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Pintscher S, Pietras R, Mielecki B, Szwalec M, Wójcik-Augustyn A, Indyka P, Rawski M, Koziej Ł, Jaciuk M, Ważny G, Glatt S, Osyczka A. Molecular basis of plastoquinone reduction in plant cytochrome b 6f. NATURE PLANTS 2024:10.1038/s41477-024-01804-x. [PMID: 39362993 DOI: 10.1038/s41477-024-01804-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 09/03/2024] [Indexed: 10/05/2024]
Abstract
A multi-subunit enzyme, cytochrome b6f (cytb6f), provides the crucial link between photosystems I and II in the photosynthetic membranes of higher plants, transferring electrons between plastoquinone (PQ) and plastocyanin. The atomic structure of cytb6f is known, but its detailed catalytic mechanism remains elusive. Here we present cryogenic electron microscopy structures of spinach cytb6f at 1.9 Å and 2.2 Å resolution, revealing an unexpected orientation of the substrate PQ in the haem ligand niche that forms the PQ reduction site (Qn). PQ, unlike Qn inhibitors, is not in direct contact with the haem. Instead, a water molecule is coordinated by one of the carbonyl groups of PQ and can act as the immediate proton donor for PQ. In addition, we identify water channels that connect Qn with the aqueous exterior of the enzyme, suggesting that the binding of PQ in Qn displaces water through these channels. The structures confirm large movements of the head domain of the iron-sulfur protein (ISP-HD) towards and away from the plastoquinol oxidation site (Qp) and define the unique position of ISP-HD when a Qp inhibitor (2,5-dibromo-3-methyl-6-isopropylbenzoquinone) is bound. This work identifies key conformational states of cytb6f, highlights fundamental differences between substrates and inhibitors and proposes a quinone-water exchange mechanism.
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Affiliation(s)
- Sebastian Pintscher
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Plant Biotechnology, Jagiellonian University, Kraków, Poland
| | - Rafał Pietras
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Molecular Biophysics, Jagiellonian University, Kraków, Poland
| | - Bohun Mielecki
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Molecular Biophysics, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Mateusz Szwalec
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Molecular Biophysics, Jagiellonian University, Kraków, Poland
| | - Anna Wójcik-Augustyn
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Molecular Biophysics, Jagiellonian University, Kraków, Poland
| | - Paulina Indyka
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Kraków, Poland
| | - Michał Rawski
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Kraków, Poland
| | - Łukasz Koziej
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland
| | - Marcin Jaciuk
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Kraków, Poland
| | - Grzegorz Ważny
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Kraków, Poland
| | - Sebastian Glatt
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland.
- Department for Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria.
| | - Artur Osyczka
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Molecular Biophysics, Jagiellonian University, Kraków, Poland.
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Matyja K. Sublethal effects of binary mixtures of Cu 2+ and Cd 2+ on Daphnia magna: Standard Dynamic Energy Budget (DEB) model analysis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 334:122142. [PMID: 37414122 DOI: 10.1016/j.envpol.2023.122142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
Dynamic Energy Budget theory (DEB) describes mass and energy fluxes that occur in living organisms. DEB models were successfully used to assess the influence of stress, including toxic substances, and changes in pH and temperature, on different organisms. In this study, the Standard DEB model was used to evaluate the toxicity of copper and cadmium ions and their binary mixtures on Daphnia magna. Both metal ions have a significant influence on daphnia growth and reproduction. Different physiological modes of action (pMoA) were applied to primary DEB model parameters. Model predictions for chosen modes of interaction of mixture components were evaluated. The goodness of model fit and the model prediction was assessed to indicate the most likely pMoA and interaction mode. Copper and cadmium influence more than one DEB model primary parameter. Different pMoAs can result in similar model fits, and therefore it is difficult to identify pMoA only by evaluation of the goodness of fit of the model to the growth and reproduction data. Some critical discussion and ideas for model development are therefore provided.
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Affiliation(s)
- Konrad Matyja
- Wroclaw University of Science and Technology, Faculty of Chemistry, Department of Micro, Nano, and Bioprocess Engineering, Ul. Norwida 4/6, 50-373, Wrocław, Poland.
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Roberts AG, Stevens JC, Szklarz GD, Scott EE, Kumar S, Shah MB, Halpert JR. Four Decades of Cytochrome P450 2B Research: From Protein Adducts to Protein Structures and Beyond. Drug Metab Dispos 2023; 51:111-122. [PMID: 36310033 PMCID: PMC11022898 DOI: 10.1124/dmd.122.001109] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 01/03/2023] Open
Abstract
This article features selected findings from the senior author and colleagues dating back to 1978 and covering approximately three-fourths of the 60 years since the discovery of cytochrome P450. Considering the vast number of P450 enzymes in this amazing superfamily and their importance for so many fields of science and medicine, including drug design and development, drug therapy, environmental health, and biotechnology, a comprehensive review of even a single topic is daunting. To make a meaningful contribution to the 50th anniversary of Drug Metabolism and Disposition, we trace the development of the research in a single P450 laboratory through the eyes of seven individuals with different backgrounds, perspectives, and subsequent career trajectories. All co-authors are united in their fascination for the structural basis of mammalian P450 substrate and inhibitor selectivity and using such information to improve drug design and therapy. An underlying theme is how technological advances enable scientific discoveries that were impossible and even inconceivable to prior generations. The work performed spans the continuum from: 1) purification of P450 enzymes from animal tissues to purification of expressed human P450 enzymes and their site-directed mutants from bacteria; 2) inhibition, metabolism, and spectral studies to isothermal titration calorimetry, deuterium exchange mass spectrometry, and NMR; 3) homology models based on bacterial P450 X-ray crystal structures to rabbit and human P450 structures in complex with a wide variety of ligands. Our hope is that humanizing the scientific endeavor will encourage new generations of scientists to make fundamental new discoveries in the P450 field. SIGNIFICANCE STATEMENT: The manuscript summarizes four decades of work from Dr. James Halpert's laboratory, whose investigations have shaped the cytochrome P450 field, and provides insightful perspectives of the co-authors. This work will also inspire future drug metabolism scientists to make critical new discoveries in the cytochrome P450 field.
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Affiliation(s)
- Arthur G Roberts
- Pharmaceutical and Biomedical Sciences Department, University of Georgia, 240 W. Green St., Athens, Georgia (A.G.R.); Unaffiliated (J.C.S.); Department of Pharmaceutical Sciences, West Virginia University, Morgantown, West Virginia (G.D.S.); Departments of Medicinal Chemistry, Pharmacology, and Biological Chemistry and the Program in Biophysics, University of Michigan, Ann Arbor, Michigan (E.E.S.); Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee (S.K.); Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York (M.B.S.); Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona (J.R.H.).
| | - Jeffrey C Stevens
- Pharmaceutical and Biomedical Sciences Department, University of Georgia, 240 W. Green St., Athens, Georgia (A.G.R.); Unaffiliated (J.C.S.); Department of Pharmaceutical Sciences, West Virginia University, Morgantown, West Virginia (G.D.S.); Departments of Medicinal Chemistry, Pharmacology, and Biological Chemistry and the Program in Biophysics, University of Michigan, Ann Arbor, Michigan (E.E.S.); Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee (S.K.); Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York (M.B.S.); Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona (J.R.H.)
| | - Grazyna D Szklarz
- Pharmaceutical and Biomedical Sciences Department, University of Georgia, 240 W. Green St., Athens, Georgia (A.G.R.); Unaffiliated (J.C.S.); Department of Pharmaceutical Sciences, West Virginia University, Morgantown, West Virginia (G.D.S.); Departments of Medicinal Chemistry, Pharmacology, and Biological Chemistry and the Program in Biophysics, University of Michigan, Ann Arbor, Michigan (E.E.S.); Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee (S.K.); Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York (M.B.S.); Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona (J.R.H.)
| | - Emily E Scott
- Pharmaceutical and Biomedical Sciences Department, University of Georgia, 240 W. Green St., Athens, Georgia (A.G.R.); Unaffiliated (J.C.S.); Department of Pharmaceutical Sciences, West Virginia University, Morgantown, West Virginia (G.D.S.); Departments of Medicinal Chemistry, Pharmacology, and Biological Chemistry and the Program in Biophysics, University of Michigan, Ann Arbor, Michigan (E.E.S.); Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee (S.K.); Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York (M.B.S.); Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona (J.R.H.)
| | - Santosh Kumar
- Pharmaceutical and Biomedical Sciences Department, University of Georgia, 240 W. Green St., Athens, Georgia (A.G.R.); Unaffiliated (J.C.S.); Department of Pharmaceutical Sciences, West Virginia University, Morgantown, West Virginia (G.D.S.); Departments of Medicinal Chemistry, Pharmacology, and Biological Chemistry and the Program in Biophysics, University of Michigan, Ann Arbor, Michigan (E.E.S.); Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee (S.K.); Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York (M.B.S.); Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona (J.R.H.)
| | - Manish B Shah
- Pharmaceutical and Biomedical Sciences Department, University of Georgia, 240 W. Green St., Athens, Georgia (A.G.R.); Unaffiliated (J.C.S.); Department of Pharmaceutical Sciences, West Virginia University, Morgantown, West Virginia (G.D.S.); Departments of Medicinal Chemistry, Pharmacology, and Biological Chemistry and the Program in Biophysics, University of Michigan, Ann Arbor, Michigan (E.E.S.); Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee (S.K.); Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York (M.B.S.); Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona (J.R.H.)
| | - James R Halpert
- Pharmaceutical and Biomedical Sciences Department, University of Georgia, 240 W. Green St., Athens, Georgia (A.G.R.); Unaffiliated (J.C.S.); Department of Pharmaceutical Sciences, West Virginia University, Morgantown, West Virginia (G.D.S.); Departments of Medicinal Chemistry, Pharmacology, and Biological Chemistry and the Program in Biophysics, University of Michigan, Ann Arbor, Michigan (E.E.S.); Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee (S.K.); Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York (M.B.S.); Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona (J.R.H.)
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Matyja K, Wasiela A, Dobicki W, Pokorny P, Trusek A. Dynamic modeling of the activated sludge microbial growth and activity under exposure to heavy metals. BIORESOURCE TECHNOLOGY 2021; 339:125623. [PMID: 34315088 DOI: 10.1016/j.biortech.2021.125623] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
The presence of heavy metals in the environment can lead to ecological and health problems. The evolution of biological systems, such as activated sludge, exposed to heavy metals is still underexplored. Therefore, this study sought to develop a model of microorganism activity and growth in activated sludge and used it to investigate the toxicity of five metals: Cu, Cd, Ni, Zn, and Ag. Patterns in the evolution of the toxic effects caused by these metals were similar at the beginning of exposure. Differences in toxicity between metal ions were noted for longer exposure times. Changes in model parameters indicate the influence of metal ions on the mass and energy balance of living cells. Decreases in new enzyme units and biomass production yields in contaminated activated sludge indicate a shift from anabolic reactions to metal homeostasis and resistance.
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Affiliation(s)
- Konrad Matyja
- Wroclaw University of Science and Technology, Faculty of Chemistry, Department of Micro, Nano, and Bioprocess Engineering, Norwida 4/6, 50-373 Wrocław, Poland.
| | - Aleksandra Wasiela
- Wroclaw University of Science and Technology, Faculty of Chemistry, Department of Micro, Nano, and Bioprocess Engineering, Norwida 4/6, 50-373 Wrocław, Poland
| | - Wojciech Dobicki
- Wrocław University of Environmental and Life Sciences, Institute of Animal Breeding, Department of Limnology and Fishery, Chelmonskiego 38C, PL-51630 Wroclaw, Poland
| | - Przemysław Pokorny
- Wrocław University of Environmental and Life Sciences, Institute of Animal Breeding, Department of Limnology and Fishery, Chelmonskiego 38C, PL-51630 Wroclaw, Poland
| | - Anna Trusek
- Wroclaw University of Science and Technology, Faculty of Chemistry, Department of Micro, Nano, and Bioprocess Engineering, Norwida 4/6, 50-373 Wrocław, Poland
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5
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Sarewicz M, Pintscher S, Pietras R, Borek A, Bujnowicz Ł, Hanke G, Cramer WA, Finazzi G, Osyczka A. Catalytic Reactions and Energy Conservation in the Cytochrome bc1 and b6f Complexes of Energy-Transducing Membranes. Chem Rev 2021; 121:2020-2108. [PMID: 33464892 PMCID: PMC7908018 DOI: 10.1021/acs.chemrev.0c00712] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Indexed: 12/16/2022]
Abstract
This review focuses on key components of respiratory and photosynthetic energy-transduction systems: the cytochrome bc1 and b6f (Cytbc1/b6f) membranous multisubunit homodimeric complexes. These remarkable molecular machines catalyze electron transfer from membranous quinones to water-soluble electron carriers (such as cytochromes c or plastocyanin), coupling electron flow to proton translocation across the energy-transducing membrane and contributing to the generation of a transmembrane electrochemical potential gradient, which powers cellular metabolism in the majority of living organisms. Cytsbc1/b6f share many similarities but also have significant differences. While decades of research have provided extensive knowledge on these enzymes, several important aspects of their molecular mechanisms remain to be elucidated. We summarize a broad range of structural, mechanistic, and physiological aspects required for function of Cytbc1/b6f, combining textbook fundamentals with new intriguing concepts that have emerged from more recent studies. The discussion covers but is not limited to (i) mechanisms of energy-conserving bifurcation of electron pathway and energy-wasting superoxide generation at the quinol oxidation site, (ii) the mechanism by which semiquinone is stabilized at the quinone reduction site, (iii) interactions with substrates and specific inhibitors, (iv) intermonomer electron transfer and the role of a dimeric complex, and (v) higher levels of organization and regulation that involve Cytsbc1/b6f. In addressing these topics, we point out existing uncertainties and controversies, which, as suggested, will drive further research in this field.
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Affiliation(s)
- Marcin Sarewicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Sebastian Pintscher
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Rafał Pietras
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Arkadiusz Borek
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Łukasz Bujnowicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Guy Hanke
- School
of Biological and Chemical Sciences, Queen
Mary University of London, London E1 4NS, U.K.
| | - William A. Cramer
- Department
of Biological Sciences, Purdue University, West Lafayette, Indiana 47907 United States
| | - Giovanni Finazzi
- Laboratoire
de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National Recherche Scientifique,
Commissariat Energie Atomique et Energies Alternatives, Institut National
Recherche l’agriculture, l’alimentation et l’environnement, 38054 Grenoble Cedex 9, France
| | - Artur Osyczka
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
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Maryasov AG, Bowman MK. Comment on “Modeling of motional EPR spectra using hindered Brownian rotational diffusion and the stochastic Liouville equation” [J. Chem. Phys. 152, 094103 (2020)]. J Chem Phys 2020; 153:027101. [DOI: 10.1063/5.0010661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alexander G. Maryasov
- N.N.Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Michael K. Bowman
- N.N.Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, USA
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Todorenko D, Timofeev N, Kovalenko I, Kukarskikh G, Matorin D, Antal T. Chromium effects on photosynthetic electron transport in pea (Pisum sativum L.). PLANTA 2019; 251:11. [PMID: 31776673 DOI: 10.1007/s00425-019-03304-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/25/2019] [Indexed: 05/02/2023]
Abstract
MAIN CONCLUSION Components of the photosynthetic electron transport chain in pea (Pisum sativum L.) leaves under in vivo conditions showed the following sensitivity to the inhibitory action of chromium(VI): intersystem electron transport > photosystem I > photosystem II. Inhibitory effects of chromium (VI) (K2Cr2O7, Cr) on the light reactions of photosynthesis were studied in vivo in Pisum sativum L. by using Multi-function Plant Efficiency Analyser (M-PEA-2). Photosynthetic parameters related to photosystem (PS) II, PSI and intersystem electron carriers were calculated from the light-induced kinetics of prompt chlorophyll a fluorescence (OJIP transient), delayed chlorophyll a fluorescence (DF), and 820 nm modulated reflection (MR). We showed that the I2 step of DF induction is sensitive to inhibition of the Q0 site of the cytochrome b6f complex. Such parameters as δRo of the JIP test related to the functional state of photosynthetic reactions beyond the PQ pool, Vred of the MR induction assigned to the overall rate of P700+ and plastocyanin reduction, and I2 step of the DF induction were significantly altered in the presence of low-dose Cr(VI). Moderate doses of Cr affected mainly PSI-related parameters including Vox and ΔMR parameters of the MR induction, whereas high-dose treatment influenced JIP test parameters φPo(= FV/FM) and ψEo related to PSII. The obtained results showed that the earliest Cr(VI) effect on the photosynthetic electron transport chain manifests itself by inhibition of the intersystem electron transport, rather, at the level of the cytochrome b6f complex. Inhibitory effects of Cr on PSI were more pronounced than those on PSII. Sensitivity of the used kinetic parameters toward the functional state of photosynthetic reactions makes this approach suitable for early diagnostics of toxic action of pollutants on plants.
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Affiliation(s)
- Daria Todorenko
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Nyurgun Timofeev
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Ilya Kovalenko
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Galina Kukarskikh
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Dmitry Matorin
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Taras Antal
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Department of Botany and Plant Ecology, Faculty of Natural Sciences and Geography, Pskov State University, Pskov, 180000, Russia.
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Taguchi AT, Ohmori D, Dikanov SA, Iwasaki T. g-Tensor Directions in the Protein Structural Frame of Hyperthermophilic Archaeal Reduced Rieske-Type Ferredoxin Explored by 13C Pulsed Electron Paramagnetic Resonance. Biochemistry 2018; 57:4074-4082. [PMID: 29890072 DOI: 10.1021/acs.biochem.8b00438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interpretation of magnetic resonance data in the context of structural and chemical biology requires prior knowledge of the g-tensor directions for paramagnetic metallo-cofactors with respect to the protein structural frame. Access to this information is often limited by the strict requirement of suitable protein crystals for single-crystal electron paramagnetic resonance (EPR) measurements or the reliance on protons (with ambiguous locations in crystal structures) near the paramagnetic metal site. Here we develop a novel pulsed EPR approach with selective 13Cβ-cysteine labeling of model [2Fe-2S] proteins to help bypass these problems. Analysis of the 13Cβ-cysteine hyperfine tensors reproduces the g-tensor of the Pseudomonas putida ISC-like [2Fe-2S] ferredoxin (FdxB). Its application to the hyperthermophilic archaeal Rieske-type [2Fe-2S] ferredoxin (ARF) from Sulfolobus solfataricus, for which the single-crystal EPR approach was not feasible, supports the best-fit g x-, g z-, and g y-tensor directions of the reduced cluster as nearly along Fe-Fe, S-S, and the cluster plane normal, respectively. These approximate principal directions of the reduced ARF g-tensor, explored by 13C pulsed EPR, are less skewed from the cluster molecular axes and are largely consistent with those previously determined by single-crystal EPR for the cytochrome bc1-associated, reduced Rieske [2Fe-2S] center. This suggests the approximate g-tensor directions are conserved across the phylogenetically and functionally divergent Rieske-type [2Fe-2S] proteins.
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Affiliation(s)
- Alexander T Taguchi
- Department of Biochemistry and Molecular Biology , Nippon Medical School , Sendagi, Tokyo 113-8602 , Japan
| | - Daijiro Ohmori
- Department of Chemistry , Juntendo University , Inzai-shi , Chiba 270-1695 , Japan
| | - Sergei A Dikanov
- Department of Veterinary Clinical Medicine , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Toshio Iwasaki
- Department of Biochemistry and Molecular Biology , Nippon Medical School , Sendagi, Tokyo 113-8602 , Japan
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9
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The cytochrome b6f complex: DFT modeling of the first step of plastoquinol oxidation by the iron-sulfur protein. J Organomet Chem 2018. [DOI: 10.1016/j.jorganchem.2018.01.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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10
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Abstract
This chapter presents an overview of structural properties of the cytochrome (Cyt) b 6 f complex and its functioning in chloroplasts. The Cyt b 6 f complex stands at the crossroad of photosynthetic electron transport pathways, providing connectivity between Photosystem (PSI) and Photosysten II (PSII) and pumping protons across the membrane into the thylakoid lumen. After a brief review of the chloroplast electron transport chain, the consideration is focused on the structural organization of the Cyt b 6 f complex and its interaction with plastoquinol (PQH2, reduced form of plastoquinone), a mediator of electron transfer from PSII to the Cyt b 6 f complex. The processes of PQH2 oxidation by the Cyt b 6 f complex have been considered within the framework of the Mitchell's Q-cycle. The overall rate of the intersystem electron transport is determined by PQH2 turnover at the quinone-binding site Qo of the Cyt b 6 f complex. The rate of PQH2 oxidation is controlled by the intrathylakoid pHin, which value determines the protonation/deprotonation events in the Qo-center. Two other regulatory mechanisms associated with the Cyt b 6 f complex are briefly overviewed: (i) redistribution of electron fluxes between alternative (linear and cyclic) pathways, and (ii) "state transitions" related to redistribution of solar energy between PSI and PSII.
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11
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Metastable radical state, nonreactive with oxygen, is inherent to catalysis by respiratory and photosynthetic cytochromes bc1/b6f. Proc Natl Acad Sci U S A 2017; 114:1323-1328. [PMID: 28115711 DOI: 10.1073/pnas.1618840114] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Oxygenic respiration and photosynthesis based on quinone redox reactions face a danger of wasteful energy dissipation by diversion of the productive electron transfer pathway through the generation of reactive oxygen species (ROS). Nevertheless, the widespread quinone oxido-reductases from the cytochrome bc family limit the amounts of released ROS to a low, perhaps just signaling, level through an as-yet-unknown mechanism. Here, we propose that a metastable radical state, nonreactive with oxygen, safely holds electrons at a local energetic minimum during the oxidation of plastohydroquinone catalyzed by the chloroplast cytochrome b6f This intermediate state is formed by interaction of a radical with a metal cofactor of a catalytic site. Modulation of its energy level on the energy landscape in photosynthetic vs. respiratory enzymes provides a possible mechanism to adjust electron transfer rates for efficient catalysis under different oxygen tensions.
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12
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Tikhonov AN. The cytochrome b6f complex at the crossroad of photosynthetic electron transport pathways. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 81:163-83. [PMID: 24485217 DOI: 10.1016/j.plaphy.2013.12.011] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 12/11/2013] [Indexed: 05/03/2023]
Abstract
Regulation of photosynthetic electron transport at the level of the cytochrome b6f complex provides efficient performance of the chloroplast electron transport chain (ETC). In this review, after brief overview of the structural organization of the chloroplast ETC, the consideration of the problem of electron transport control is focused on the plastoquinone (PQ) turnover and its interaction with the b6f complex. The data available show that the rates of plastoquinol (PQH2) formation in PSII and its diffusion to the b6f complex do not limit the overall rate of electron transfer between photosystem II (PSII) and photosystem I (PSI). Analysis of experimental and theoretical data demonstrates that the rate-limiting step in the intersystem chain of electron transport is determined by PQH2 oxidation at the Qo-site of the b6f complex, which is accompanied by the proton release into the thylakoid lumen. The acidification of the lumen causes deceleration of PQH2 oxidation, thus impeding the intersystem electron transport. Two other mechanisms of regulation of the intersystem electron transport have been considered: (i) "state transitions" associated with the light-induced redistribution of solar energy between PSI and PSII, and (ii) redistribution of electron fluxes between alternative pathways (noncyclic electron transport and cyclic electron flow around PSI).
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Rasmussen M, Minteer SD. Investigating the mechanism of thylakoid direct electron transfer for photocurrent generation. Electrochim Acta 2014. [DOI: 10.1016/j.electacta.2013.06.081] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Tikhonov AN. pH-dependent regulation of electron transport and ATP synthesis in chloroplasts. PHOTOSYNTHESIS RESEARCH 2013; 116:511-34. [PMID: 23695653 DOI: 10.1007/s11120-013-9845-y] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Accepted: 04/25/2013] [Indexed: 05/02/2023]
Abstract
This review is focused on pH-dependent mechanisms of regulation of photosynthetic electron transport and ATP synthesis in chloroplasts. The light-induced acidification of the thylakoid lumen is known to decelerate the plastoquinol oxidation by the cytochrome b 6 f complex, thus impeding the electron flow between photosystem II and photosystem I. Acidification of the lumen also triggers the dissipation of excess energy in the light-harvesting antenna of photosystem II, thereby protecting the photosynthetic apparatus against a solar stress. After brief description of structural and functional organization of the chloroplast electron transport chain, our attention is focused on the nature of the rate-limiting step of electron transfer between photosystem II and photosystem I. In the context of pH-dependent mechanism of photosynthetic control in chloroplasts, the mechanisms of plastoquinol oxidation by the cytochrome b 6 f complex have been considered. The light-induced alkalization of stroma is another factor of pH-dependent regulation of electron transport in chloroplasts. Alkalization of stroma induces activation of the Bassham-Benson-Calvin cycle reactions, thereby promoting efflux of electrons from photosystem I to NADP(+). The mechanisms of the light-induced activation of ATP synthase are briefly considered.
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Affiliation(s)
- Alexander N Tikhonov
- Department of Biophysics, Faculty of Physics, M. V. Lomonosov, Moscow State University, Moscow, Russia,
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Nguyen-Deroche TLN, Caruso A, Le TT, Bui TV, Schoefs B, Tremblin G, Morant-Manceau A. Zinc affects differently growth, photosynthesis, antioxidant enzyme activities and phytochelatin synthase expression of four marine diatoms. ScientificWorldJournal 2012; 2012:982957. [PMID: 22645501 PMCID: PMC3356767 DOI: 10.1100/2012/982957] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 01/10/2012] [Indexed: 01/05/2023] Open
Abstract
Zinc-supplementation (20 μM) effects on growth, photosynthesis, antioxidant enzyme activities (superoxide dismutase, ascorbate peroxidase, catalase), and the expression of phytochelatin synthase gene were investigated in four marine diatoms (Amphora acutiuscula, Nitzschia palea, Amphora coffeaeformis and Entomoneis paludosa). Zn-supplementation reduced the maximum cell density. A linear relationship was found between the evolution of gross photosynthesis and total chlorophyll content. The Zn treatment decreased the electron transport rate except in A. coffeaeformis and in E. paludosa at high irradiance. A linear relationship was found between the efficiency of light to evolve oxygen and the size of the light-harvesting antenna. The external carbonic anhydrase activity was stimulated in Zn-supplemented E. paludosa but was not correlated with an increase of photosynthesis. The total activity of the antioxidant enzymes did not display any clear increase except in ascorbate peroxidase activity in N. palea. The phytochelatin synthase gene was identified in the four diatoms, but its expression was only revealed in N. palea, without a clear difference between control and Zn-supplemented cells. Among the four species, A. paludosa was the most sensitive and A. coffeaeformis, the most tolerant. A. acutiuscula seemed to be under metal starvation, whereas, to survive, only N. palea developed several stress responses.
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Affiliation(s)
- Thi Le Nhung Nguyen-Deroche
- Mer, Molécules, Santé, EA 2160, LUNAM Université, Faculté des Sciences et Techniques, Université du Maine, Avenue Olivier Messiaen, 72085 Le Mans cedex 9, France
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Kallas T. Cytochrome b 6 f Complex at the Heart of Energy Transduction and Redox Signaling. PHOTOSYNTHESIS 2012. [DOI: 10.1007/978-94-007-1579-0_21] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Cooley JW. A structural model for across membrane coupling between the Qo and Qi active sites of cytochrome bc1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1842-8. [DOI: 10.1016/j.bbabio.2010.05.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 05/19/2010] [Accepted: 05/23/2010] [Indexed: 12/22/2022]
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18
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Sarewicz M, Dutka M, Froncisz W, Osyczka A. Magnetic interactions sense changes in distance between heme b(L) and the iron-sulfur cluster in cytochrome bc(1). Biochemistry 2009; 48:5708-20. [PMID: 19415898 PMCID: PMC2697599 DOI: 10.1021/bi900511b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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During the operation of cytochrome bc1, a key enzyme of biological energy conversion, the iron−sulfur head domain of one of the subunits of the catalytic core undergoes a large-scale movement from the catalytic quinone oxidation Qo site to cytochrome c1. This changes a distance between the two iron−two sulfur (FeS) cluster and other cofactors of the redox chains. Although the role and the mechanism of this movement have been intensely studied, they both remain poorly understood, partly because the movement itself is not easily traceable experimentally. Here, we take advantage of magnetic interactions between the reduced FeS cluster and oxidized heme bL to use dipolar enhancement of phase relaxation of the FeS cluster as a spectroscopic parameter which with a unique clarity and specificity senses changes in the distance between those two cofactors. The dipolar relaxation curves measured by EPR at Q-band in a glass state of frozen solution (i.e., under the conditions trapping a dynamic distribution of FeS positions that existed in a liquid phase) of isolated cytochrome bc1 were compared with the curves calculated for the FeS cluster occupying distinct positions in various crystals of cytochrome bc1. This comparison revealed the existence of a broad distribution of the FeS positions in noninhibited cytochrome bc1 and demonstrated that the average equilibrium position is modifiable by inhibitors or mutations. To explain the results, we assume that changes in the equilibrium distribution of the FeS positions are the result of modifications of the orienting potential gradient in which the diffusion of the FeS head domain takes place. The measured changes in the phase relaxation enhancement provide the first direct experimental description of changes in the strength of dipolar coupling between the FeS cluster and heme bL.
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Affiliation(s)
- Marcin Sarewicz
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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The Cytochrome bc 1 and Related bc Complexes: The Rieske/Cytochrome b Complex as the Functional Core of a Central Electron/Proton Transfer Complex. THE PURPLE PHOTOTROPHIC BACTERIA 2009. [DOI: 10.1007/978-1-4020-8815-5_23] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Yamashita E, Zhang H, Cramer WA. Structure of the cytochrome b6f complex: quinone analogue inhibitors as ligands of heme cn. J Mol Biol 2007; 370:39-52. [PMID: 17498743 PMCID: PMC1993820 DOI: 10.1016/j.jmb.2007.04.011] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Revised: 04/01/2007] [Accepted: 04/04/2007] [Indexed: 11/24/2022]
Abstract
A native structure of the cytochrome b(6)f complex with improved resolution was obtained from crystals of the complex grown in the presence of divalent cadmium. Two Cd(2+) binding sites with different occupancy were determined: (i) a higher affinity site, Cd1, which bridges His143 of cytochrome f and the acidic residue, Glu75, of cyt b(6); in addition, Cd1 is coordinated by 1-2 H(2)O or 1-2 Cl(-); (ii) a second site, Cd2, of lower affinity for which three identified ligands are Asp58 (subunit IV), Glu3 (PetG subunit) and Glu4 (PetM subunit). Binding sites of quinone analogue inhibitors were sought to map the pathway of transfer of the lipophilic quinone across the b(6)f complex and to define the function of the novel heme c(n). Two sites were found for the chromone ring of the tridecyl-stigmatellin (TDS) quinone analogue inhibitor, one near the p-side [2Fe-2S] cluster. A second TDS site was found on the n-side of the complex facing the quinone exchange cavity as an axial ligand of heme c(n). A similar binding site proximal to heme c(n) was found for the n-side inhibitor, NQNO. Binding of these inhibitors required their addition to the complex before lipid used to facilitate crystallization. The similar binding of NQNO and TDS as axial ligands to heme c(n) implies that this heme utilizes plastoquinone as a natural ligand, thus defining an electron transfer complex consisting of hemes b(n), c(n), and PQ, and the pathway of n-side reduction of the PQ pool. The NQNO binding site explains several effects associated with its inhibitory action: the negative shift in heme c(n) midpoint potential, the increased amplitude of light-induced heme b(n) reduction, and an altered EPR spectrum attributed to interaction between hemes c(n) and b(n). A decreased extent of heme c(n) reduction by reduced ferredoxin in the presence of NQNO allows observation of the heme c(n) Soret band in a chemical difference spectrum.
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Cape JL, Bowman MK, Kramer DM. Understanding the cytochrome bc complexes by what they don't do. The Q-cycle at 30. TRENDS IN PLANT SCIENCE 2006; 11:46-55. [PMID: 16352458 DOI: 10.1016/j.tplants.2005.11.007] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2005] [Revised: 10/20/2005] [Accepted: 11/25/2005] [Indexed: 05/05/2023]
Abstract
The cytochrome (cyt) bc(1), b(6)f and related complexes are central components of the respiratory and photosynthetic electron transport chains. These complexes carry out an extraordinary sequence of electron and proton transfer reactions that conserve redox energy in the form of a trans-membrane proton motive force for use in synthesizing ATP and other processes. Thirty years ago, Peter Mitchell proposed a general turnover mechanism for these complexes, which he called the Q-cycle. Since that time, many opposing schemes have challenged the Q-cycle but, with the accumulation of large amounts of biochemical, kinetic, thermodynamic and high-resolution structural data, the Q-cycle has triumphed as the accepted model, although some of the intermediate steps are poorly understood and still controversial. One of the major research questions concerning the cyt bc(1) and b(6)f complexes is how these enzymes suppress deleterious and dissipative side reactions. In particular, most Q-cycle models involve reactive semiquinone radical intermediates that can reduce O(2) to superoxide and lead to cellular oxidative stress. Current models to explain the avoidance of side reactions involve unprecedented or unusual enzyme mechanisms, the testing of which will involve new theoretical and experimental approaches.
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Affiliation(s)
- Jonathan L Cape
- Institute of Biological Chemistry, Washington State University, 289 Clark Hall, Pullman, WA 99164-6314, USA
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Cooley JW, Ohnishi T, Daldal F. Binding dynamics at the quinone reduction (Qi) site influence the equilibrium interactions of the iron sulfur protein and hydroquinone oxidation (Qo) site of the cytochrome bc1 complex. Biochemistry 2005; 44:10520-32. [PMID: 16060661 PMCID: PMC1360200 DOI: 10.1021/bi050571+] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Multiple instances of low-potential electron-transport pathway inhibitors that affect the structure of the cytochrome (cyt) bc(1) complex to varying degrees, ranging from changes in hydroquinone (QH(2)) oxidation and cyt c(1) reduction kinetics to proteolytic accessibility of the hinge region of the iron-sulfur-containing subunit (Fe/S protein), have been reported. However, no instance has been documented of any ensuing change on the environment(s) of the [2Fe-2S] cluster. In this work, this issue was addressed in detail by taking advantage of the increased spectral and spatial resolution obtainable with orientation-dependent electron paramagnetic resonance (EPR) spectroscopic analysis of ordered membrane preparations. For the first time, perturbation of the low-potential electron-transport pathway by Q(i)-site inhibitors or various mutations was shown to change the EPR spectra of both the cyt b hemes and the [2Fe-2S] cluster of the Fe/S protein. In particular, two interlinked effects of Q(i)-site modifications on the Fe/S subunit, one changing the local environment of its [2Fe-2S] cluster and a second affecting the mobility of this subunit, are revealed. Remarkably, different inhibitors and mutations at or near the Q(i) site induce these two effects differently, indicating that the events occurring at the Q(i) site affect the global structure of the cyt bc(1). Furthermore, occupancy of discrete Q(i)-site subdomains differently impede the location of the Fe/S protein at the Q(o) site. These findings led us to propose that antimycin A and HQNO mimic the presence of QH(2) and Q at the Q(i) site, respectively. Implications of these findings in respect to the Q(o)-Q(i) sites communications and to multiple turnovers of the cyt bc(1) are discussed.
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Affiliation(s)
| | - Tomoko Ohnishi
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, PA 19104
| | - Fevzi Daldal
- Department of Biology, Plant Science Institute and
- *To whom correspondence should be addressed: Phone: (215) 898-4394 Fax: (215) 898-8780 E-mail:
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Cooley JW, Ohnishi T, Daldal F. Binding dynamics at the quinone reduction (Qi) site influence the equilibrium interactions of the iron sulfur protein and hydroquinone oxidation (Qo) site of the cytochrome bc1 complex. Biochemistry 2005. [PMID: 16060661 DOI: 10.1021/bi050571] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multiple instances of low-potential electron-transport pathway inhibitors that affect the structure of the cytochrome (cyt) bc(1) complex to varying degrees, ranging from changes in hydroquinone (QH(2)) oxidation and cyt c(1) reduction kinetics to proteolytic accessibility of the hinge region of the iron-sulfur-containing subunit (Fe/S protein), have been reported. However, no instance has been documented of any ensuing change on the environment(s) of the [2Fe-2S] cluster. In this work, this issue was addressed in detail by taking advantage of the increased spectral and spatial resolution obtainable with orientation-dependent electron paramagnetic resonance (EPR) spectroscopic analysis of ordered membrane preparations. For the first time, perturbation of the low-potential electron-transport pathway by Q(i)-site inhibitors or various mutations was shown to change the EPR spectra of both the cyt b hemes and the [2Fe-2S] cluster of the Fe/S protein. In particular, two interlinked effects of Q(i)-site modifications on the Fe/S subunit, one changing the local environment of its [2Fe-2S] cluster and a second affecting the mobility of this subunit, are revealed. Remarkably, different inhibitors and mutations at or near the Q(i) site induce these two effects differently, indicating that the events occurring at the Q(i) site affect the global structure of the cyt bc(1). Furthermore, occupancy of discrete Q(i)-site subdomains differently impede the location of the Fe/S protein at the Q(o) site. These findings led us to propose that antimycin A and HQNO mimic the presence of QH(2) and Q at the Q(i) site, respectively. Implications of these findings in respect to the Q(o)-Q(i) sites communications and to multiple turnovers of the cyt bc(1) are discussed.
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Affiliation(s)
- Jason W Cooley
- Department of Biology, Plant Science Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Mulkidjanian AY. Ubiquinol oxidation in the cytochrome bc1 complex: Reaction mechanism and prevention of short-circuiting. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1709:5-34. [PMID: 16005845 DOI: 10.1016/j.bbabio.2005.03.009] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2004] [Revised: 12/01/2004] [Accepted: 03/22/2005] [Indexed: 11/26/2022]
Abstract
This review is focused on the mechanism of ubiquinol oxidation by the cytochrome bc1 complex (bc1). This integral membrane complex serves as a "hub" in the vast majority of electron transfer chains. The bc1 oxidizes a ubiquinol molecule to ubiquinone by a unique "bifurcated" reaction where the two released electrons go to different acceptors: one is accepted by the mobile redox active domain of the [2Fe-2S] iron-sulfur Rieske protein (FeS protein) and the other goes to cytochrome b. The nature of intermediates in this reaction remains unclear. It is also debatable how the enzyme prevents short-circuiting that could happen if both electrons escape to the FeS protein. Here, I consider a reaction mechanism that (i) agrees with the available experimental data, (ii) entails three traits preventing the short-circuiting in bc1, and (iii) exploits the evident structural similarity of the ubiquinone binding sites in the bc1 and the bacterial photosynthetic reaction center (RC). Based on the latter congruence, it is suggested that the reaction route of ubiquinol oxidation by bc1 is a reversal of that leading to the ubiquinol formation in the RC. The rate-limiting step of ubiquinol oxidation is then the re-location of a ubiquinol molecule from its stand-by site within cytochrome b into a catalytic site, which is formed only transiently, after docking of the mobile redox domain of the FeS protein to cytochrome b. In the catalytic site, the quinone ring is stabilized by Glu-272 of cytochrome b and His-161 of the FeS protein. The short circuiting is prevented as long as: (i) the formed semiquinone anion remains bound to the reduced FeS domain and impedes its undocking, so that the second electron is forced to go to cytochrome b; (ii) even after ubiquinol is fully oxidized, the reduced FeS domain remains docked to cytochrome b until electron(s) pass through cytochrome b; (iii) if cytochrome b becomes (over)reduced, the binding and oxidation of further ubiquinol molecules is hampered; the reason is that the Glu-272 residue is turned towards the reduced hemes of cytochrome b and is protonated to stabilize the surplus negative charge; in this state, this residue cannot participate in the binding/stabilization of a ubiquinol molecule.
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Affiliation(s)
- Armen Y Mulkidjanian
- Max Planck Institute of Biophysics, Department of Biophysical Chemistry, Max-von-Laue-Str. 3, D-60438 Frankfurt-am-Main, Germany.
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Liu XD, Shen YG. Salt-induced redox-independent phosphorylation of light harvesting chlorophyll a/b proteins in Dunaliella salina thylakoid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1706:215-9. [PMID: 15694349 DOI: 10.1016/j.bbabio.2004.11.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2004] [Revised: 10/27/2004] [Accepted: 11/10/2004] [Indexed: 11/22/2022]
Abstract
This study investigated the regulation of the major light harvesting chlorophyll a/b protein (LHCII) phosphorylation in Dunaliella salina thylakoid membranes. We found that both light and NaCl could induce LHCII phosphorylation in D. salina thylakoid membranes. Treatments with oxidants (ferredoxin and NADP) or photosynthetic electron flow inhibitors (DCMU, DBMIB, and stigmatellin) inhibited LHCII phosphorylation induced by light but not that induced by NaCl. Furthermore, neither addition of CuCl(2), an inhibitor of cytochrome b(6)f complex reduction, nor oxidizing treatment with ferricyanide inhibited light- or NaCl-induced LHCII phosphorylation, and both salts even induced LHCII phosphorylation in dark-adapted D. salina thylakoid membranes as other salts did. Together, these results indicate that the redox state of the cytochrome b(6)f complex is likely involved in light- but not salt-induced LHCII phosphorylation in D. salina thylakoid membranes.
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Affiliation(s)
- Xian-De Liu
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
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Kramer DM, Roberts AG, Muller F, Cape J, Bowman MK. Q-cycle bypass reactions at the Qo site of the cytochrome bc1 (and related) complexes. Methods Enzymol 2004; 382:21-45. [PMID: 15047094 DOI: 10.1016/s0076-6879(04)82002-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Affiliation(s)
- David M Kramer
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, USA
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Eggink LL, LoBrutto R, Brune DC, Brusslan J, Yamasato A, Tanaka A, Hoober JK. Synthesis of chlorophyll b: localization of chlorophyllide a oxygenase and discovery of a stable radical in the catalytic subunit. BMC PLANT BIOLOGY 2004; 4:5. [PMID: 15086960 PMCID: PMC406501 DOI: 10.1186/1471-2229-4-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2003] [Accepted: 04/15/2004] [Indexed: 05/24/2023]
Abstract
BACKGROUND Assembly of stable light-harvesting complexes (LHCs) in the chloroplast of green algae and plants requires synthesis of chlorophyll (Chl) b, a reaction that involves oxygenation of the 7-methyl group of Chl a to a formyl group. This reaction uses molecular oxygen and is catalyzed by chlorophyllide a oxygenase (CAO). The amino acid sequence of CAO predicts mononuclear iron and Rieske iron-sulfur centers in the protein. The mechanism of synthesis of Chl b and localization of this reaction in the chloroplast are essential steps toward understanding LHC assembly. RESULTS Fluorescence of a CAO-GFP fusion protein, transiently expressed in young pea leaves, was found at the periphery of mature chloroplasts and on thylakoid membranes by confocal fluorescence microscopy. However, when membranes from partially degreened cells of Chlamydomonas reinhardtii cw15 were resolved on sucrose gradients, full-length CAO was detected by immunoblot analysis only on the chloroplast envelope inner membrane. The electron paramagnetic resonance spectrum of CAO included a resonance at g = 4.3, assigned to the predicted mononuclear iron center. Instead of a spectrum of the predicted Rieske iron-sulfur center, a nearly symmetrical, approximately 100 Gauss peak-to-trough signal was observed at g = 2.057, with a sensitivity to temperature characteristic of an iron-sulfur center. A remarkably stable radical in the protein was revealed by an isotropic, 9 Gauss peak-to-trough signal at g = 2.0042. Fragmentation of the protein after incorporation of 125I- identified a conserved tyrosine residue (Tyr-422 in Chlamydomonas and Tyr-518 in Arabidopsis) as the radical species. The radical was quenched by chlorophyll a, an indication that it may be involved in the enzymatic reaction. CONCLUSION CAO was found on the chloroplast envelope and thylakoid membranes in mature chloroplasts but only on the envelope inner membrane in dark-grown C. reinhardtii cells. Such localization provides further support for the envelope membranes as the initial site of Chl b synthesis and assembly of LHCs during chloroplast development. Identification of a tyrosine radical in the protein provides insight into the mechanism of Chl b synthesis.
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Affiliation(s)
- Laura L Eggink
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501, USA
- Center for the Study of Early Events in Photosynthesis, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Russell LoBrutto
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501, USA
- Center for the Study of Early Events in Photosynthesis, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Daniel C Brune
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA
- Center for the Study of Early Events in Photosynthesis, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Judy Brusslan
- Department of Biological Science, California State University, Long Beach, California 90840-3702, USA
| | - Akihiro Yamasato
- The Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - Ayumi Tanaka
- The Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - J Kenneth Hoober
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501, USA
- Center for the Study of Early Events in Photosynthesis, Arizona State University, Tempe, Arizona 85287-1604, USA
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Hervás M, Navarro JA, De La Rosa MA. Electron transfer between membrane complexes and soluble proteins in photosynthesis. Acc Chem Res 2003; 36:798-805. [PMID: 14567714 DOI: 10.1021/ar020084b] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photosynthesis consists of a series of endergonic redox reactions, with light as the source of energy, chlorophyll as the energy converter, and electrons flowing through membrane and soluble proteins. Here, we give an account of the most recent results on the structure-function relationships of the membrane-embedded complexes cytochrome b(6)-f and photosystem I and of the two soluble proteins (cytochrome c(6) and plastocyanin) that serve as alternative electron carriers between them. Particular attention is paid to the evolutionary aspects of the reaction mechanism and transient protein-protein interactions between the membrane complexes and their partners in cyanobacteria, eukaryotic algae, and plants.
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Affiliation(s)
- Manuel Hervás
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla y Consejo Superior de Investigaciones Científicas, Américo Vespucio s/n, 41092-Sevilla, Spain
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Yan J, Cramer WA. Functional insensitivity of the cytochrome b6f complex to structure changes in the hinge region of the Rieske iron-sulfur protein. J Biol Chem 2003; 278:20925-33. [PMID: 12672829 DOI: 10.1074/jbc.m212616200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Structure analysis of the cytochrome bc1 complex in the presence and absence of Qp quinol analog inhibitors implied that a large amplitude motion of the Rieske iron-sulfur protein (ISP) is required to mediate electron transfer from ubiquinol to cytochrome c1. Studies of the functional consequences of mutagenesis of an 8-residue ISP "hinge" region in the bc1 complex showed it to be sensitive to structure perturbation, implying that optimum flexibility and length are required for the large amplitude motion. Mutagenesis-function analysis carried out on the ISP hinge region of the cytochrome b6 f complex using the cyanobacterium Synechococcus sp. PCC 7002 showed the following. (i) Of three petC genes, only that in the petCA operon codes for functional ISP. (ii) The function of the complex was insensitive to changes in the hinge region that increased flexibility, decreased flexibility by substitutions of 4-6 Pro residues, shortened the hinge by a 1-residue deletion, or elongated it by insertion of 4 residues. The latter change increased sensitivity to Qp inhibitors, whereas deletion of 2 residues resulted in a loss of inhibitor sensitivity and a decrease in activity, indicating a minimum hinge length of 7 residues required for optimum binding of ISP at the Qp site. Thus, in contrast to the bc1 complex, the function of the b6 f complex was insensitive to sequence changes in the ISP hinge that altered its length or flexibility. This implies that either the barriers to motion or the amplitude of ISP motion required for function is smaller than in the bc1 complex.
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Affiliation(s)
- Jiusheng Yan
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-2054,USA
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Soriano GM, Guo LW, De Vitry C, Kallas T, Cramer WA. Electron transfer from the Rieske iron-sulfur protein (ISP) to cytochrome f in vitro. Is a guided trajectory of the ISP necessary for competent docking? J Biol Chem 2002; 277:41865-71. [PMID: 12207018 DOI: 10.1074/jbc.m205772200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The time course of electron transfer in vitro between soluble domains of the Rieske iron-sulfur protein (ISP) and cytochrome f subunits of the cytochrome b(6)f complex of oxygenic photosynthesis was measured by stopped-flow mixing. The domains were derived from Chlamydomonas reinhardtii and expressed in Escherichia coli. The expressed 142-residue soluble ISP apoprotein was reconstituted with the [2Fe-2S] cluster. The second-order rate constant, k(2)((ISP-f)) = 1.5 x 10(6) m(-1) s(-1), for ISP to cytochrome f electron transfer was <10(-2) of the rate constant at low ionic strength, k(2)((f-PC))(> 200 x 10(6) m(-1) s(-1)), for the reduction of plastocyanin by cytochrome f, and approximately 1/30 of k(2)((f-PC)) at the ionic strength estimated for the thylakoid interior. In contrast to k(2)((f-PC)), k(2)((ISP-f)) was independent of pH and ionic strength, implying no significant role of electrostatic interactions. Effective pK values of 6.2 and 8.3, respectively, of oxidized and reduced ISP were derived from the pH dependence of the amplitude of cytochrome f reduction. The first-order rate constant, k(1)((ISP-f)), predicted from k(2)((ISP-f)) is approximately 10 and approximately 150 times smaller than the millisecond and microsecond phases of cytochrome f reduction observed in vivo. It is proposed that in the absence of electrostatic guidance, a productive docking geometry for fast electron transfer is imposed by the guided trajectory of the ISP extrinsic domain. The requirement of a specific electrically neutral docking configuration for ISP electron transfer is consistent with structure data for the related cytochrome bc(1) complex.
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Affiliation(s)
- Glenda M Soriano
- Department of Biological Sciences and Program in Biochemistry/Molecular Biology, Purdue University, West Lafayette, Indiana 47907-1392, USA
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