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Vilyanen D, Pavlov I, Naydov I, Ivanov B, Kozuleva M. Peculiarities of DNP-INT and DBMIB as inhibitors of the photosynthetic electron transport. PHOTOSYNTHESIS RESEARCH 2024; 161:79-92. [PMID: 38108927 DOI: 10.1007/s11120-023-01063-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023]
Abstract
Inhibitory analysis is a useful tool for studying cytochrome b6f complex in the photosynthetic electron transport chain. Here, we examine the inhibitory efficiency of two widely used inhibitors of the plastoquinol oxidation in the cytochrome b6f complex, namely 2,4-dinitrophenyl ether of 2-iodo-4-nitrothymol (DNP-INT) and 2,5-dibromo-3-methyl-6-isopropylbenzoquinone (DBMIB). Using isolated thylakoids from pea and arabidopsis, we demonstrate that inhibitory activity of DNP-INT and DBMIB is enhanced by increasing irradiance, and this effect is due to the increase in the rate of electron transport. However, the accumulation of protons in the thylakoid lumen at low light intensity has opposite effects on the inhibitory activity of DNP-INT and DBMIB, namely increasing the activity of DNP-INT and restricting the activity of DBMIB. These results allow for the refinement of the conditions under which the use of these inhibitors leads to the complete inhibition of plastoquinol oxidation in the cytochrome b6f complex, thereby broadening our understanding of the operation of the cytochrome b6f complex under conditions of steady-state electron transport.
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Affiliation(s)
- Daria Vilyanen
- Federal Research Center, Institute of Basic Biological Problems of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia
| | - Ilya Pavlov
- Saint Petersburg State University, Saint Petersburg, Russia
| | - Ilya Naydov
- Federal Research Center, Institute of Basic Biological Problems of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia
| | - Boris Ivanov
- Federal Research Center, Institute of Basic Biological Problems of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia
| | - Marina Kozuleva
- Federal Research Center, Institute of Basic Biological Problems of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia.
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2
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Markevich NI, Markevich LN. Computational Modeling Analysis of Kinetics of Fumarate Reductase Activity and ROS Production during Reverse Electron Transfer in Mitochondrial Respiratory Complex II. Int J Mol Sci 2023; 24:ijms24098291. [PMID: 37175997 PMCID: PMC10179487 DOI: 10.3390/ijms24098291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/23/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Reverse electron transfer in mitochondrial complex II (CII) plays an important role in hypoxia/anoxia, in particular, in ischemia, when the blood supply to an organ is disrupted and oxygen is not available. A computational model of CII was developed in this work to facilitate the quantitative analysis of the kinetics of quinol-fumarate reduction as well as ROS production during reverse electron transfer in CII. The model consists of 20 ordinary differential equations and 7 moiety conservation equations. The parameter values were determined at which the kinetics of electron transfer in CII in both forward and reverse directions would be explained simultaneously. The possibility of the existence of the "tunnel diode" behavior in the reverse electron transfer in CII, where the driving force is QH2, was tested. It was found that any high concentrations of QH2 and fumarate are insufficient for the appearance of a tunnel effect. The results of computer modeling show that the maximum rate of succinate production cannot provide a high concentration of succinate in ischemia. Furthermore, computational modeling results predict a very low rate of ROS production, about 50 pmol/min/mg mitochondrial protein, which is considerably less than 1000 pmol/min/mg protein observed in CII in forward direction.
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Affiliation(s)
- Nikolay I Markevich
- Institute of Theoretical and Experimental Biophysics of RAS, Pushchino, Moscow 142290, Russia
| | - Lubov N Markevich
- Institute of Cell Biophysics of RAS, Pushchino, Moscow 142290, Russia
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3
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An eco-friendly electrochemical process for the formation of a new desloratadine derivative and its antibacterial susceptibility. Report of a new type of ortho-quinhydrone complex. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.140518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Yuan S, Schmidt HM, Wood KC, Straub AC. CoenzymeQ in cellular redox regulation and clinical heart failure. Free Radic Biol Med 2021; 167:321-334. [PMID: 33753238 DOI: 10.1016/j.freeradbiomed.2021.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/22/2021] [Accepted: 03/08/2021] [Indexed: 12/12/2022]
Abstract
Coenzyme Q (CoQ) is ubiquitously embedded in lipid bilayers of various cellular organelles. As a redox cycler, CoQ shuttles electrons between mitochondrial complexes and extramitochondrial reductases and oxidases. In this way, CoQ is crucial for maintaining the mitochondrial function, ATP synthesis, and redox homeostasis. Cardiomyocytes have a high metabolic rate and rely heavily on mitochondria to provide energy. CoQ levels, in both plasma and the heart, correlate with heart failure in patients, indicating that CoQ is critical for cardiac function. Moreover, CoQ supplementation in clinics showed promising results for treating heart failure. This review provides a comprehensive view of CoQ metabolism and its interaction with redox enzymes and reactive species. We summarize the clinical trials and applications of CoQ in heart failure and discuss the caveats and future directions to improve CoQ therapeutics.
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Affiliation(s)
- Shuai Yuan
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Heidi M Schmidt
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Katherine C Wood
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adam C Straub
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.
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5
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Wise CE, Ledinina AE, Yuly JL, Artz JH, Lubner CE. The role of thermodynamic features on the functional activity of electron bifurcating enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148377. [PMID: 33453185 DOI: 10.1016/j.bbabio.2021.148377] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 11/25/2022]
Abstract
Electron bifurcation is a biological mechanism to drive a thermodynamically unfavorable redox reaction through direct coupling with an exergonic reaction. This process allows microorganisms to generate high energy reducing equivalents in order to sustain life and is often found in anaerobic metabolism, where the energy economy of the cell is poor. Recent work has revealed details of the redox energy landscapes for a variety of electron bifurcating enzymes, greatly expanding the understanding of how energy is transformed by this unique mechanism. Here we highlight the plasticity of these emerging landscapes, what is known regarding their mechanistic underpinnings, and provide a context for interpreting their biochemical activity within the physiological framework. We conclude with an outlook for propelling the field toward an integrative understanding of the impact of electron bifurcation.
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Affiliation(s)
| | | | | | - Jacob H Artz
- National Renewable Energy Laboratory, Golden, CO, USA
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6
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Springett R. The proton pumping mechanism of the bc 1 complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148352. [PMID: 33338489 DOI: 10.1016/j.bbabio.2020.148352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 11/17/2020] [Accepted: 12/08/2020] [Indexed: 02/07/2023]
Abstract
The bc1 complex is a proton pump of the mitochondrial electron transport chain which transfers electrons from ubiquinol to cytochrome c. It operates via the modified Q cycle in which the two electrons from oxidation of ubiquinol at the Qo center are bifurcated such that the first electron is passed to Cytc via an iron sulfur center and c1 whereas the second electron is passed across the membrane by bL and bH to reduce ubiquinone at the Qi center. Proton pumping occurs because oxidation of ubiquinol at the Qo center releases protons to the P-side and reduction of ubiquinone at the Qi center takes up protons from the N-side. However, the mechanisms which prevent the thermodynamically more favorable short circuit reactions and so ensure precise bifurcation and proton pumping are not known. Here we use statistical thermodynamics to show that reaction steps that originate from high energy states cannot support high flux even when they have large rate constants. We show how the chemistry of ubiquinol oxidation and the structure of the Qo site can result in free energy profiles that naturally suppress flux through the short circuit pathways while allowing high rates of bifurcation. These predictions are confirmed through in-silico simulations using a Markov state model.
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Affiliation(s)
- Roger Springett
- Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, United Kingdom.
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7
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Luévano-Martínez LA, Girard RMBM, Alencar MB, Silber AM. ATP regulates the activity of an alternative oxidase in Trypanosoma brucei. FEBS Lett 2020; 594:2150-2158. [PMID: 32279308 DOI: 10.1002/1873-3468.13790] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 02/05/2023]
Abstract
The reduced mitochondrial respiratory chain from the bloodstream forms of Trypanosoma brucei is composed of only a membrane-bound glycerol-3-phosphate dehydrogenase and an alternative oxidase. Since these enzymes are not proton pumps, their functions are restricted to the maintenance of the redox balance in the glycosome by means of the dihydroxyacetone phosphate/glycerol-3-phosphate shuttle. Additionally, an F1 Fo -ATP synthase functions as an ATP-hydrolysing enzyme to establish the proton motive force necessary to maintain the basic functions of mitochondria. In this report, we studied the interplay between the alternative oxidase and ATP synthase, and we found that, in addition to its role as a proton pump, ATP synthase contributes to maintain safe levels of ATP to prevent the inhibition of the alternative oxidase by ATP.
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Affiliation(s)
- Luis Alberto Luévano-Martínez
- Laboratory of Biochemistry of Tryps - LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Richard M B M Girard
- Laboratory of Biochemistry of Tryps - LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Mayke Bezerra Alencar
- Laboratory of Biochemistry of Tryps - LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Ariel Mariano Silber
- Laboratory of Biochemistry of Tryps - LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil
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8
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Song Z, Hu Y, Iorga BI, Vallières C, Fisher N, Meunier B. Mutational analysis of the Q i-site proton pathway in yeast cytochrome bc 1 complex. Biochem Biophys Res Commun 2020; 523:615-619. [PMID: 31941609 DOI: 10.1016/j.bbrc.2019.12.102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 12/19/2019] [Indexed: 11/18/2022]
Abstract
The respiratory cytochrome bc1 complex functions as a protonmotive ubiquinol:cytochrome c oxidoreductase. Lysine 228 (K228) located within the quinol reduction (Qi) site of the bc1 complex, has been reported as a key residue for proton transfer during the redox chemistry cycle to substrate quinone at Qi. In yeast, while single mutations had no effect, the combination of K228L and F225L resulted in a severe respiratory growth defect and inhibition of O2 consumption in intact cells. The inhibition was overcome by uncoupling the mitochondrial membrane or by suppressor mutations in the region of K228L-F225L. We propose that the K228L mutation introduces energetic (and kinetic) barriers into normal electron- and proton transfer chemistry at Qi, which are relieved by dissipation of the opposing protonmotive force or through the restoration of favourable intraprotein proton transfer networks via suppressor mutation.
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Affiliation(s)
- Zehua Song
- Translational Research Institute, Henan Provincial People's Hospital, School of Medicine, Henan University, Zhengzhou, China
| | - Yangfeng Hu
- Translational Research Institute, Henan Provincial People's Hospital, School of Medicine, Henan University, Zhengzhou, China
| | - Bogdan I Iorga
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - Cindy Vallières
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Nicholas Fisher
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA.
| | - Brigitte Meunier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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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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Wilson CA, Crofts AR. Dissecting the pattern of proton release from partial process involved in ubihydroquinone oxidation in the Q-cycle. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:531-543. [PMID: 29625088 DOI: 10.1016/j.bbabio.2018.03.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/18/2018] [Accepted: 03/28/2018] [Indexed: 12/01/2022]
Abstract
A key feature of the modified Q-cycle of the cytochrome bc1 and related complexes is a bifurcation of QH2 oxidation involving electron transfer to two different acceptor chains, each coupled to proton release. We have studied the kinetics of proton release in chromatophore vesicles from Rhodobacter sphaeroides, using the pH-sensitive dye neutral red to follow pH changes inside on activation of the photosynthetic chain, focusing on the bifurcated reaction, in which 4H+are released on complete turnover of the Q-cycle (2H+/ubiquinol (QH2) oxidized). We identified different partial processes of the Qo-site reaction, isolated through use of specific inhibitors, and correlated proton release with electron transfer processes by spectrophotometric measurement of cytochromes or electrochromic response. In the presence of myxothiazol or azoxystrobin, the proton release observed reflected oxidation of the Rieske iron‑sulfur protein. In the absence of Qo-site inhibitors, the pH change measured represented the convolution of this proton release with release of protons on turnover of the Qo-site, involving formation of the ES-complex and oxidation of the semiquinone intermediate. Turnover also regenerated the reduced iron-sulfur protein, available for further oxidation on a second turnover. Proton release was well-matched with the rate limiting step on oxidation of QH2 on both turnovers. However, a minor lag in proton release found at pH 7 but not at pH 8 might suggest that a process linked to rapid proton release on oxidation of the intermediate semiquinone involves a group with a pK in that range.
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Affiliation(s)
- Charles A Wilson
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States.
| | - Antony R Crofts
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States
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11
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Analysis of a Functional Dimer Model of Ubiquinol Cytochrome c Oxidoreductase. Biophys J 2017; 113:1599-1612. [PMID: 28978450 PMCID: PMC5627346 DOI: 10.1016/j.bpj.2017.08.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 08/04/2017] [Accepted: 08/10/2017] [Indexed: 11/21/2022] Open
Abstract
Ubiquinol cytochrome c oxidoreductase (bc1 complex) serves as an important electron junction in many respiratory systems. It funnels electrons coming from NADH and ubiquinol to cytochrome c, but it is also capable of producing significant amounts of the free radical superoxide. In situ and in other experimental systems, the enzyme exists as a dimer. But until recently, it was believed to operate as a functional monomer. Here we show that a functional dimer model is capable of explaining both kinetic and superoxide production rate data. The model consists of six electronic states characterized by the number of electrons deposited on the complex. It is fully reversible and strictly adheres to the thermodynamics governing the reactions. A total of nine independent data sets were used to parameterize the model. To explain the data with a consistent set of parameters, it was necessary to incorporate intramonomer Coulombic effects between hemes bL and bH and intermonomer Coulombic effects between bL hemes. The fitted repulsion energies fall within the theoretical range of electrostatic calculations. In addition, model analysis demonstrates that the Q pool is mostly oxidized under normal physiological operation but can switch to a more reduced state when reverse electron transport conditions are in place.
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12
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Abstract
Respiratory chain dysfunction plays an important role in human disease and aging. It is now well established that the individual respiratory complexes can be organized into supercomplexes, and structures for these macromolecular assemblies, determined by electron cryo-microscopy, have been described recently. Nevertheless, the reason why supercomplexes exist remains an enigma. The widely held view that they enhance catalysis by channeling substrates is challenged by both structural and biophysical information. Here, we evaluate and discuss data and hypotheses on the structures, roles, and assembly of respiratory-chain supercomplexes and propose a future research agenda to address unanswered questions.
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Affiliation(s)
- Dusanka Milenkovic
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9b, 50931 Cologne, Germany
| | - James N Blaza
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9b, 50931 Cologne, Germany; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden.
| | - Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK.
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13
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Tessensohn ME, Ng SJ, Chan KK, Gan SL, Sims NF, Koh YR, Webster RD. Impurities in Nitrile Solvents Commonly Used for Electrochemistry, and their Effects on Voltammetric Data. ChemElectroChem 2016. [DOI: 10.1002/celc.201600266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Malcolm E. Tessensohn
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
| | - Shu Jun Ng
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
| | - Kwok Kiong Chan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
| | - Sher Li Gan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
| | - Natalie F. Sims
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
| | - Yu Rong Koh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
| | - Richard D. Webster
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
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14
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Complex I function in mitochondrial supercomplexes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:991-1000. [DOI: 10.1016/j.bbabio.2016.01.013] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/20/2016] [Accepted: 01/22/2016] [Indexed: 02/02/2023]
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15
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Impact of Antioxidants on Cardiolipin Oxidation in Liposomes: Why Mitochondrial Cardiolipin Serves as an Apoptotic Signal? OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2016; 2016:8679469. [PMID: 27313834 PMCID: PMC4899610 DOI: 10.1155/2016/8679469] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 02/29/2016] [Accepted: 03/17/2016] [Indexed: 01/08/2023]
Abstract
Molecules of mitochondrial cardiolipin (CL) get selectively oxidized upon oxidative stress, which triggers the intrinsic apoptotic pathway. In a chemical model most closely resembling the mitochondrial membrane-liposomes of pure bovine heart CL-we compared ubiquinol-10, ubiquinol-6, and alpha-tocopherol, the most widespread naturally occurring antioxidants, with man-made, quinol-based amphiphilic antioxidants. Lipid peroxidation was induced by addition of an azo initiator in the absence and presence of diverse antioxidants, respectively. The kinetics of CL oxidation was monitored via formation of conjugated dienes at 234 nm. We found that natural ubiquinols and ubiquinol-based amphiphilic antioxidants were equally efficient in protecting CL liposomes from peroxidation; the chromanol-based antioxidants, including alpha-tocopherol, were 2-3 times less efficient. Amphiphilic antioxidants, but not natural ubiquinols and alpha-tocopherol, were able, additionally, to protect the CL bilayer from oxidation by acting from the water phase. We suggest that the previously reported therapeutic efficiency of mitochondrially targeted amphiphilic antioxidants is owing to their ability to protect those CL molecules that are inaccessible to natural hydrophobic antioxidants, being trapped within respiratory supercomplexes. The high susceptibility of such occluded CL molecules to oxidation may have prompted their recruitment as apoptotic signaling molecules by nature.
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16
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Hagras MA, Hayashi T, Stuchebrukhov AA. Quantum Calculations of Electron Tunneling in Respiratory Complex III. J Phys Chem B 2015; 119:14637-51. [DOI: 10.1021/acs.jpcb.5b09424] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Muhammad A. Hagras
- Department of Chemistry, University of California, One Shields
Avenue, Davis, California 95616, United States
| | - Tomoyuki Hayashi
- Department of Chemistry, University of California, One Shields
Avenue, Davis, California 95616, United States
| | - Alexei A. Stuchebrukhov
- Department of Chemistry, University of California, One Shields
Avenue, Davis, California 95616, United States
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17
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Kinetic evidence against partitioning of the ubiquinone pool and the catalytic relevance of respiratory-chain supercomplexes. Proc Natl Acad Sci U S A 2014; 111:15735-40. [PMID: 25331896 DOI: 10.1073/pnas.1413855111] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In mitochondria, four respiratory-chain complexes drive oxidative phosphorylation by sustaining a proton-motive force across the inner membrane that is used to synthesize ATP. The question of how the densely packed proteins of the inner membrane are organized to optimize structure and function has returned to prominence with the characterization of respiratory-chain supercomplexes. Supercomplexes are increasingly accepted structural entities, but their functional and catalytic advantages are disputed. Notably, substrate "channeling" between the enzymes in supercomplexes has been proposed to confer a kinetic advantage, relative to the rate provided by a freely accessible, common substrate pool. Here, we focus on the mitochondrial ubiquinone/ubiquinol pool. We formulate and test three conceptually simple predictions of the behavior of the mammalian respiratory chain that depend on whether channeling in supercomplexes is kinetically important, and on whether the ubiquinone pool is partitioned between pathways. Our spectroscopic and kinetic experiments demonstrate how the metabolic pathways for NADH and succinate oxidation communicate and catalyze via a single, universally accessible ubiquinone/ubiquinol pool that is not partitioned or channeled. We reevaluate the major piece of contrary evidence from flux control analysis and find that the conclusion of substrate channeling arises from the particular behavior of a single inhibitor; we explain why different inhibitors behave differently and show that a robust flux control analysis provides no evidence for channeling. Finally, we discuss how the formation of respiratory-chain supercomplexes may confer alternative advantages on energy-converting membranes.
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Lokhmatikov AV, Voskoboynikova NE, Cherepanov DA, Sumbatyan NV, Korshunova GA, Skulachev MV, Steinhoff HJ, Skulachev VP, Mulkidjanian AY. Prevention of peroxidation of cardiolipin liposomes by quinol-based antioxidants. BIOCHEMISTRY (MOSCOW) 2014; 79:1081-100. [DOI: 10.1134/s0006297914100101] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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19
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Trefz T, Kabir MK, Jain R, Patrick BO, Hicks RG. Unconventional redox properties of hydroquinones with intramolecular OH−N hydrogen bonds. CAN J CHEM 2014. [DOI: 10.1139/cjc-2014-0175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The redox (chemical and electrochemical) properties of several hydroquinones are reported in which the OH protons are engaged in intramolecular hydrogen bonds to a nitrogen-based acceptor (pyridine or amine). The 1,4-hydroquinones generally undergo reversible oxidation to quinones in which both OH protons have transferred to the pendant bases; the oxidation processes are generally chemically and electrochemically reversible, in stark contrast with normal hydroquinones, which are oxidized irreversibly (via proton loss) to quinones. The oxidation processes, believed to occur in concerted proton/electron transfer steps, are at much lower potentials for the hydrogen-bonded derivatives relative to unsubstituted derivatives. In contrast, isomeric 1,3-hydroquinones (resorcinols) are oxidized irreversibly at relatively high potentials. The stability of some of the 1,4-hydroquinone oxidized species permits their isolation and characterization both spectroscopically and structurally. Somewhat surprisingly, in the oxidized species in which the proton is now located on the nitrogen base, the characterization data indicate that there is no NH−O hydrogen bond. Relationships between the particulars of the redox properties of the hydroquinones (potentials, reversibility/stability) and molecular structure are discussed.
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Affiliation(s)
- Tyler Trefz
- Department of Chemistry, University of Victoria, P.O. Box 3065 STN CSC, Victoria, BC V8W 3V6, Canada
| | - Md. Khayrul Kabir
- Department of Chemistry, University of Victoria, P.O. Box 3065 STN CSC, Victoria, BC V8W 3V6, Canada
| | - Rajsapan Jain
- Department of Chemistry, University of Victoria, P.O. Box 3065 STN CSC, Victoria, BC V8W 3V6, Canada
| | - Brian O. Patrick
- Crystallography Laboratory, Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Robin G. Hicks
- Department of Chemistry, University of Victoria, P.O. Box 3065 STN CSC, Victoria, BC V8W 3V6, Canada
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Computer modeling of electron and proton transport in chloroplasts. Biosystems 2014; 121:1-21. [PMID: 24835748 DOI: 10.1016/j.biosystems.2014.04.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 04/27/2014] [Accepted: 04/28/2014] [Indexed: 11/21/2022]
Abstract
Photosynthesis is one of the most important biological processes in biosphere, which provides production of organic substances from atmospheric CO2 and water at expense of solar energy. In this review, we contemplate computer models of oxygenic photosynthesis in the context of feedback regulation of photosynthetic electron transport in chloroplasts, the energy-transducing organelles of the plant cell. We start with a brief overview of electron and proton transport processes in chloroplasts coupled to ATP synthesis and consider basic regulatory mechanisms of oxygenic photosynthesis. General approaches to computer simulation of photosynthetic processes are considered, including the random walk models of plastoquinone diffusion in thylakoid membranes and deterministic approach to modeling electron transport in chloroplasts based on the mass action law. Then we focus on a kinetic model of oxygenic photosynthesis that includes key stages of the linear electron transport, alternative pathways of electron transfer around photosystem I (PSI), transmembrane proton transport and ATP synthesis in chloroplasts. This model includes different regulatory processes: pH-dependent control of the intersystem electron transport, down-regulation of photosystem II (PSII) activity (non-photochemical quenching), the light-induced activation of the Bassham-Benson-Calvin (BBC) cycle. The model correctly describes pH-dependent feedback control of electron transport in chloroplasts and adequately reproduces a variety of experimental data on induction events observed under different experimental conditions in intact chloroplasts (variations of CO2 and O2 concentrations in atmosphere), including a complex kinetics of P700 (primary electron donor in PSI) photooxidation, CO2 consumption in the BBC cycle, and photorespiration. Finally, we describe diffusion-controlled photosynthetic processes in chloroplasts within the framework of the model that takes into account complex architecture of chloroplasts and lateral heterogeneity of lamellar system of thylakoids. The lateral profiles of pH in the thylakoid lumen and in the narrow gap between grana thylakoids have been calculated under different metabolic conditions. Analyzing topological aspects of diffusion-controlled stages of electron and proton transport in chloroplasts, we conclude that along with the NPQ mechanism of attenuation of PSII activity and deceleration of PQH2 oxidation by the cytochrome b6f complex caused by the lumen acidification, the intersystem electron transport may be down-regulated due to the light-induced alkalization of the narrow partition between adjacent thylakoids of grana. The computer models of electron and proton transport described in this article may be integrated as appropriate modules into a comprehensive model of oxygenic photosynthesis.
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21
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Functional role of mitochondrial respiratory supercomplexes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:427-43. [DOI: 10.1016/j.bbabio.2013.11.002] [Citation(s) in RCA: 224] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 10/30/2013] [Accepted: 11/02/2013] [Indexed: 12/30/2022]
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22
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Cartron ML, Olsen JD, Sener M, Jackson PJ, Brindley AA, Qian P, Dickman MJ, Leggett GJ, Schulten K, Neil Hunter C. Integration of energy and electron transfer processes in the photosynthetic membrane of Rhodobacter sphaeroides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1769-80. [PMID: 24530865 DOI: 10.1016/j.bbabio.2014.02.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 02/03/2014] [Accepted: 02/05/2014] [Indexed: 02/04/2023]
Abstract
Photosynthesis converts absorbed solar energy to a protonmotive force, which drives ATP synthesis. The membrane network of chlorophyll-protein complexes responsible for light absorption, photochemistry and quinol (QH2) production has been mapped in the purple phototrophic bacterium Rhodobacter (Rba.) sphaeroides using atomic force microscopy (AFM), but the membrane location of the cytochrome bc1 (cytbc1) complexes that oxidise QH2 to quinone (Q) to generate a protonmotive force is unknown. We labelled cytbc1 complexes with gold nanobeads, each attached by a Histidine10 (His10)-tag to the C-terminus of cytc1. Electron microscopy (EM) of negatively stained chromatophore vesicles showed that the majority of the cytbc1 complexes occur as dimers in the membrane. The cytbc1 complexes appeared to be adjacent to reaction centre light-harvesting 1-PufX (RC-LH1-PufX) complexes, consistent with AFM topographs of a gold-labelled membrane. His-tagged cytbc1 complexes were retrieved from chromatophores partially solubilised by detergent; RC-LH1-PufX complexes tended to co-purify with cytbc1 whereas LH2 complexes became detached, consistent with clusters of cytbc1 complexes close to RC-LH1-PufX arrays, but not with a fixed, stoichiometric cytbc1-RC-LH1-PufX supercomplex. This information was combined with a quantitative mass spectrometry (MS) analysis of the RC, cytbc1, ATP synthase, cytaa3 and cytcbb3 membrane protein complexes, to construct an atomic-level model of a chromatophore vesicle comprising 67 LH2 complexes, 11 LH1-RC-PufX dimers & 2 RC-LH1-PufX monomers, 4 cytbc1 dimers and 2 ATP synthases. Simulation of the interconnected energy, electron and proton transfer processes showed a half-maximal ATP turnover rate for a light intensity equivalent to only 1% of bright sunlight. Thus, the photosystem architecture of the chromatophore is optimised for growth at low light intensities.
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Affiliation(s)
- Michaël L Cartron
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - John D Olsen
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Melih Sener
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Philip J Jackson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK; ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - Amanda A Brindley
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Pu Qian
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Mark J Dickman
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - Graham J Leggett
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, UK
| | - Klaus Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
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Analysis of the kinetics and bistability of ubiquinol:cytochrome c oxidoreductase. Biophys J 2014; 105:343-55. [PMID: 23870256 DOI: 10.1016/j.bpj.2013.05.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 03/28/2013] [Accepted: 05/13/2013] [Indexed: 11/21/2022] Open
Abstract
Ubiquinol:cytochrome c oxidoreductase, bc1 complex, is the enzyme in the respiratory chain of mitochondria responsible for the transfer reducing potential from ubiquinol to cytochrome c coupled to the movement of charge against the electrostatic potential across the mitochondrial inner membrane. The complex is also implicated in the generation of reactive oxygen species under certain conditions and is thus a contributor to cellular oxidative stress. Here, a biophysically detailed, thermodynamically consistent model of the bc1 complex for mammalian mitochondria is developed. The model incorporates the major redox centers near the Qo- and Qi-site of the enzyme, includes the pH-dependent redox reactions, accounts for the effect of the proton-motive force of the reaction rate, and simulates superoxide production at the Qo-site. The model consists of six distinct states characterized by the mobile electron distribution in the enzyme. Within each state, substates that correspond to various electron localizations exist in a rapid equilibrium distribution. The steady-state equation for the six-state system is parameterized using five independent data sets and validated in comparison to additional experimental data. Model analysis suggests that the pH-dependence on turnover is primarily due to the pKa values of cytochrome bH and Rieske iron sulfur protein. A previously proposed kinetic scheme at the Qi-site where ubiquinone binds to only the reduced enzyme and ubiquinol binds to only the oxidized enzyme is shown to be thermodynamically infeasible. Moreover, the model is able to reproduce the bistability phenomenon where at a given overall flux through the enzyme, different rates of superoxide production are attained when the enzyme is differentially reduced.
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Antal TK, Kovalenko IB, Rubin AB, Tyystjärvi E. Photosynthesis-related quantities for education and modeling. PHOTOSYNTHESIS RESEARCH 2013; 117:1-30. [PMID: 24162971 DOI: 10.1007/s11120-013-9945-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Accepted: 10/07/2013] [Indexed: 05/24/2023]
Abstract
A quantitative understanding of the photosynthetic machinery depends largely on quantities, such as concentrations, sizes, absorption wavelengths, redox potentials, and rate constants. The present contribution is a collection of numbers and quantities related mainly to photosynthesis in higher plants. All numbers are taken directly from a literature or database source and the corresponding reference is provided. The numerical values, presented in this paper, provide ranges of values, obtained in specific experiments for specific organisms. However, the presented numbers can be useful for understanding the principles of structure and function of photosynthetic machinery and for guidance of future research.
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Affiliation(s)
- Taras K Antal
- Biological Faculty, Moscow State University, Vorobyevi Gory, 119992, Moscow, Russia
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25
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Nedielkov R, Steffen W, Steuber J, Möller HM. NMR reveals double occupancy of quinone-type ligands in the catalytic quinone binding site of the Na+-translocating NADH:Quinone oxidoreductase from Vibrio cholerae. J Biol Chem 2013; 288:30597-30606. [PMID: 24003222 DOI: 10.1074/jbc.m112.435750] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The sodium ion-translocating NADH:quinone oxidoreductase (Na(+)-NQR) from the pathogen Vibrio cholerae exploits the free energy liberated during oxidation of NADH with ubiquinone to pump sodium ions across the cytoplasmic membrane. The Na(+)-NQR consists of four membrane-bound subunits NqrBCDE and the peripheral NqrF and NqrA subunits. NqrA binds ubiquinone-8 as well as quinones with shorter prenyl chains (ubiquinone-1 and ubiquinone-2). Here we show that the quinone derivative 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB), a known inhibitor of the bc1 and b6f complexes found in mitochondria and chloroplasts, also inhibits quinone reduction by the Na(+)-NQR in a mixed inhibition mode. Tryptophan fluorescence quenching and saturation transfer difference NMR experiments in the presence of Na(+)-NQR inhibitor (DBMIB or 2-n-heptyl-4-hydroxyquinoline N-oxide) indicate that two quinone analog ligands are bound simultaneously by the NqrA subunit with very similar interaction constants as observed with the holoenzyme complex. We conclude that the catalytic site of quinone reduction is located on NqrA. The two ligands bind to an extended binding pocket in direct vicinity to each other as demonstrated by interligand Overhauser effects between ubiquinone-1 and DBMIB or 2-n-heptyl-4-hydroxyquinoline N-oxide, respectively. We propose that a similar spatially close arrangement of the native quinone substrates is also operational in vivo, enhancing the catalytic efficiency during the final electron transfer steps in the Na(+)-NQR.
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Affiliation(s)
- Ruslan Nedielkov
- From the Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany and
| | - Wojtek Steffen
- the Department of Microbiology, University of Hohenheim (Stuttgart), 70599 Stuttgart, Germany
| | - Julia Steuber
- the Department of Microbiology, University of Hohenheim (Stuttgart), 70599 Stuttgart, Germany.
| | - Heiko M Möller
- From the Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany and.
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26
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Efremov RG, Sazanov LA. The coupling mechanism of respiratory complex I — A structural and evolutionary perspective. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1785-95. [DOI: 10.1016/j.bbabio.2012.02.015] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 02/09/2012] [Accepted: 02/14/2012] [Indexed: 11/27/2022]
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27
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Verkhovskaya M, Bloch DA. Energy-converting respiratory Complex I: on the way to the molecular mechanism of the proton pump. Int J Biochem Cell Biol 2012; 45:491-511. [PMID: 22982742 DOI: 10.1016/j.biocel.2012.08.024] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 08/27/2012] [Accepted: 08/28/2012] [Indexed: 12/16/2022]
Abstract
In respiring organisms the major energy transduction flux employs the transmembrane electrochemical proton gradient as a physical link between exergonic redox reactions and endergonic ADP phosphorylation. Establishing the gradient involves electrogenic, transmembrane H(+) translocation by the membrane-embedded respiratory complexes. Among others, Complex I (NADH:ubiquinone oxidoreductase) is the most structurally complex and functionally enigmatic respiratory enzyme; its molecular mechanism is as yet unknown. Here we highlight recent progress and discuss the catalytic events during Complex I turnover in relation to their role in energy conversion and to the enzyme structure.
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Affiliation(s)
- Marina Verkhovskaya
- Helsinki Bioenergetics Group, Institute of Biotechnology, PO Box 65 (Viikinkaari 1) FIN-00014 University of Helsinki, Finland.
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28
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Baymann F, Schoepp-Cothenet B, Lebrun E, van Lis R, Nitschke W. Phylogeny of Rieske/cytb complexes with a special focus on the Haloarchaeal enzymes. Genome Biol Evol 2012; 4:720-9. [PMID: 22798450 PMCID: PMC3509893 DOI: 10.1093/gbe/evs056] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Rieske/cytochrome b (Rieske/cytb) complexes are proton pumping quinol oxidases that are present in most bacteria and Archaea. The phylogeny of their subunits follows closely the 16S-rRNA phylogeny, indicating that chemiosmotic coupling was already present in the last universal common ancestor of Archaea and bacteria. Haloarchaea are the only organisms found so far that acquired Rieske/cytb complexes via interdomain lateral gene transfer. They encode two Rieske/cytb complexes in their genomes; one of them is found in genetic context with nitrate reductase genes and has its closest relatives among Actinobacteria and the Thermus/Deinococcus group. It is likely to function in nitrate respiration. The second Rieske/cytb complex of Haloarchaea features a split cytochrome b sequence as do Cyanobacteria, chloroplasts, Heliobacteria, and Bacilli. It seems that Haloarchaea acquired this complex from an ancestor of the above-mentioned phyla. Its involvement in the bioenergetic reaction chains of Haloarchaea is unknown. We present arguments in favor of the hypothesis that the ancestor of Haloarchaea, which relied on a highly specialized bioenergetic metabolism, that is, methanogenesis, and was devoid of quinones and most enzymes of anaerobic or aerobic bioenergetic reaction chains, integrated laterally transferred genes into its genome to respond to a change in environmental conditions that made methanogenesis unfavorable.
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29
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Hirosawa S, Arai S, Takeoka S. A TEMPO-conjugated fluorescent probe for monitoring mitochondrial redox reactions. Chem Commun (Camb) 2012; 48:4845-7. [PMID: 22506265 DOI: 10.1039/c2cc30603d] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a mitochondrial targeted redox probe (MitoRP) that comprises a nitroxide radical (TEMPO) moiety and coumarin 343. Using isolated mitochondria in the presence/absence of substrates and inhibitors of oxidative phosphorylation, we demonstrated that MitoRP is a useful probe to monitor the electron flow associated with complex I.
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Affiliation(s)
- Shota Hirosawa
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University (TWIns), Tokyo 162-8480, Japan
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30
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Fusing proteins as an approach to study bioenergetic enzymes and processes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1847-51. [PMID: 22484274 DOI: 10.1016/j.bbabio.2012.03.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 03/21/2012] [Accepted: 03/22/2012] [Indexed: 11/21/2022]
Abstract
Fusing proteins is an attractive genetic tool used in several biochemical and biophysical investigations. Within a group of redox proteins, certain fusion constructs appear to provide valuable templates for spectroscopy with which specific bioenergetic questions can be addressed. Here we briefly summarize three different cases of fusions reported for bacterial cytochrome bc(1) (prokaryotic equivalent of mitochondrial respiratory complex III), a common component of electron transport chains. These fusions were used to study supramolecular organization of enzymatic complexes in bioenergetic membrane, influence of the accessory subunits on the activity and stability of the complex, and molecular mechanism of operation of the enzyme in the context of its dimeric structure. Besides direct connotation to molecular bioenergetics, these fusions also appeared interesting from the protein design, biogenesis, and assembly points of view. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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31
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Stoichiometry of proton translocation by respiratory complex I and its mechanistic implications. Proc Natl Acad Sci U S A 2012; 109:4431-6. [PMID: 22392981 DOI: 10.1073/pnas.1120949109] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Complex I (NADH-ubiquinone oxidoreductase) in the respiratory chain of mitochondria and several bacteria functions as a redox-driven proton pump that contributes to the generation of the protonmotive force across the inner mitochondrial or bacterial membrane and thus to the aerobic synthesis of ATP. The stoichiometry of proton translocation is thought to be 4 H(+) per NADH oxidized (2 e(-)). Here we show that a H(+)/2 e(-) ratio of 3 appears more likely on the basis of the recently determined H(+)/ATP ratio of the mitochondrial F(1)F(o)-ATP synthase of animal mitochondria and of a set of carefully determined ATP/2 e(-) ratios for different segments of the mitochondrial respiratory chain. This lower H(+)/2 e(-) ratio of 3 is independently supported by thermodynamic analyses of experiments with both mitochondria and submitochondrial particles. A reduced H(+)/2 e(-) stoichiometry of 3 has important mechanistic implications for this proton pump. In a rough mechanistic model, we suggest a concerted proton translocation mechanism in the three homologous and tightly packed antiporter-like subunits L, M, and N of the proton-translocating membrane domain of complex I.
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32
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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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Questioning the functional relevance of mitochondrial supercomplexes by time-resolved analysis of the respiratory chain. Proc Natl Acad Sci U S A 2011; 108:E1027-34. [PMID: 22011573 DOI: 10.1073/pnas.1109510108] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Mitochondria are the powerhouses of eukaryotic cells as they feed metabolism with its major substrate. Oxidative-phosphorylation relies on the generation, by an electron/proton transfer chain, of an electrochemical transmembrane potential utilized to synthesize ATP. Although these fundamental principles are not a matter of debate, the emerging picture of the respiratory chain diverges from the linear and fluid scheme. Indeed, a growing number of pieces of evidence point to membrane compartments that possibly restrict the diffusion of electron carriers, and to supramolecular assembly of various complexes within various kinds of supercomplexes that modulate the thermodynamic and kinetic properties of the components of the chain. Here, we describe a method that allows the unprecedented time-resolved study of the respiratory chain in intact cells that is aimed at assessing these hypotheses. We show that, in yeast, cytochrome c is not trapped within supercomplexes and encounters no particular restriction to its diffusion which questions the functional relevance of these supramolecular edifices.
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34
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A two-state stabilization-change mechanism for proton-pumping complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1364-9. [DOI: 10.1016/j.bbabio.2011.04.006] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2011] [Revised: 04/17/2011] [Accepted: 04/19/2011] [Indexed: 11/18/2022]
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35
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Castellani M, Havens J, Kleinschroth T, Millett F, Durham B, Malatesta F, Ludwig B. The acidic domain of cytochrome c₁ in paracoccus denitrificans, analogous to the acidic subunits in eukaryotic bc₁ complexes, is not involved in the electron transfer reaction to its native substrate cytochrome c(552). BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1383-9. [PMID: 21856278 DOI: 10.1016/j.bbabio.2011.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 08/03/2011] [Accepted: 08/05/2011] [Indexed: 11/19/2022]
Abstract
The cytochrome bc(1) complex is a key component in several respiratory pathways. One of the characteristics of the eukaryotic complex is the presence of a small acidic subunit, which is thought to guide the interaction of the complex with its electron acceptor and facilitate electron transfer. Paracoccus denitrificans represents the only example of a prokaryotic organism in which a highly acidic domain is covalently fused to the cytochrome c(1) subunit. In this work, a deletion variant lacking this acidic domain has been produced and purified by affinity chromatography. The complex is fully intact as shown by its X-ray structure, and is a dimer (Kleinschroth et al., subm.) compared to the tetrameric (dimer-of-dimer) state of the wild-type. The variant complex is studied by steady-state kinetics and flash photolysis, showing wild type turnover and a virtually identical interaction with its substrate cytochrome c(552).
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Affiliation(s)
- Michela Castellani
- Institute of Biochemistry, Molecular Genetics, Goethe University, D-60438 Frankfurt am Main and Cluster of Excellence "Macromolecular Complexes" (CEF-MC), D-60438 Frankfurt am Main, Germany
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36
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De los Rios Castillo D, Zarco-Zavala M, Olvera-Sanchez S, Pardo JP, Juarez O, Martinez F, Mendoza-Hernandez G, García-Trejo JJ, Flores-Herrera O. Atypical cristae morphology of human syncytiotrophoblast mitochondria: role for complex V. J Biol Chem 2011; 286:23911-9. [PMID: 21572045 DOI: 10.1074/jbc.m111.252056] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mitochondrial complexes I, III(2), and IV from human cytotrophoblast and syncytiotrophoblast associate to form supercomplexes or respirasomes, with the following stoichiometries: I(1):(III(2))(1) and I(1):(III(2))(1-2):IV(1-4). The content of respirasomes was similar in both cell types after isolating mitochondria. However, syncytiotrophoblast mitochondria possess low levels of dimeric complex V and do not have orthodox cristae morphology. In contrast, cytotrophoblast mitochondria show normal cristae morphology and a higher content of ATP synthase dimer. Consistent with the dimerizing role of the ATPase inhibitory protein (IF(1)) (García, J. J., Morales-Ríos, E., Cortés-Hernandez, P., and Rodríguez-Zavala, J. S. (2006) Biochemistry 45, 12695-12703), higher relative amounts of IF(1) were observed in cytotrophoblast when compared with syncytiotrophoblast mitochondria. Therefore, there is a correlation between dimerization of complex V, IF(1) expression, and the morphology of mitochondrial cristae in human placental mitochondria. The possible relationship between cristae architecture and the physiological function of the syncytiotrophoblast mitochondria is discussed.
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Affiliation(s)
- Daniela De los Rios Castillo
- Department of Biochemistry and Molecular Biology, Medicine Faculty, National Autonomous University of Mexico, 04510 Mexico City, Mexico
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Lee DW, El Khoury Y, Francia F, Zambelli B, Ciurli S, Venturoli G, Hellwig P, Daldal F. Zinc inhibition of bacterial cytochrome bc(1) reveals the role of cytochrome b E295 in proton release at the Q(o) site. Biochemistry 2011; 50:4263-72. [PMID: 21500804 DOI: 10.1021/bi200230e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cytochrome (cyt) bc(1) complex (cyt bc(1)) plays a major role in the electrogenic extrusion of protons across the membrane responsible for the proton motive force to produce ATP. Proton-coupled electron transfer underlying the catalysis of cyt bc(1) is generally accepted, but the molecular basis of coupling and associated proton efflux pathway(s) remains unclear. Herein we studied Zn(2+)-induced inhibition of Rhodobacter capsulatus cyt bc(1) using enzyme kinetics, isothermal titration calorimetry (ITC), and electrochemically induced Fourier transform infrared (FTIR) difference spectroscopy with the purpose of understanding the Zn(2+) binding mechanism and its inhibitory effect on cyt bc(1) function. Analogous studies were conducted with a mutant of cyt b, E295, a residue previously proposed to bind Zn(2+) on the basis of extended X-ray absorption fine-structure spectroscopy. ITC analysis indicated that mutation of E295 to valine, a noncoordinating residue, results in a decrease in Zn(2+) binding affinity. The kinetic study showed that wild-type cyt bc(1) and its E295V mutant have similar levels of apparent K(m) values for decylbenzohydroquinone as a substrate (4.9 ± 0.2 and 3.1 ± 0.4 μM, respectively), whereas their K(I) values for Zn(2+) are 8.3 and 38.5 μM, respectively. The calorimetry-based K(D) values for the high-affinity site of cyt bc(1) are on the same order of magnitude as the K(I) values derived from the kinetic analysis. Furthermore, the FTIR signal of protonated acidic residues was perturbed in the presence of Zn(2+), whereas the E295V mutant exhibited no significant change in electrochemically induced FTIR difference spectra measured in the presence and absence of Zn(2+). Our overall results indicate that the proton-active E295 residue near the Q(o) site of cyt bc(1) can bind directly to Zn(2+), resulting in a decrease in the electron transferring activity without changing drastically the redox potentials of the cofactors of the enzyme. We conclude that E295 is involved in proton efflux coupled to electron transfer at the Q(o) site of cyt bc(1).
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Affiliation(s)
- Dong-Woo Lee
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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Chien LF, Wu YC, Chen HP. Mitochondrial energy metabolism in young bamboo rhizomes from Bambusa oldhamii and Phyllostachys edulis during shooting stage. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2011; 49:449-457. [PMID: 21334908 DOI: 10.1016/j.plaphy.2011.01.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 01/13/2011] [Accepted: 01/24/2011] [Indexed: 05/30/2023]
Abstract
The energy metabolism of mitochondria in young rhizomes of the bamboo species Bambusa oldhamii, which favors shooting during the summer, and Phyllostachys edulis, which favors shooting during the winter, was characterized. The mitochondrial energy-converting system was clarified in terms of respiratory activity and structural organization. The respiration rates were measured at 15, 28, and 42 °C by NADH, succinate, and malate oxidation. NADH was shown to act as an efficient substrate regardless of the temperature. The structural organization of functional mitochondrial respiratory supercomplexes was studied using blue native PAGE and in-gel activity staining. In both species, almost 90% of the total complex I was assembled into supercomplexes, and P. edulis contained a greater amount of complex-I-comprising supercomplexes than B. oldhamii. Approximately 50% of complex III and 75% of complex V were included in supercomplexes, whereas P. edulis mitochondria possessed a greater amount of complex-V-comprising supercomplexes. The alternative oxidase (AOX), plant mitochondrial uncoupling protein (PUCP), plant mitochondrial potassium channel (PmitoK(ATP)), rotenone-insensitive external/internal NADH:ubiquinone oxidoreductase [NDH(e/i)], and superoxide dismutase (SOD) activities of the energy-dissipating systems were investigated. P. edulis mitochondria had higher levels of the PUCP1 and AOX1 proteins than B. oldhamii mitochondria. The activity of PmitoK(ATP) in P. edulis was higher than that in B. oldhamii. However, P. edulis mitochondria possessed lower NDH(e/i) and SOD activities than B. oldhamii mitochondria. The results suggest that the adaptation of P. edulis to a cooler environment may correlate with its greater abundance of functional mitochondrial supercomplexes and the higher energy-dissipating capacity of its AOX, PUCP and PmitoK(ATP) relative to B. oldhamii.
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Affiliation(s)
- Lee-Feng Chien
- Department of Life Sciences, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan.
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Treberg JR, Brand MD. A model of the proton translocation mechanism of complex I. J Biol Chem 2011; 286:17579-84. [PMID: 21454533 DOI: 10.1074/jbc.m111.227751] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Despite decades of speculation, the proton pumping mechanism of complex I (NADH-ubiquinone oxidoreductase) is unknown and continues to be controversial. Recent descriptions of the architecture of the hydrophobic region of complex I have resolved one vital issue: this region appears to have multiple proton transporters that are mechanically interlinked. Thus, transduction of conformational changes to drive the transmembrane transporters linked by a "connecting rod" during the reduction of ubiquinone (Q) can account for two or three of the four protons pumped per NADH oxidized. The remaining proton(s) must be pumped by direct coupling at the Q-binding site. Here, we present a mixed model based on a crucial constraint: the strong dependence on the pH gradient across the membrane (ΔpH) of superoxide generation at the Q-binding site of complex I. This model combines direct and indirect coupling mechanisms to account for the pumping of the four protons. It explains the observed properties of the semiquinone in the Q-binding site, the rapid superoxide production from this site during reverse electron transport, its low superoxide production during forward electron transport except in the presence of inhibitory Q-analogs and high protonmotive force, and the strong dependence of both modes of superoxide production on ΔpH.
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Affiliation(s)
- Jason R Treberg
- Buck Institute for Research on Aging, Novato, California 94945, USA.
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Ivanov BN. Cooperation of photosystem I with the plastoquinone pool in oxygen reduction in higher plant chloroplasts. BIOCHEMISTRY (MOSCOW) 2011; 73:112-8. [DOI: 10.1134/s0006297908010173] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lemmer C, Bouvet M, Meunier-Prest R. Proton coupled electron transfer of ubiquinone Q2 incorporated in a self-assembled monolayer. Phys Chem Chem Phys 2011; 13:13327-32. [DOI: 10.1039/c0cp02700f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Wu J, Bauer CE. RegB kinase activity is controlled in part by monitoring the ratio of oxidized to reduced ubiquinones in the ubiquinone pool. mBio 2010; 1:e00272-10. [PMID: 21157513 PMCID: PMC3000548 DOI: 10.1128/mbio.00272-10] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 11/10/2010] [Indexed: 01/08/2023] Open
Abstract
RegB is a membrane-spanning sensor kinase responsible for redox regulation of a wide variety of metabolic processes in numerous proteobacterial species. Here we show that full-length RegB purified from Escherichia coli membranes contains bound ubiquinone. Four conserved residues in the membrane-spanning domain of RegB are shown to have important roles in ubiquinone binding in vitro and redox sensing in vivo. Isothermal titration calorimetry measurements, coupled with kinase assays under oxidizing and reducing conditions, indicate that RegB weakly binds both oxidized ubiquinone and reduced ubiquinone (ubiquinol) with nearly equal affinity and that oxidized ubiquinone inhibits kinase activity without promoting a redox reaction. We propose a model in which ubiquinone/ubiquinol bound to RegB readily equilibrates with ubiquinones/ubiquinols in the membrane, allowing the kinase activity to be tuned by the redox state of the ubiquinone pool. This noncatalytic role of ubiquinone in controlling RegB activity is distinct from that of other known ubiquinone-binding proteins, which use ubiquinone as an electron donor or acceptor.
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Affiliation(s)
- Jiang Wu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
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Song Y, Buettner GR. Thermodynamic and kinetic considerations for the reaction of semiquinone radicals to form superoxide and hydrogen peroxide. Free Radic Biol Med 2010; 49:919-62. [PMID: 20493944 PMCID: PMC2936108 DOI: 10.1016/j.freeradbiomed.2010.05.009] [Citation(s) in RCA: 224] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 05/10/2010] [Accepted: 05/12/2010] [Indexed: 10/19/2022]
Abstract
The quinone/semiquinone/hydroquinone triad (Q/SQ(*-)/H(2)Q) represents a class of compounds that has great importance in a wide range of biological processes. The half-cell reduction potentials of these redox couples in aqueous solutions at neutral pH, E degrees ', provide a window to understanding the thermodynamic and kinetic characteristics of this triad and their associated chemistry and biochemistry in vivo. Substituents on the quinone ring can significantly influence the electron density "on the ring" and thus modify E degrees' dramatically. E degrees' of the quinone governs the reaction of semiquinone with dioxygen to form superoxide. At near-neutral pH the pK(a)'s of the hydroquinone are outstanding indicators of the electron density in the aromatic ring of the members of these triads (electrophilicity) and thus are excellent tools to predict half-cell reduction potentials for both the one-electron and two-electron couples, which in turn allow estimates of rate constants for the reactions of these triads. For example, the higher the pK(a)'s of H(2)Q, the lower the reduction potentials and the higher the rate constants for the reaction of SQ(*-) with dioxygen to form superoxide. However, hydroquinone autoxidation is controlled by the concentration of di-ionized hydroquinone; thus, the lower the pK(a)'s the less stable H(2)Q to autoxidation. Catalysts, e.g., metals and quinone, can accelerate oxidation processes; by removing superoxide and increasing the rate of formation of quinone, superoxide dismutase can accelerate oxidation of hydroquinones and thereby increase the flux of hydrogen peroxide. The principal reactions of quinones are with nucleophiles via Michael addition, for example, with thiols and amines. The rate constants for these addition reactions are also related to E degrees'. Thus, pK(a)'s of a hydroquinone and E degrees ' are central to the chemistry of these triads.
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Affiliation(s)
- Yang Song
- College of Pharmaceutical Sciences, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Southwest University, Chongqing, 400715, People's Republic of China
- Free Radical and Radiation Biology Program, The University of Iowa, Iowa City, IA 52242-1181, USA
| | - Garry R. Buettner
- Free Radical and Radiation Biology Program, The University of Iowa, Iowa City, IA 52242-1181, USA
- Human Toxicology Program, The University of Iowa, Iowa City, IA 52242-1181, USA
- Corresponding author. Free Radical and Radiation Biology, ESR Facility, Med Labs B180, The University of Iowa Iowa City, IA 52242-1181. Fax: +1 319 335 8039. (G.R. Buettner)
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Hsueh KL, Westler WM, Markley JL. NMR investigations of the Rieske protein from Thermus thermophilus support a coupled proton and electron transfer mechanism. J Am Chem Soc 2010; 132:7908-18. [PMID: 20496909 PMCID: PMC2882753 DOI: 10.1021/ja1026387] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The Rieske protein component of the cytochrome bc complex contains a [2Fe−2S] cluster ligated by two cysteines and two histidines. We report here the pKa values of each of the imidazole rings of the two ligating histidines (His134 and His154) in the oxidized and reduced states of the Rieske protein from Thermus thermophilus (TtRp) as determined by NMR spectroscopy. Knowledge of these pKa values is of critical interest because of their pertinence to the mechanism of electron and proton transfer in the bifurcated Q-cycle. Although we earlier had observed the pH dependence of a 15N NMR signal from each of the two ligand histidines in oxidized TtRp (Lin, I. J.; Chen, Y.; Fee, J. A.; Song, J.; Westler, W. M.; Markley, J. L.J. Am. Chem. Soc.2006, 132, 10672−10673), the strong paramagnetism of the [2Fe−2S] cluster prevented the assignment of these signals by conventional methods. Our approach here was to take advantage of the unique histidine−leucine (His134−Leu135) sequence and to use residue-selective labeling to establish a key sequence-specific assignment, which was then extended. Analysis of the pH dependence of assigned 13C′, 13Cα, and 15Nε2 signals from the two histidine cluster ligands led to unambiguous assignment of the pKa values of oxidized and reduced TtRp. The results showed that the pKa of His134 changes from 9.1 in oxidized to ∼12.3 in reduced TtRp, whereas the pKa of His154 changes from 7.4 in oxidized to ∼12.6 in reduced TtRp. This establishes His154, which is close to the quinone when the Rieske protein is in the cytochrome b site, as the residue experiencing the remarkable redox-dependent pKa shift. Secondary structural analysis of oxidized and reduced TtRp based upon our extensive chemical shift assignments rules out a large conformational change between the oxidized and reduced states. Therefore, TtRp likely translocates between the cytochrome b and cytochrome c sites by passive diffusion. Our results are most consistent with a mechanism involving the coupled transfer of an electron and transfer of the proton across the hydrogen bond between the hydroquinone and His154 at the cytochrome b site.
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Affiliation(s)
- Kuang-Lung Hsueh
- Graduate Program in Biophysics, 433 Babcock Drive, University of Wisconsin, Madison, Wisconsin 53706, USA
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Selivanov VA, Votyakova TV, Zeak JA, Trucco M, Roca J, Cascante M. Bistability of mitochondrial respiration underlies paradoxical reactive oxygen species generation induced by anoxia. PLoS Comput Biol 2009; 5:e1000619. [PMID: 20041200 PMCID: PMC2789320 DOI: 10.1371/journal.pcbi.1000619] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Accepted: 11/17/2009] [Indexed: 11/18/2022] Open
Abstract
Increased production of reactive oxygen species (ROS) in mitochondria underlies major systemic diseases, and this clinical problem stimulates a great scientific interest in the mechanism of ROS generation. However, the mechanism of hypoxia-induced change in ROS production is not fully understood. To mathematically analyze this mechanism in details, taking into consideration all the possible redox states formed in the process of electron transport, even for respiratory complex III, a system of hundreds of differential equations must be constructed. Aimed to facilitate such tasks, we developed a new methodology of modeling, which resides in the automated construction of large sets of differential equations. The detailed modeling of electron transport in mitochondria allowed for the identification of two steady state modes of operation (bistability) of respiratory complex III at the same microenvironmental conditions. Various perturbations could induce the transition of respiratory chain from one steady state to another. While normally complex III is in a low ROS producing mode, temporal anoxia could switch it to a high ROS producing state, which persists after the return to normal oxygen supply. This prediction, which we qualitatively validated experimentally, explains the mechanism of anoxia-induced cell damage. Recognition of bistability of complex III operation may enable novel therapeutic strategies for oxidative stress and our method of modeling could be widely used in systems biology studies. The levels of reactive oxygen species (ROS) that are generated as a side product of mitochondrial respiratory electron transport largely define the extent of oxidative stress in living cells. Free radicals formed in electron transport, such as ubisemiquinone, could pass their non-paired electron directly to oxygen, thus producing superoxide radical that gives rise to a variety of ROS. It is well known in clinical practice that upon recommencing oxygen supply after anoxia a tissue produces much more ROS than before the anoxia, and the state of high ROS production is stable. The mechanism of switching from low to high ROS production by temporal anoxia was unknown, in part because of the lack of detailed mathematical description of hundreds of redox states of respiratory complexes, which are formed in the process of electron transport. A new methodology of automated construction of large systems of differential equations allowed us to describe the system in detail and predicts that the mechanism of paradoxical effect of anoxia-reoxygenation could be defined by the properties of complex III of mitochondrial respiratory chain. Our experiments confirmed that the effect of hypoxia-reoxygenation is confined by intramitochondrial processes since it is observed in isolated mitochondria.
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Affiliation(s)
- Vitaly A. Selivanov
- Departament de Bioquimica i Biologia Molecular, Facultat de Biologia, Institut de Biomedicina at Universitat de Barcelona IBUB and IDIBAPS Hospital Clinic, Barcelona, Catalunya, Spain
- Hospital Clínic, IDIBAPS, CIBERES; Universitat de Barcelona, Barcelona, Catalunya, Spain
- A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Tatyana V. Votyakova
- Department of Pediatrics, The University of Pittsburgh School of Medicine and The Children's Hospital of Pittsburgh, Diabetes Institute, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (TVV); (MC)
| | - Jennifer A. Zeak
- Department of Pediatrics, The University of Pittsburgh School of Medicine and The Children's Hospital of Pittsburgh, Diabetes Institute, Pittsburgh, Pennsylvania, United States of America
| | - Massimo Trucco
- Department of Pediatrics, The University of Pittsburgh School of Medicine and The Children's Hospital of Pittsburgh, Diabetes Institute, Pittsburgh, Pennsylvania, United States of America
| | - Josep Roca
- Hospital Clínic, IDIBAPS, CIBERES; Universitat de Barcelona, Barcelona, Catalunya, Spain
| | - Marta Cascante
- Departament de Bioquimica i Biologia Molecular, Facultat de Biologia, Institut de Biomedicina at Universitat de Barcelona IBUB and IDIBAPS Hospital Clinic, Barcelona, Catalunya, Spain
- * E-mail: (TVV); (MC)
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Abstract
Complex I (NADH:quinone oxidoreductase) is crucial to respiration in many aerobic organisms. In mitochondria, it oxidizes NADH (to regenerate NAD+ for the tricarboxylic acid cycle and fatty-acid oxidation), reduces ubiquinone (the electrons are ultimately used to reduce oxygen to water) and transports protons across the mitochondrial inner membrane (to produce and sustain the protonmotive force that supports ATP synthesis and transport processes). Complex I is also a major contributor to reactive oxygen species production in the cell. Understanding the mechanisms of energy transduction and reactive oxygen species production by complex I is not only a significant intellectual challenge, but also a prerequisite for understanding the roles of complex I in disease, and for the development of effective therapies. One approach to defining a complicated reaction mechanism is to break it down into manageable parts that can be tackled individually, before being recombined and integrated to produce the complete picture. Thus energy transduction by complex I comprises NADH oxidation by a flavin mononucleotide, intramolecular electron transfer from the flavin to bound quinone along a chain of iron–sulfur clusters, quinone reduction and proton translocation. More simply, molecular oxygen is reduced by the flavin, to form the reactive oxygen species superoxide and hydrogen peroxide. The present review summarizes and evaluates experimental data that pertain to the reaction mechanisms of complex I, and describes and discusses contemporary mechanistic hypotheses, proposals and models.
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Lhee S, Kolling DRJ, Nair SK, Dikanov SA, Crofts AR. Modifications of protein environment of the [2Fe-2S] cluster of the bc1 complex: effects on the biophysical properties of the rieske iron-sulfur protein and on the kinetics of the complex. J Biol Chem 2009; 285:9233-48. [PMID: 20023300 DOI: 10.1074/jbc.m109.043505] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The rate-determining step in the overall turnover of the bc(1) complex is electron transfer from ubiquinol to the Rieske iron-sulfur protein (ISP) at the Q(o)-site. Structures of the ISP from Rhodobacter sphaeroides show that serine 154 and tyrosine 156 form H-bonds to S-1 of the [2Fe-2S] cluster and to the sulfur atom of the cysteine liganding Fe-1 of the cluster, respectively. These are responsible in part for the high potential (E(m)(,7) approximately 300 mV) and low pK(a) (7.6) of the ISP, which determine the overall reaction rate of the bc(1) complex. We have made site-directed mutations at these residues, measured thermodynamic properties using protein film voltammetry to evaluate the E(m) and pK(a) values of ISPs, explored the local proton environment through two-dimensional electron spin echo envelope modulation, and characterized function in strains S154T, S154C, S154A, Y156F, and Y156W. Alterations in reaction rate were investigated under conditions in which concentration of one substrate (ubiquinol or ISP(ox)) was saturating and the other was varied, allowing calculation of kinetic terms and relative affinities. These studies confirm that H-bonds to the cluster or its ligands are important determinants of the electrochemical characteristics of the ISP, likely through electron affinity of the interacting atom and the geometry of the H-bonding neighborhood. The calculated parameters were used in a detailed Marcus-Brønsted analysis of the dependence of rate on driving force and pH. The proton-first-then-electron model proposed accounts naturally for the effects of mutation on the overall reaction.
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Affiliation(s)
- Sangmoon Lhee
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, USA
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Castellani M, Covian R, Kleinschroth T, Anderka O, Ludwig B, Trumpower BL. Direct demonstration of half-of-the-sites reactivity in the dimeric cytochrome bc1 complex: enzyme with one inactive monomer is fully active but unable to activate the second ubiquinol oxidation site in response to ligand binding at the ubiquinone reduction site. J Biol Chem 2009; 285:502-10. [PMID: 19892700 DOI: 10.1074/jbc.m109.072959] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We previously proposed that the dimeric cytochrome bc(1) complex exhibits half-of-the-sites reactivity for ubiquinol oxidation and rapid electron transfer between bc(1) monomers (Covian, R., Kleinschroth, T., Ludwig, B., and Trumpower, B. L. (2007) J. Biol. Chem. 282, 22289-22297). Here, we demonstrate the previously proposed half-of-the-sites reactivity and intermonomeric electron transfer by characterizing the kinetics of ubiquinol oxidation in the dimeric bc(1) complex from Paracoccus denitrificans that contains an inactivating Y147S mutation in one or both cytochrome b subunits. The enzyme with a Y147S mutation in one cytochrome b subunit was catalytically fully active, whereas the activity of the enzyme with a Y147S mutation in both cytochrome b subunits was only 10-16% of that of the enzyme with fully wild-type or heterodimeric cytochrome b subunits. Enzyme with one inactive cytochrome b subunit was also indistinguishable from the dimer with two wild-type cytochrome b subunits in rate and extent of reduction of cytochromes b and c(1) by ubiquinol under pre-steady-state conditions in the presence of antimycin. However, the enzyme with only one mutated cytochrome b subunit did not show the stimulation in the steady-state rate that was observed in the wild-type dimeric enzyme at low concentrations of antimycin, confirming that the half-of-the-sites reactivity for ubiquinol oxidation can be regulated in the wild-type dimer by binding of inhibitor to one ubiquinone reduction site.
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Affiliation(s)
- Michela Castellani
- Institute of Biochemistry, Molecular Genetics, Goethe University and Cluster of Excellence Macromolecular Complexes Frankfurt am Main, D-60438 Frankfurt am Main, Germany
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Lenaz G, Genova ML. Structural and functional organization of the mitochondrial respiratory chain: a dynamic super-assembly. Int J Biochem Cell Biol 2009; 41:1750-1772. [PMID: 19711505 DOI: 10.1016/j.biocel.2009.04.003] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The structural organization of the mitochondrial oxidative phosphorylation (OXPHOS) system has received large attention in the past and most investigations led to the conclusion that the respiratory enzymatic complexes are randomly dispersed in the lipid bilayer of the inner membrane and functionally connected by fast diffusion of smaller redox components, Coenzyme Q and cytochrome c. More recent investigations by native gel electrophoresis, however, have shown the existence of supramolecular associations of the respiratory complexes, confirmed by electron microscopy analysis and single particle image processing. Flux control analysis has demonstrated that Complexes I and III in mammalian mitochondria and Complexes I, III, and IV in plant mitochondria kinetically behave as single units with control coefficients approaching unity for each single component, suggesting the existence of substrate channelling within the supercomplexes. The reasons why the presence of substrate channelling for Coenzyme Q and cytochrome c was overlooked in the past are analytically discussed. The review also discusses the forces and the conditions responsible for the formation of the supramolecular units. The function of the supercomplexes appears not to be restricted to kinetic advantages in electron transfer: we discuss evidence on their role in the stability and assembly of the individual complexes and in preventing excess oxygen radical formation. Finally, there is increasing evidence that disruption of the supercomplex organization leads to functional derangements responsible for pathological changes.
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Affiliation(s)
- Giorgio Lenaz
- Dipartimento di Biochimica G. Moruzzi, Università di Bologna, Via Irnerio 48, 40126 Bologna, Italy.
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Lenaz G, Genova ML. Mobility and function of Coenzyme Q (ubiquinone) in the mitochondrial respiratory chain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:563-73. [DOI: 10.1016/j.bbabio.2009.02.019] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Revised: 02/23/2009] [Accepted: 02/23/2009] [Indexed: 11/29/2022]
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