 mV. Analysis of the simulations illustrates that hydrogen-bonding interactions between tyrosine and water increase the redox potentials by ∼100-250 mV, with significant variations because of the fluctuating protein environment. This QM/MM approach enables the calculation of proton-coupled redox potentials of tyrosine and other residues such as tryptophan in a variety of protein systems.
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23
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Blomberg MRA. Role of the Two Metals in the Active Sites of Heme Copper Oxidases-A Study of NO Reduction in cbb3 Cytochrome c Oxidase. Inorg Chem 2020; 59:11542-11553. [PMID: 32799475 DOI: 10.1021/acs.inorgchem.0c01351] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The superfamily of heme copper oxidases reduces molecular oxygen or nitric oxide, and the active sites comprise a high-spin heme group (a3 or b3) and a non-heme metal (CuB or FeB). The cbb3 C family of cytochrome c oxidases, with the high-spin heme b3 and CuB in the active site, is a subfamily of the heme copper oxidases that can reduce both molecular oxygen, which is the main substrate, and nitric oxide. The mechanism for NO reduction in cbb3 oxidase is studied here using hybrid density functional theory and compared to other cytochrome c oxidases (A and B families), with a high-spin heme a3 and CuB in the active site, and to cytochrome c dependent NO reductase, with a high-spin heme b3 and a non-heme FeB in the active site. It is found that the reaction mechanism and the detailed reaction energetics of the cbb3 oxidases are not similar to those of cytochrome c dependent NO reductase, which has the same type of high-spin heme group but a different non-heme metal. This is in contrast to earlier expectations. Instead, the NO reduction mechanism in cbb3 oxidases is very similar to that in the other cytochrome c oxidases, with the same non-heme metal, CuB, and is independent of the type of high-spin heme group. The conclusion is that the type of non-heme metal (CuB or FeB) in the active site of the heme copper oxidases is more important for the reaction mechanisms than the type of high-spin heme, at least for the NO reduction reaction. The reason is that the proton-coupled reduction potentials of the active site cofactors determine the energetics for the NO reduction reaction, and they depend to a larger extent on the non-heme metal. Observed differences in NO reduction reactivity among the various cytochrome c oxidases may be explained by differences outside the BNC, affecting the rate of proton transfer, rather than in the BNC itself.
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24
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Nilsen-Moe A, Reinhardt CR, Glover SD, Liang L, Hammes-Schiffer S, Hammarström L, Tommos C. Proton-Coupled Electron Transfer from Tyrosine in the Interior of a de novo Protein: Mechanisms and Primary Proton Acceptor. J Am Chem Soc 2020; 142:11550-11559. [PMID: 32479070 PMCID: PMC7315633 DOI: 10.1021/jacs.0c04655] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Proton-coupled
electron transfer (PCET) from tyrosine produces
a neutral tyrosyl radical (Y•) that is vital to
many catalytic redox reactions. To better understand how the protein
environment influences the PCET properties of tyrosine, we have studied
the radical formation behavior of Y32 in the α3Y model protein. The previously solved α3Y solution NMR structure shows that Y32 is sequestered
∼7.7 ± 0.3 Å below the protein surface without any
primary proton acceptors nearby. Here we present transient absorption
kinetic data and molecular dynamics (MD) simulations to resolve the
PCET mechanism associated with Y32 oxidation. Y32• was generated in a bimolecular reaction with
[Ru(bpy)3]3+ formed by flash photolysis. At
pH > 8, the rate constant of Y32• formation
(kPCET) increases by one order of magnitude
per pH unit, corresponding to a proton-first mechanism via tyrosinate
(PTET). At lower pH < 7.5, the pH dependence is weak and shows
a previously measured KIE ≈ 2.5, which best fits a concerted
mechanism. kPCET is independent of phosphate
buffer concentration at pH 6.5. This provides clear evidence that
phosphate buffer is not the primary proton acceptor. MD simulations
show that one to two water molecules can enter the hydrophobic cavity
of α3Y and hydrogen bond to Y32, as well
as the possibility of hydrogen-bonding interactions between Y32 and E13, through structural fluctuations that
reorient surrounding side chains. Our results illustrate how protein
conformational motions can influence the redox reactivity of a tyrosine
residue and how PCET mechanisms can be tuned by changing the pH even
when the PCET occurs within the interior of a protein.
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Affiliation(s)
- Astrid Nilsen-Moe
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, Uppsala 75120, Sweden
| | - Clorice R Reinhardt
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Starla D Glover
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, Uppsala 75120, Sweden
| | - Li Liang
- Departments of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, United States
| | | | - Leif Hammarström
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, Uppsala 75120, Sweden
| | - Cecilia Tommos
- Departments of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, United States.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, United States
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Odella E, Mora SJ, Wadsworth BL, Goings JJ, Gervaldo MA, Sereno LE, Groy TL, Gust D, Moore TA, Moore GF, Hammes-Schiffer S, Moore AL. Proton-coupled electron transfer across benzimidazole bridges in bioinspired proton wires. Chem Sci 2020; 11:3820-3828. [PMID: 34122850 PMCID: PMC8152432 DOI: 10.1039/c9sc06010c] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Designing molecular platforms for controlling proton and electron movement in artificial photosynthetic systems is crucial to efficient catalysis and solar energy conversion. The transfer of both protons and electrons during a reaction is known as proton-coupled electron transfer (PCET) and is used by nature in myriad ways to provide low overpotential pathways for redox reactions and redox leveling, as well as to generate bioenergetic proton currents. Herein, we describe theoretical and electrochemical studies of a series of bioinspired benzimidazole-phenol (BIP) derivatives and a series of dibenzimidazole-phenol (BI2P) analogs with each series bearing the same set of terminal proton-accepting (TPA) groups. The set of TPAs spans more than 6 pKa units. These compounds have been designed to explore the role of the bridging benzimidazole(s) in a one-electron oxidation process coupled to intramolecular proton translocation across either two (the BIP series) or three (the BI2P series) acid/base sites. These molecular constructs feature an electrochemically active phenol connected to the TPA group through a benzimidazole-based bridge, which together with the phenol and TPA group form a covalent framework supporting a Grotthuss-type hydrogen-bonded network. Infrared spectroelectrochemistry demonstrates that upon oxidation of the phenol, protons translocate across this well-defined hydrogen-bonded network to a TPA group. The experimental data show the benzimidazole bridges are non-innocent participants in the PCET process in that the addition of each benzimidazole unit lowers the redox potential of the phenoxyl radical/phenol couple by 60 mV, regardless of the nature of the TPA group. Using a series of hypothetical thermodynamic steps, density functional theory calculations correctly predicted the dependence of the redox potential of the phenoxyl radical/phenol couple on the nature of the final protonated species and provided insight into the thermodynamic role of dibenzimidazole units in the PCET process. This information is crucial for developing molecular “dry proton wires” with these moieties, which can transfer protons via a Grotthuss-type mechanism over long distances without the intervention of water molecules. Experimental and theoretical methods characterize the thermodynamics of electrochemically driven proton-coupled electron transfer processes in bioinspired constructs involving multiple proton translocations over Grotthus-type proton wires.![]()
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Affiliation(s)
- Emmanuel Odella
- School of Molecular Sciences, Arizona State University Tempe Arizona 85287-1604 USA
| | - S Jimena Mora
- School of Molecular Sciences, Arizona State University Tempe Arizona 85287-1604 USA
| | - Brian L Wadsworth
- School of Molecular Sciences, Arizona State University Tempe Arizona 85287-1604 USA
| | - Joshua J Goings
- Department of Chemistry, Yale University New Haven Connecticut 06520-8107 USA
| | - Miguel A Gervaldo
- Departamento de Química, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto Agencia Postal No 3 5800 Río Cuarto Córdoba Argentina
| | - Leonides E Sereno
- Departamento de Química, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto Agencia Postal No 3 5800 Río Cuarto Córdoba Argentina
| | - Thomas L Groy
- School of Molecular Sciences, Arizona State University Tempe Arizona 85287-1604 USA
| | - Devens Gust
- School of Molecular Sciences, Arizona State University Tempe Arizona 85287-1604 USA
| | - Thomas A Moore
- School of Molecular Sciences, Arizona State University Tempe Arizona 85287-1604 USA
| | - Gary F Moore
- School of Molecular Sciences, Arizona State University Tempe Arizona 85287-1604 USA
| | | | - Ana L Moore
- School of Molecular Sciences, Arizona State University Tempe Arizona 85287-1604 USA
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26
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The structure of the oxidized state of cytochrome c oxidase - experiments and theory compared. J Inorg Biochem 2020; 206:111020. [PMID: 32062501 DOI: 10.1016/j.jinorgbio.2020.111020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/31/2020] [Accepted: 02/05/2020] [Indexed: 11/22/2022]
Abstract
Cytochrome c oxidase (CcO), the terminal enzyme in the respiratory chain, reduces molecular oxygen to water. Experimental data on the midpoint potentials of the heme iron/copper active site cofactors do not match the overall reaction energetics, and are also in conflict with the observed efficiency of energy conservation in CcO. Therefore it has been postulated that the ferric/cupric intermediate (the oxidized state) exists in two forms. One form, labelled OH, is presumably involved during catalytic turnover, and should have a high CuB midpoint potential due to a metastable high energy structure. When no more electrons are supplied, the OH state supposedly relaxes to the resting form, labelled O, with a lower energy and a lower midpoint potential. It has been suggested that there is a pure geometrical difference between the OH and O states, obtained by moving a water molecule inside the active site. It is shown here that the difference between the two forms of the oxidized state must be of a more chemical nature. The reason is that all types of geometrically relaxed structures of the oxidized intermediate have similar energies, all with a high proton coupled reduction potential in accordance with the postulated OH state. One hypothesized chemical modification of the OH state is the transfer of an extra proton, possibly internal, into the active site. Such a protonated state has several properties that agree with experimental data on the relaxed oxidized state, including a decreased midpoint potential.
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27
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Patel A, Patel G, Banerjee S. Visible Light-Emitting Diode Light-Driven Cu 0.9Fe 0.1@RCAC-Catalyzed Highly Selective Aerobic Oxidation of Alcohols and Oxidative Azo-Coupling of Anilines: Tandem One Pot Oxidation-Condensation to Imidazoles and Imines. ACS OMEGA 2019; 4:22445-22455. [PMID: 31909327 PMCID: PMC6941188 DOI: 10.1021/acsomega.9b03096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
Here, we have demonstrated visible light-emitting diode light-driven selective and efficient aerobic oxidation of primary/secondary alcohols to aldehydes/ketones and oxidative azo-coupling of anilines using biomass rice husk-derived chemically activated carbon sheet-supported copper-iron bimetallic hybrid nanomaterials (Cu x Fe1-x @RCAC) under oxidant and additive-free conditions. The catalytic activity of the Cu x Fe1-x @RCAC materials has been investigated for the oxidation of alcohols and anilines, and Cu0.9Fe0.1@RCAC was established as the best catalyst. Moreover, a tandem one-pot protocol has been developed for the sequential oxidation of alcohols followed by condensation to functionalized imidazole and imine derivatives in high isolated yields. The hybrid materials were highly robust and stable under the reaction conditions and were recovered simply by filtration and recycled up to 12th run without considerable loss in catalytic activity.
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Mani P, Devadas S, Gurusamy T, Karthik PE, Ratheesh BP, Ramanujam K, Mandal S. Sodalite-type Cu-based Three-dimensional Metal-Organic Framework for Efficient Oxygen Reduction Reaction. Chem Asian J 2019; 14:4814-4818. [PMID: 31697018 DOI: 10.1002/asia.201901242] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/06/2019] [Indexed: 11/10/2022]
Abstract
Inspired by copper-based oxygen reduction biocatalysts, we have studied the electrocatalytic behavior of a Cu-based MOF (Cu-BTT) for oxygen reduction reaction (ORR) in alkaline medium. This catalyst reduces the oxygen at the onset (Eonset ) and half-wave potential (E1/2 ) of 0. 940 V and 0.778 V, respectively. The high halfway potential supports the good activity of Cu-BTT MOF. The high ORR catalytic activity can be interpreted by the presence of nitrogen-rich ligand (tetrazole) and the generation of nascent copper(I) during the reaction. In addition to the excellent activity, Cu-BTT MOF showed exceptional stability too, which was confirmed through chronoamperometry study, where current was unchanged up to 12 h. Further, the 4-electrons transfer of ORR kinetics was confirmed by hydrodynamic voltammetry. The oxygen active center namely copper(I) generation during ORR has been understood by the reduction peak in cyclic voltammetry as well in the XPS analysis.
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Affiliation(s)
- Prabu Mani
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, Kerala, 695551, India
| | - Sharat Devadas
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, Kerala, 695551, India
| | - Tamilselvi Gurusamy
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Pitchiah Esakki Karthik
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, Kerala, 695551, India
| | - Balu P Ratheesh
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, Kerala, 695551, India
| | | | - Sukhendu Mandal
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, Kerala, 695551, India
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29
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Vilhjálmsdóttir J, Albertsson I, Blomberg MRA, Ädelroth P, Brzezinski P. Proton transfer in uncoupled variants of cytochrome c oxidase. FEBS Lett 2019; 594:813-822. [PMID: 31725900 DOI: 10.1002/1873-3468.13679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/31/2019] [Accepted: 11/09/2019] [Indexed: 11/08/2022]
Abstract
Cytochrome c oxidase is a membrane-bound redox-driven proton pump that harbors two proton-transfer pathways, D and K, which are used at different stages of the reaction cycle. Here, we address the question if a D pathway with a modified energy landscape for proton transfer could take over the role of the K pathway when the latter is blocked by a mutation. Our data indicate that structural alterations near the entrance of the D pathway modulate energy barriers that influence proton transfer to the proton-loading site. The data also suggest that during reduction of the catalytic site, its protonation has to occur via the K pathway and that this proton transfer to the catalytic site cannot take place through the D pathway.
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Affiliation(s)
- Jóhanna Vilhjálmsdóttir
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden
| | - Ingrid Albertsson
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden
| | - Margareta R A Blomberg
- Department of Organic Chemistry, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden
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30
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Blomberg MRA. The mechanism for oxygen reduction in the C family cbb 3 cytochrome c oxidases - Implications for the proton pumping stoichiometry. J Inorg Biochem 2019; 203:110866. [PMID: 31706225 DOI: 10.1016/j.jinorgbio.2019.110866] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/12/2019] [Accepted: 09/15/2019] [Indexed: 11/16/2022]
Abstract
Cytochrome c oxidases (CcOs) couple the exergonic reduction of molecular oxygen to proton pumping across the membrane in which they are embedded, thereby conserving a significant part of the free energy. The A family CcOs are known to pump four protons per oxygen molecule, while there is no consensus regarding the proton pumping stoichiometry for the C family cbb3 oxidases. Hybrid density functional theory is used here to investigate the catalytic mechanism for oxygen reduction in cbb3 oxidases. A surprising result is that the barrier for O O bond cleavage at the mixed valence reduction level seems to be too high compared to the overall reaction rate of the enzyme. It is therefore suggested that the O O bond is cleaved only after the first proton coupled reduction step, and that this reduction step most likely is not coupled to proton pumping. Furthermore, since the cbb3 oxidases have only one proton channel leading to the active site, it is proposed that the activated EH intermediate, suggested to be responsible for proton pumping in one of the reduction steps in the A family, cannot be involved in the catalytic cycle for cbb3, which results in the lack of proton pumping also in the E to R reduction step. In summary, the calculations indicate that only two protons are pumped per oxygen molecule in cbb3 oxidases. However, more experimental information on this divergent enzyme is needed, e.g. whether the flow of electrons resembles that in the other more well-studied CcO families.
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Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden.
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31
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Capitanio G, Palese LL, Papa F, Papa S. Allosteric Cooperativity in Proton Energy Conversion in A1-Type Cytochrome c Oxidase. J Mol Biol 2019; 432:534-551. [PMID: 31626808 DOI: 10.1016/j.jmb.2019.09.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/06/2019] [Accepted: 09/24/2019] [Indexed: 12/30/2022]
Abstract
Cytochrome c oxidase (CcO), the CuA, heme a, heme a3, CuB enzyme of respiratory chain, converts the free energy released by aerobic cytochrome c oxidation into a membrane electrochemical proton gradient (ΔμH+). ΔμH+ derives from the membrane anisotropic arrangement of dioxygen reduction to two water molecules and transmembrane proton pumping from a negative (N) space to a positive (P) space separated by the membrane. Spectroscopic, potentiometric, and X-ray crystallographic analyses characterize allosteric cooperativity of dioxygen binding and reduction with protonmotive conformational states of CcO. These studies show that allosteric cooperativity stabilizes the favorable conformational state for conversion of redox energy into a transmembrane ΔμH+.
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Affiliation(s)
- Giuseppe Capitanio
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Luigi Leonardo Palese
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Francesco Papa
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Sergio Papa
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124 Bari, Italy; Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy.
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32
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Geometric and Electronic Structure Contributions to O-O Cleavage and the Resultant Intermediate Generated in Heme-Copper Oxidases. J Am Chem Soc 2019; 141:10068-10081. [PMID: 31146528 DOI: 10.1021/jacs.9b04271] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study investigates the mechanism of O-O bond cleavage in heme-copper oxidase (HCO) enzymes, combining experimental and computational insights from enzyme intermediates and synthetic models. It is determined that HCOs undergo a proton-initiated O-O cleavage mechanism where a single water molecule in the active site enables proton transfer (PT) from the cross-linked tyrosine to a peroxo ligand bridging the heme FeIII and CuII, and multiple H-bonding interactions lower the tyrosine p Ka. Due to sterics within the active site, the proton must either transfer initially to the O(Fe) (a high-energy intermediate), or from another residue over a ∼10 Å distance to reach the O(Cu) atom directly. While the distance between the H+ donor (Tyr) and acceptor (O(Cu)) results in a barrier to PT, this separation is critical for the low barrier to O-O cleavage as it enhances backbonding from Fe into the O22- σ* orbital. Thus, PT from Tyr precedes O-O elongation and is rate-limiting, consistent with available kinetic data. The electron transfers from tyrosinate after the barrier via a superexchange pathway provided by the cross-link, generating intermediate PM. PM is evaluated using available experimental data. The geometric structure contains an FeIV═O that is H-bonded to the CuII-OH. The electronic structure is a singlet, where the FeIV and CuII are antiferromagnetically coupled through the H-bond between the oxo(Fe) and hydroxo(Cu) ligands, while the CuII and Tyr• are ferromagnetically coupled due their delocalization into orthogonal magnetic orbitals on the cross-linked His residue. These findings provide critical insights into the mechanism of efficient O2 reduction in HCOs, and the nature of the PM intermediate that couples this reaction to proton pumping.
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33
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Schaefer AW, Ehudin MA, Quist DA, Tang JA, Karlin KD, Solomon EI. Spin Interconversion of Heme-Peroxo-Copper Complexes Facilitated by Intramolecular Hydrogen-Bonding Interactions. J Am Chem Soc 2019; 141:4936-4951. [PMID: 30836005 PMCID: PMC6457345 DOI: 10.1021/jacs.9b00118] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Synthetic peroxo-bridged high-spin (HS) heme-(μ-η2:η1-O22-)-Cu(L) complexes incorporating (as part of the copper ligand) intramolecular hydrogen-bond (H-bond) capabilities and/or steric effects are herein demonstrated to affect the complex's electronic and geometric structure, notably impacting the spin state. An H-bonding interaction with the peroxo core favors a low-spin (LS) heme-(μ-η1:η1-O22-)-Cu(L) structure, resulting in a reversible temperature-dependent interconversion of spin state (5 coordinate HS to 6 coordinate LS). The LS state dominates at low temperatures, even in the absence of a strong trans-axial heme ligand. Lewis base addition inhibits the H-bond facilitated spin interconversion by competition for the H-bond donor, illustrating the precise H-bonding interaction required to induce spin-crossover (SCO). Resonance Raman spectroscopy (rR) shows that the H-bonding pendant interacts with the bridging peroxide ligand to stabilize the LS but not the HS state. The H-bond (to the Cu-bound O atom) acts to weaken the O-O bond and strengthen the Fe-O bond, exhibiting ν(M-O) and ν(O-O) values comparable to analogous known LS complexes with a strong donating trans-axial ligand, 1,5-dicyclohexylimidazole, (DCHIm)heme-(μ-η1:η1-O22-)-Cu(L). Variable-temperature (-90 to -130 °C) UV-vis and 2H NMR spectroscopies confirm the SCO process and implicate the involvement of solvent binding. Examining a case of solvent binding without SCO, thermodynamic parameters were obtained from a van't Hoff analysis, accounting for its contribution in SCO. Taken together, these data provide evidence for the H-bond group facilitating a core geometry change and allowing solvent to bind, stabilizing a LS state. The rR data, complemented by DFT analysis, reveal a stronger H-bonding interaction with the peroxo core in the LS compared to the HS complexes, which enthalpically favors the LS state. These insights enhance our fundamental understanding of secondary coordination sphere influences in metalloenzymes.
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Affiliation(s)
- Andrew W. Schaefer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Melanie A. Ehudin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David A. Quist
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joel A. Tang
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D. Karlin
- Department of Chemistry, 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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34
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Blomberg MRA. Active Site Midpoint Potentials in Different Cytochrome c Oxidase Families: A Computational Comparison. Biochemistry 2019; 58:2028-2038. [PMID: 30892888 DOI: 10.1021/acs.biochem.9b00093] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome c oxidase (C cO) is the terminal enzyme in the respiratory electron transport chain, reducing molecular oxygen to water. The binuclear active site in C cO comprises a high-spin heme associated with a CuB complex and a redox active tyrosine. The electron transport in the respiratory chain is driven by increasing midpoint potentials of the involved cofactors, resulting in a release of free energy, which is stored by coupling the electron transfer to proton translocation across a membrane, building up an electrochemical gradient. In this context, the midpoint potentials of the active site cofactors in the C cOs are of special interest, since they determine the driving forces for the individual oxygen reduction steps and thereby affect the efficiency of the proton pumping. It has been difficult to obtain useful information on some of these midpoint potentials from experiments. However, since each of the reduction steps in the catalytic cycle of oxygen reduction to water corresponds to the formation of an O-H bond, they can be calculated with a reasonably high accuracy using quantum chemical methods. From the calculated O-H bond strengths, the proton-coupled midpoint potentials of the active site cofactors can be estimated. Using models representing the different families of C cO's (A, B, and C), the calculations give midpoint potentials that should be relevant during catalytic turnover. The calculations also suggest possible explanations for why some experimentally measured potentials deviate significantly from the calculated ones, i.e., for CuB in all oxidase families, and for heme b3 in the C family.
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Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory , Stockholm University , Stockholm SE-106 91 , Sweden
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35
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Ehudin MA, Schaefer AW, Adam SM, Quist DA, Diaz DE, Tang JA, Solomon EI, Karlin KD. Influence of intramolecular secondary sphere hydrogen-bonding interactions on cytochrome c oxidase inspired low-spin heme-peroxo-copper complexes. Chem Sci 2019; 10:2893-2905. [PMID: 30996867 PMCID: PMC6431958 DOI: 10.1039/c8sc05165h] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/03/2019] [Indexed: 11/21/2022] Open
Abstract
Dioxygen reduction by heme-copper oxidases is a critical biochemical process, wherein hydrogen bonding is hypothesized to participate in the critical step involving the active-site reductive cleavage of the O-O bond. Sixteen novel synthetic heme-(μ-O2 2-)-Cu(XTMPA) complexes, whose design is inspired by the cytochrome c oxidase active site structure, were generated in an attempt to form the first intramolecular H-bonded complexes. Derivatives of the "parent" ligand (XTMPA, TMPA = (tris((2-pyridyl)methyl)amine)) possessing one or two amine pendants preferentially form an H-bond with the copper-bound O-atom of the peroxide bridge. This is evidenced by a characteristic blue shift in the ligand-to-metal charge transfer (LMCT) bands observed in UV-vis spectroscopy (consistent with lowering of the peroxo π* relative to the iron orbitals) and a weakening of the O-O bond determined by resonance Raman spectroscopy (rR), with support from Density Functional Theory (DFT) calculations. Remarkably, with the TMPA-based infrastructure (versus similar heme-peroxo-copper complexes with different copper ligands), the typically undetected Cu-O stretch for these complexes was observed via rR, affording critical insights into the nature of the O-O peroxo core for the complexes studied. While amido functionalities have been shown to have greater H-bonding capabilities than their amino counterparts, in these heme-peroxo-copper complexes amido substituents distort the local geometry such that H-bonding with the peroxo core only imparts a weak electronic effect; optimal H-bonding interactions are observed by employing two amino groups on the copper ligand. The amino-substituted systems presented in this work reveal a key orientational anisotropy in H-bonding to the peroxo core for activating the O-O bond, offering critical insights into effective O-O cleavage chemistry. These findings indirectly support computational and protein structural studies suggesting the presence of an interstitial H-bonding water molecule in the CcO active site, which is critical for the desired reactivity. The results are evaluated with appropriate controls and discussed with respect to potential O2-reduction capabilities.
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Affiliation(s)
- Melanie A Ehudin
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , USA .
| | - Andrew W Schaefer
- Department of Chemistry , Stanford University , Stanford , California 94305 , USA .
| | - Suzanne M Adam
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , USA .
| | - David A Quist
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , USA .
| | - Daniel E Diaz
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , USA .
| | - Joel A Tang
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , USA .
| | - Edward I Solomon
- Department of Chemistry , Stanford University , Stanford , California 94305 , USA .
| | - Kenneth D Karlin
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , USA .
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36
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Abstract
Photosystem II (PSII) uses water as the terminal electron donor, producing oxygen in the Mn4CaO5 oxygen evolving complex (OEC), while cytochrome c oxidase (CcO) reduces O2 to water in its heme–Cu binuclear center (BNC). Each protein is oriented in the membrane to add to the proton gradient. The OEC, which releases protons, is located near the P-side (positive, at low-pH) of the membrane. In contrast, the BNC is in the middle of CcO, so the protons needed for O2 reduction must be transferred from the N-side (negative, at high pH). In addition, CcO pumps protons from N- to P-side, coupled to the O2 reduction chemistry, to store additional energy. Thus, proton transfers are directly coupled to the OEC and BNC redox chemistry, as well as needed for CcO proton pumping. The simulations that study the changes in proton affinity of the redox active sites and the surrounding protein at different states of the reaction cycle, as well as the changes in hydration that modulate proton transfer paths, are described.
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37
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Thammavongsy Z, Mercer IP, Yang JY. Promoting proton coupled electron transfer in redox catalysts through molecular design. Chem Commun (Camb) 2019; 55:10342-10358. [DOI: 10.1039/c9cc05139b] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mini-review on using the secondary coordination sphere to facilitate multi-electron, multi-proton catalysis.
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Affiliation(s)
| | - Ian P. Mercer
- Department of Chemistry
- University of California
- Irvine
- USA
| | - Jenny Y. Yang
- Department of Chemistry
- University of California
- Irvine
- USA
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38
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Siegbahn PEM, Blomberg MRA. A Systematic DFT Approach for Studying Mechanisms of Redox Active Enzymes. Front Chem 2018; 6:644. [PMID: 30627530 PMCID: PMC6309562 DOI: 10.3389/fchem.2018.00644] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 12/11/2018] [Indexed: 02/03/2023] Open
Abstract
When DFT has been applied to study mechanisms of redox processes a common procedure has been to study the results for many different functionals. For redox reactions involving the first row transition metals, this approach has given very different results for different functionals. The conclusion has been that DFT cannot be used for these reactions. In the meantime, results with strong predictability have been generated, most noteworthy for photosystem II, where all DFT predictions have been verified by experiments performed later. In order to obtain these predictive results using DFT, an alternative, systematic approach has been used, where the key differences between the results for different functionals can be rationalized by using a single parameter, rather than using the very large number of differences in the functionals.
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Affiliation(s)
- Per E M Siegbahn
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm, Sweden
| | - Margareta R A Blomberg
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm, Sweden
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Adam SM, Wijeratne GB, Rogler PJ, Diaz DE, Quist DA, Liu JJ, Karlin KD. Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function. Chem Rev 2018; 118:10840-11022. [PMID: 30372042 PMCID: PMC6360144 DOI: 10.1021/acs.chemrev.8b00074] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.
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Affiliation(s)
- Suzanne M. Adam
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gayan B. Wijeratne
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Patrick J. Rogler
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Daniel E. Diaz
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David A. Quist
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jeffrey J. Liu
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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40
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Odella E, Mora SJ, Wadsworth BL, Huynh MT, Goings JJ, Liddell PA, Groy TL, Gervaldo M, Sereno LE, Gust D, Moore TA, Moore GF, Hammes-Schiffer S, Moore AL. Controlling Proton-Coupled Electron Transfer in Bioinspired Artificial Photosynthetic Relays. J Am Chem Soc 2018; 140:15450-15460. [DOI: 10.1021/jacs.8b09724] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emmanuel Odella
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - S. Jimena Mora
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Brian L. Wadsworth
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Mioy T. Huynh
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Joshua J. Goings
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Paul A. Liddell
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Thomas L. Groy
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Miguel Gervaldo
- Departamento de Química, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Agencia Postal No. 3, 5800 Río Cuarto, Córdoba, Argentina
| | - Leónides E. Sereno
- Departamento de Química, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Agencia Postal No. 3, 5800 Río Cuarto, Córdoba, Argentina
| | - Devens Gust
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Thomas A. Moore
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Gary F. Moore
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Ana L. Moore
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
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41
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Blomberg MRA, Ädelroth P. Mechanisms for enzymatic reduction of nitric oxide to nitrous oxide - A comparison between nitric oxide reductase and cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:1223-1234. [PMID: 30248312 DOI: 10.1016/j.bbabio.2018.09.368] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/23/2018] [Accepted: 09/17/2018] [Indexed: 12/22/2022]
Abstract
Cytochrome c oxidases (CcO) reduce O2 to H2O in the respiratory chain of mitochondria and many aerobic bacteria. In addition, some species of CcO can also reduce NO to N2O and water while others cannot. Here, the mechanism for NO-reduction in CcO is investigated using quantum mechanical calculations. Comparison is made to the corresponding reaction in a "true" cytochrome c-dependent NO reductase (cNOR). The calculations show that in cNOR, where the reduction potentials are low, the toxic NO molecules are rapidly reduced, while the higher reduction potentials in CcO lead to a slower or even impossible reaction, consistent with experimental observations. In both enzymes the reaction is initiated by addition of two NO molecules to the reduced active site, forming a hyponitrite intermediate. In cNOR, N2O can then be formed using only the active-site electrons. In contrast, in CcO, one proton-coupled reduction step most likely has to occur before N2O can be formed, and furthermore, proton transfer is most likely rate-limiting. This can explain why different CcO species with the same heme a3-Cu active site differ with respect to NO reduction efficiency, since they have a varying number and/or properties of proton channels. Finally, the calculations also indicate that a conserved active site valine plays a role in reducing the rate of NO reduction in CcO.
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Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden.
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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42
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Wikström M, Sharma V. Proton pumping by cytochrome c oxidase – A 40 year anniversary. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:692-698. [DOI: 10.1016/j.bbabio.2018.03.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 03/14/2018] [Indexed: 12/21/2022]
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43
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Control of transmembrane charge transfer in cytochrome c oxidase by the membrane potential. Nat Commun 2018; 9:3187. [PMID: 30093670 PMCID: PMC6085328 DOI: 10.1038/s41467-018-05615-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 07/09/2018] [Indexed: 11/08/2022] Open
Abstract
The respiratory chain in mitochondria is composed of membrane-bound proteins that couple electron transfer to proton translocation across the inner membrane. These charge-transfer reactions are regulated by the proton electrochemical gradient that is generated and maintained by the transmembrane charge transfer. Here, we investigate this feedback mechanism in cytochrome c oxidase in intact inner mitochondrial membranes upon generation of an electrochemical potential by hydrolysis of ATP. The data indicate that a reaction step that involves proton uptake to the catalytic site and presumably proton translocation is impaired by the potential, but electron transfer is not affected. These results define the order of electron and proton-transfer reactions and suggest that the proton pump is regulated by the transmembrane electrochemical gradient through control of internal proton transfer rather than by control of electron transfer.
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44
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Farahvash A, Stuchebrukhov A. Investigating the Many Roles of Internal Water in Cytochrome c Oxidase. J Phys Chem B 2018; 122:7625-7635. [PMID: 30011995 DOI: 10.1021/acs.jpcb.7b11920] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cytochrome c oxidase (C cO) is the terminal enzyme in the respiratory electron transport chain. As part of its catalytic cycle, C cO transfers protons to its Fe-Cu binuclear center (BNC) to reduce oxygen, and in addition, it pumps protons across the mitochondrial inner, or bacterial, membrane where it is located. It is believed that this proton transport is facilitated by a network of water chains inside the enzyme. Here we present an analysis of the hydration of C cO, including the BNC region, using a semi-empirical hydration program, Dowser++, recently developed in our group. Using high-resolution X-ray data, we show that Dowser++ predictions match very accurately the water molecules seen in the D- and K-channels of C cO, as well as in the vicinity of its BNC. Moreover, Dowser++ predicts many more internal water molecules than is typically seen in the experiment. However, no significant hydration of the catalytic cavity in C cO described recently in the literature is observed. As Dowser++ itself does not account for structural changes of the protein, this result supports the earlier assessment that the proposed wetting transition in the catalytic cavity can only either be due to structural rearrangements of BNC, possibly induced by the charges during the catalytic cycle, or occur transiently, in concert with the proton transfer. Molecular dynamics simulations were performed to investigate the global dynamic nature of Dowser++ waters in C cO, and the results suggest a consistent explanation as to why some predicted water molecules would be missing in the experimental structures. Furthermore, in light of the significant protein hydration predicted by Dowser++, the dielectric constant of the hydrated cavities in C cO was also investigated using the Fröhlich-Kirkwood model; the results indicate that in the cavities where water is packed sufficiently densely the dielectric constant can approach values comparable even to that of bulk water.
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Affiliation(s)
- Ardavan Farahvash
- Department of Chemistry , University of California-Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Alexei Stuchebrukhov
- Department of Chemistry , University of California-Davis , One Shields Avenue , Davis , California 95616 , United States
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45
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Supekar S, Kaila VRI. Dewetting transitions coupled to K-channel activation in cytochrome c oxidase. Chem Sci 2018; 9:6703-6710. [PMID: 30310604 PMCID: PMC6115622 DOI: 10.1039/c8sc01587b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/08/2018] [Indexed: 12/20/2022] Open
Abstract
Cytochrome c oxidase (CcO) drives aerobic respiratory chains in all organisms by transducing the free energy from oxygen reduction into an electrochemical proton gradient across a biological membrane.
Cytochrome c oxidase (CcO) drives aerobic respiratory chains in all organisms by transducing the free energy from oxygen reduction into an electrochemical proton gradient across a biological membrane. CcO employs the so-called D- and K-channels for proton uptake, but the molecular mechanism for activation of the K-channel has remained elusive for decades. We show here by combining large-scale atomistic molecular simulations with graph-theoretical water network analysis, and hybrid quantum/classical (QM/MM) free energy calculations, that the K-channel is activated by formation of a reactive oxidized intermediate in the binuclear heme a3/CuB active site. This state induces electrostatic, hydration, and conformational changes that lower the barrier for proton transfer along the K-channel by dewetting pathways that connect the D-channel with the active site. Our combined results reconcile previous experimental findings and indicate that water dynamics plays a decisive role in the proton pumping machinery in CcO.
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Affiliation(s)
- Shreyas Supekar
- Department Chemie , Technische Universität München , Lichtenbergstraße 4 , D-85748 Garching , Germany .
| | - Ville R I Kaila
- Department Chemie , Technische Universität München , Lichtenbergstraße 4 , D-85748 Garching , Germany .
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46
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47
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Lee W, Kasanmascheff M, Huynh M, Quartararo A, Costentin C, Bejenke I, Nocera DG, Bennati M, Tommos C, Stubbe J. Properties of Site-Specifically Incorporated 3-Aminotyrosine in Proteins To Study Redox-Active Tyrosines: Escherichia coli Ribonucleotide Reductase as a Paradigm. Biochemistry 2018; 57:3402-3415. [PMID: 29630358 DOI: 10.1021/acs.biochem.8b00160] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
3-Aminotyrosine (NH2Y) has been a useful probe to study the role of redox active tyrosines in enzymes. This report describes properties of NH2Y of key importance for its application in mechanistic studies. By combining the tRNA/NH2Y-RS suppression technology with a model protein tailored for amino acid redox studies (α3X, X = NH2Y), the formal reduction potential of NH2Y32(O•/OH) ( E°' = 395 ± 7 mV at pH 7.08 ± 0.05) could be determined using protein film voltammetry. We find that the Δ E°' between NH2Y32(O•/OH) and Y32(O•/OH) when measured under reversible conditions is ∼300-400 mV larger than earlier estimates based on irreversible voltammograms obtained on aqueous NH2Y and Y. We have also generated D6-NH2Y731-α2 of ribonucleotide reductase (RNR), which when incubated with β2/CDP/ATP generates the D6-NH2Y731•-α2/β2 complex. By multifrequency electron paramagnetic resonance (35, 94, and 263 GHz) and 34 GHz 1H ENDOR spectroscopies, we determined the hyperfine coupling (hfc) constants of the amino protons that establish RNH2• planarity and thus minimal perturbation of the reduction potential by the protein environment. The amount of Y in the isolated NH2Y-RNR incorporated by infidelity of the tRNA/NH2Y-RS pair was determined by a generally useful LC-MS method. This information is essential to the utility of this NH2Y probe to study any protein of interest and is employed to address our previously reported activity associated with NH2Y-substituted RNRs.
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Affiliation(s)
| | - Müge Kasanmascheff
- Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 Germany
| | - Michael Huynh
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 United States
| | | | - Cyrille Costentin
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 United States.,Laboratoire d'Electrochimie Moléculaire, Unité Mixte de Recherche Université - CNRS No 7591 , Université Paris Diderot, Sorbonne Paris Cité , Bâtiment Lavoisier, 15 rue Jean de Baïf , 75205 Paris Cedex 13 , France
| | - Isabel Bejenke
- Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 Germany
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 United States
| | - Marina Bennati
- Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 Germany
| | - Cecilia Tommos
- Department of Biochemistry and Biophysics , University of Pennsylvania Perelman School of Medicine , Philadelphia , Pennsylvania 19104 , United States
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48
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Wikström M, Krab K, Sharma V. Oxygen Activation and Energy Conservation by Cytochrome c Oxidase. Chem Rev 2018; 118:2469-2490. [PMID: 29350917 PMCID: PMC6203177 DOI: 10.1021/acs.chemrev.7b00664] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
This review focuses on the type
A cytochrome c oxidases (CcO), which
are found in all mitochondria
and also in several aerobic bacteria. CcO catalyzes
the respiratory reduction of dioxygen (O2) to water by
an intriguing mechanism, the details of which are fairly well understood
today as a result of research for over four decades. Perhaps even
more intriguingly, the membrane-bound CcO couples
the O2 reduction chemistry to translocation of protons
across the membrane, thus contributing to generation of the electrochemical
proton gradient that is used to drive the synthesis of ATP as catalyzed
by the rotary ATP synthase in the same membrane. After reviewing the
structure of the core subunits of CcO, the active
site, and the transfer paths of electrons, protons, oxygen, and water,
we describe the states of the catalytic cycle and point out the few
remaining uncertainties. Finally, we discuss the mechanism of proton
translocation and the controversies in that area that still prevail.
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Affiliation(s)
- Mårten Wikström
- Institute of Biotechnology , University of Helsinki , P.O. Box 56 , Helsinki FI-00014 , Finland
| | - Klaas Krab
- Department of Molecular Cell Physiology , Vrije Universiteit , P.O. Box 7161 , Amsterdam 1007 MC , The Netherlands
| | - Vivek Sharma
- Institute of Biotechnology , University of Helsinki , P.O. Box 56 , Helsinki FI-00014 , Finland.,Department of Physics , University of Helsinki , P.O. Box 64 , Helsinki FI-00014 , Finland
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49
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Fukuzumi S, Lee YM, Nam W. Mechanisms of Two-Electron versus Four-Electron Reduction of Dioxygen Catalyzed by Earth-Abundant Metal Complexes. ChemCatChem 2017. [DOI: 10.1002/cctc.201701064] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Shunichi Fukuzumi
- Department of Chemistry and Nano Science; Ewha Womans University; Seoul 03760 Korea
- Faculty of Science and Engineering; Meijo University; SENTAN, Japan, Science and Technology Agency, JST; Nagoya Aichi 468-8502 Japan
| | - Yong-Min Lee
- Department of Chemistry and Nano Science; Ewha Womans University; Seoul 03760 Korea
| | - Wonwoo Nam
- Department of Chemistry and Nano Science; Ewha Womans University; Seoul 03760 Korea
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50
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Hromada SE, Hilbrands AM, Wolf EM, Ross JL, Hegg TR, Roth AG, Hollowell MT, Anderson CE, Benson DE. Protein oxidation involved in Cys-Tyr post-translational modification. J Inorg Biochem 2017; 176:168-174. [PMID: 28917639 DOI: 10.1016/j.jinorgbio.2017.08.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 08/15/2017] [Accepted: 08/30/2017] [Indexed: 11/19/2022]
Abstract
Some post-translationally modified tyrosines can perform reversible redox chemistry similar to metal cofactors. The most studied of these tyrosine modifications is the intramolecular thioether-crosslinked 3'-(S-cysteinyl)-tyrosine (Cys-Tyr) in galactose oxidase. This Cu-mediated tyrosine modification in galactose oxidase involves direct electron transfer (inner-sphere) to the coordinated tyrosine. Mammalian cysteine dioxygenase enzymes also contain a Cys-Tyr that is formed, presumably, through outer-sphere electron transfer from a non-heme iron center ~6Å away from the parent residues. An orphan protein (BF4112), amenable to UV spectroscopic characterization, has also been shown to form Cys-Tyr between Tyr 52 and Cys 98 by an adjacent Cu2+ ion-loaded, mononuclear metal ion binding site. Native Cys-Tyr fluorescence under denaturing conditions provides a more robust methodology for Cys-Tyr yield determination. Cys-Tyr specificity, relative to 3,3'-dityrosine, was provided in this fluorescence assay by guanidinium chloride. Replacing Tyr 52 with Phe or the Cu2+ ion with a Zn2+ ion abolished Cys-Tyr formation. The Cys-Tyr fluorescence-based yields were decreased but not completely removed by surface Tyr mutations to Phe (Y4F/Y109F, 50%) and Cys 98 to Ser (25%). The small absorbance and fluorescence emission intensities for C98S BF4112 were surprising until a significantly red-shifted emission was observed. The red-shifted emission spectrum and monomer to dimer shift seen by reducing, denaturing SDS-PAGE demonstrate a surface tyrosyl radical product (dityrosine) when Cys 98 is replaced with Ser. These results demonstrate surface tyrosine oxidation in BF4112 during Cys-Tyr formation and that protein oxidation can be a significant side reaction in forming protein derived cofactors.
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Affiliation(s)
- Susan E Hromada
- Department of Chemistry & Biochemistry, Calvin College, Grand Rapids, MI 49546, United States
| | - Adam M Hilbrands
- Department of Chemistry & Biochemistry, Calvin College, Grand Rapids, MI 49546, United States
| | - Elysa M Wolf
- Department of Chemistry & Biochemistry, Calvin College, Grand Rapids, MI 49546, United States
| | - Jackson L Ross
- Department of Chemistry & Biochemistry, Calvin College, Grand Rapids, MI 49546, United States
| | - Taylor R Hegg
- Department of Chemistry & Biochemistry, Calvin College, Grand Rapids, MI 49546, United States
| | - Andrew G Roth
- Department of Chemistry & Biochemistry, Calvin College, Grand Rapids, MI 49546, United States
| | - Matthew T Hollowell
- Department of Chemistry & Biochemistry, Calvin College, Grand Rapids, MI 49546, United States
| | - Carolyn E Anderson
- Department of Chemistry & Biochemistry, Calvin College, Grand Rapids, MI 49546, United States
| | - David E Benson
- Department of Chemistry & Biochemistry, Calvin College, Grand Rapids, MI 49546, United States.
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