1
|
Harmer JR, Hakopian S, Niks D, Hille R, Bernhardt PV. Redox Characterization of the Complex Molybdenum Enzyme Formate Dehydrogenase from Cupriavidus necator. J Am Chem Soc 2023; 145:25850-25863. [PMID: 37967365 DOI: 10.1021/jacs.3c10199] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The oxygen-tolerant and molybdenum-dependent formate dehydrogenase FdsDABG from Cupriavidus necator is capable of catalyzing both formate oxidation to CO2 and the reverse reaction (CO2 reduction to formate) at neutral pH, which are both reactions of great importance to energy production and carbon capture. FdsDABG is replete with redox cofactors comprising seven Fe/S clusters, flavin mononucleotide, and a molybdenum ion coordinated by two pyranopterin dithiolene ligands. The redox potentials of these centers are described herein and assigned to specific cofactors using combinations of potential-dependent continuous wave and pulse EPR spectroscopy and UV/visible spectroelectrochemistry on both the FdsDABG holoenzyme and the FdsBG subcomplex. These data represent the first redox characterization of a complex metal dependent formate dehydrogenase and provide an understanding of the highly efficient catalytic formate oxidation and CO2 reduction activity that are associated with the enzyme.
Collapse
Affiliation(s)
- Jeffrey R Harmer
- Centre for Advanced Imaging, University of Queensland, Brisbane 4072, Australia
| | - Sheron Hakopian
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Dimitri Niks
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Russ Hille
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
| |
Collapse
|
2
|
Strotmann L, Harter C, Gerasimova T, Ritter K, Jessen HJ, Wohlwend D, Friedrich T. H 2O 2 selectively damages the binuclear iron-sulfur cluster N1b of respiratory complex I. Sci Rep 2023; 13:7652. [PMID: 37169846 PMCID: PMC10175503 DOI: 10.1038/s41598-023-34821-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023] Open
Abstract
NADH:ubiquinone oxidoreductase, respiratory complex I, plays a major role in cellular energy metabolism by coupling electron transfer with proton translocation. Electron transfer is catalyzed by a flavin mononucleotide and a series of iron-sulfur (Fe/S) clusters. As a by-product of the reaction, the reduced flavin generates reactive oxygen species (ROS). It was suggested that the ROS generated by the respiratory chain in general could damage the Fe/S clusters of the complex. Here, we show that the binuclear Fe/S cluster N1b is specifically damaged by H2O2, however, only at high concentrations. But under the same conditions, the activity of the complex is hardly affected, since N1b can be easily bypassed during electron transfer.
Collapse
Affiliation(s)
- Lisa Strotmann
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Caroline Harter
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Tatjana Gerasimova
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Kevin Ritter
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Henning J Jessen
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany.
| |
Collapse
|
3
|
Lubner CE, Artz JH, Mulder DW, Oza A, Ward RJ, Williams SG, Jones AK, Peters JW, Smalyukh II, Bharadwaj VS, King PW. A site-differentiated [4Fe-4S] cluster controls electron transfer reactivity of Clostridium acetobutylicum [FeFe]-hydrogenase I. Chem Sci 2022; 13:4581-4588. [PMID: 35656134 PMCID: PMC9019909 DOI: 10.1039/d1sc07120c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/24/2022] [Indexed: 01/11/2023] Open
Abstract
One of the many functions of reduction–oxidation (redox) cofactors is to mediate electron transfer in biological enzymes catalyzing redox-based chemical transformation reactions. There are numerous examples of enzymes that utilize redox cofactors to form electron transfer relays to connect catalytic sites to external electron donors and acceptors. The compositions of relays are diverse and tune transfer thermodynamics and kinetics towards the chemical reactivity of the enzyme. Diversity in relay design is exemplified among different members of hydrogenases, enzymes which catalyze reversible H2 activation, which also couple to diverse types of donor and acceptor molecules. The [FeFe]-hydrogenase I from Clostridium acetobutylicum (CaI) is a member of a large family of structurally related enzymes where interfacial electron transfer is mediated by a terminal, non-canonical, His-coordinated, [4Fe–4S] cluster. The function of His coordination was examined by comparing the biophysical properties and reactivity to a Cys substituted variant of CaI. This demonstrated that His coordination strongly affected the distal [4Fe–4S] cluster spin state, spin pairing, and spatial orientations of molecular orbitals, with a minor effect on reduction potential. The deviations in these properties by substituting His for Cys in CaI, correlated with pronounced changes in electron transfer and reactivity with the native electron donor–acceptor ferredoxin. The results demonstrate that differential coordination of the surface localized [4Fe–4S]His cluster in CaI is utilized to control intermolecular and intramolecular electron transfer where His coordination creates a physical and electronic environment that enables facile electron exchange between electron carrier molecules and the iron–sulfur cluster relay for coupling to reversible H2 activation at the catalytic site. Histidine coordination of the distal [4Fe–4S] cluster in [FeFe]-hydrogenase was demonstrated to tune the cluster spin-states, spin-pairing and surrounding molecular orbitals to enable more facile electron transfer compared to cysteine coordination.![]()
Collapse
Affiliation(s)
| | - Jacob H Artz
- National Renewable Energy Laboratory Golden Colorado USA
| | - David W Mulder
- National Renewable Energy Laboratory Golden Colorado USA
| | - Aisha Oza
- National Renewable Energy Laboratory Golden Colorado USA
| | - Rachel J Ward
- Department of Physics, University of Colorado Boulder Boulder Colorado USA
| | - S Garrett Williams
- School of Molecular Sciences, Arizona State University Tempe Arizona USA.,Sandia National Laboratories Albuquerque New Mexico USA
| | - Anne K Jones
- School of Molecular Sciences, Arizona State University Tempe Arizona USA
| | - John W Peters
- Institute of Biological Chemistry, Washington State University Pullman Washington USA
| | - Ivan I Smalyukh
- Department of Physics, University of Colorado Boulder Boulder Colorado USA.,Renewable and Sustainable Energy Institute, National Renewable Energy Laboratory and University of Colorado Boulder Boulder Colorado USA
| | | | - Paul W King
- National Renewable Energy Laboratory Golden Colorado USA .,Renewable and Sustainable Energy Institute, National Renewable Energy Laboratory and University of Colorado Boulder Boulder Colorado USA
| |
Collapse
|
4
|
Chaturvedi A. Reaction Rate Theory-Based Mathematical Approximation for the Amount of Time it Takes For Cellular Respiration to Occur. COMPUTATIONAL AND MATHEMATICAL BIOPHYSICS 2022. [DOI: 10.1515/cmb-2022-0132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
The venerable process of cellular respiration is essential for cells to produce energy from glucose molecules, in order to carry out cellular work. The process is responsible for producing molecules of ATP, a molecule which is thermodynamically coupled with other biochemical and biophysical processes in order to provide energy for such processes to occur. While the process of cellular respiration is essential to biology, one cycle of the process occurs only in a matter of milliseconds, and so, it would be impractical to measure the time it takes for the process to occur through conventional means. Therefore, using concepts from reaction rate theory, particularly Marcus Theory of electron transfer, Michaelis-Menten kinetics for enzymatic catalysis, and the hard-sphere model of collision theory, I formulate and propose a mathematical approximation for the amount of time it takes for cellular respiration to occur. Through this heuristic approach, quantitatively knowing the amount of time it takes for one cycle of cellular respiration to occur could potentially have future applications in biological research.
Collapse
|
5
|
Schimpf J, Oppermann S, Gerasimova T, Santos Seica AF, Hellwig P, Grishkovskaya I, Wohlwend D, Haselbach D, Friedrich T. Structure of the peripheral arm of a minimalistic respiratory complex I. Structure 2021; 30:80-94.e4. [PMID: 34562374 DOI: 10.1016/j.str.2021.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/09/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
Respiratory complex I drives proton translocation across energy-transducing membranes by NADH oxidation coupled with (ubi)quinone reduction. In humans, its dysfunction is associated with neurodegenerative diseases. The Escherichia coli complex represents the structural minimal form of an energy-converting NADH:ubiquinone oxidoreductase. Here, we report the structure of the peripheral arm of the E. coli complex I consisting of six subunits, the FMN cofactor, and nine iron-sulfur clusters at 2.7 Å resolution obtained by cryo electron microscopy. While the cofactors are in equivalent positions as in the complex from other species, individual subunits are adapted to the absence of supernumerary proteins to guarantee structural stability. The catalytically important subunits NuoC and D are fused resulting in a specific architecture of functional importance. Striking features of the E. coli complex are scrutinized by mutagenesis and biochemical characterization of the variants. Moreover, the arrangement of the subunits sheds light on the unknown assembly of the complex.
Collapse
Affiliation(s)
- Johannes Schimpf
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Sabrina Oppermann
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Tatjana Gerasimova
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany; Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CMC, Université de Strasbourg CNRS, 4 Rue Blaise Pascal, 67081 Strasbourg, France
| | - Ana Filipa Santos Seica
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CMC, Université de Strasbourg CNRS, 4 Rue Blaise Pascal, 67081 Strasbourg, France
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CMC, Université de Strasbourg CNRS, 4 Rue Blaise Pascal, 67081 Strasbourg, France; University of Strasbourg, Institute for Advanced Studies (USIAS), 5 Allée du Général Rouvillois, 67083 Strasbourg, France
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany.
| |
Collapse
|
6
|
Mitochondria-targeted magnolol inhibits OXPHOS, proliferation, and tumor growth via modulation of energetics and autophagy in melanoma cells. Cancer Treat Res Commun 2020; 25:100210. [PMID: 32987287 PMCID: PMC7883397 DOI: 10.1016/j.ctarc.2020.100210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/01/2020] [Accepted: 09/15/2020] [Indexed: 12/19/2022]
Abstract
Introduction: Melanoma is an aggressive form of skin cancer for which there are no effective drugs for prolonged treatment. The existing kinase inhibitor antiglycolytic drugs (B-Raf serine/threonine kinase or BRAF inhibitors) are effective for a short time followed by a rapid onset of drug resistance. Presentation of case: Here, we show that a mitochondria-targeted analog of magnolol, Mito-magnolol (Mito-MGN), inhibits oxidative phosphorylation (OXPHOS) and proliferation of melanoma cells more potently than untargeted magnolol. Mito-MGN also inhibited tumor growth in murine melanoma xenografts. Mito-MGN decreased mitochondrial membrane potential and modulated energetic and mitophagy signaling proteins. Discussion: Results indicate that Mito-MGN is significantly more potent than the FDA-approved OXPHOS inhibitor in inhibiting proliferation of melanoma cells. Conclusion: These findings have implications in the treatment of melanomas with enhanced OXPHOS status due to metabolic reprogramming or drug resistance.
Collapse
|
7
|
Melin F, Hellwig P. Redox Properties of the Membrane Proteins from the Respiratory Chain. Chem Rev 2020; 120:10244-10297. [DOI: 10.1021/acs.chemrev.0c00249] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Frederic Melin
- Chimie de la Matière Complexe UMR 7140, Laboratoire de Bioelectrochimie et Spectroscopie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
| | - Petra Hellwig
- Chimie de la Matière Complexe UMR 7140, Laboratoire de Bioelectrochimie et Spectroscopie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
| |
Collapse
|
8
|
Tran KN, Niu S, Ichiye T. Reduction potential calculations of the Fe–S clusters in
Thermus thermophilus
respiratory complex I. J Comput Chem 2019; 40:1248-1256. [DOI: 10.1002/jcc.25785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 12/12/2018] [Accepted: 01/06/2019] [Indexed: 01/12/2023]
Affiliation(s)
- Kelly N. Tran
- Department of ChemistryGeorgetown University Washington District of Columbia, 20057
| | - Shuqiang Niu
- Department of ChemistryGeorgetown University Washington District of Columbia, 20057
| | - Toshiko Ichiye
- Department of ChemistryGeorgetown University Washington District of Columbia, 20057
| |
Collapse
|
9
|
Schuller JM, Birrell JA, Tanaka H, Konuma T, Wulfhorst H, Cox N, Schuller SK, Thiemann J, Lubitz W, Sétif P, Ikegami T, Engel BD, Kurisu G, Nowaczyk MM. Structural adaptations of photosynthetic complex I enable ferredoxin-dependent electron transfer. Science 2018; 363:257-260. [PMID: 30573545 DOI: 10.1126/science.aau3613] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/06/2018] [Indexed: 12/22/2022]
Abstract
Photosynthetic complex I enables cyclic electron flow around photosystem I, a regulatory mechanism for photosynthetic energy conversion. We report a 3.3-angstrom-resolution cryo-electron microscopy structure of photosynthetic complex I from the cyanobacterium Thermosynechococcus elongatus. The model reveals structural adaptations that facilitate binding and electron transfer from the photosynthetic electron carrier ferredoxin. By mimicking cyclic electron flow with isolated components in vitro, we demonstrate that ferredoxin directly mediates electron transfer between photosystem I and complex I, instead of using intermediates such as NADPH (the reduced form of nicotinamide adenine dinucleotide phosphate). A large rate constant for association of ferredoxin to complex I indicates efficient recognition, with the protein subunit NdhS being the key component in this process.
Collapse
Affiliation(s)
- Jan M Schuller
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
| | - James A Birrell
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Hideaki Tanaka
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.,Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
| | - Tsuyoshi Konuma
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hannes Wulfhorst
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany.,Daiichi Sankyo Deutschland GmbH, Zielstattstr. 48, 81379 München, Germany
| | - Nicholas Cox
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany.,Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Sandra K Schuller
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Jacqueline Thiemann
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Pierre Sétif
- Institut de Biologie Intégrative de la Cellule (I2BC), IBITECS, CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette, France
| | - Takahisa Ikegami
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Benjamin D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan. .,Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
| | - Marc M Nowaczyk
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany.
| |
Collapse
|
10
|
Burschel S, Kreuzer Decovic D, Nuber F, Stiller M, Hofmann M, Zupok A, Siemiatkowska B, Gorka M, Leimkühler S, Friedrich T. Iron-sulfur cluster carrier proteins involved in the assembly of Escherichia coli
NADH:ubiquinone oxidoreductase (complex I). Mol Microbiol 2018; 111:31-45. [DOI: 10.1111/mmi.14137] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 09/10/2018] [Accepted: 09/19/2018] [Indexed: 01/26/2023]
Affiliation(s)
- Sabrina Burschel
- Albert-Ludwigs-Universität, Institut für Biochemie; Albertstr. 21 D-79104 Freiburg Germany
| | - Doris Kreuzer Decovic
- Albert-Ludwigs-Universität, Institut für Biochemie; Albertstr. 21 D-79104 Freiburg Germany
- Spemann Graduate School of Biology and Medicine (SGBM); University of Freiburg; Germany
| | - Franziska Nuber
- Albert-Ludwigs-Universität, Institut für Biochemie; Albertstr. 21 D-79104 Freiburg Germany
| | - Marie Stiller
- Albert-Ludwigs-Universität, Institut für Biochemie; Albertstr. 21 D-79104 Freiburg Germany
| | - Maud Hofmann
- Albert-Ludwigs-Universität, Institut für Biochemie; Albertstr. 21 D-79104 Freiburg Germany
| | - Arkadiusz Zupok
- University of Potsdam; Institut für Biochemie und Biologie; Karl-Liebknecht-Str. 24-25 14476 Potsdam-Golm Germany
| | - Beata Siemiatkowska
- Max-Planck-Institute of Molecular Plant Physiology; Am Mühlenberg 1 14476 Potsdam-Golm Germany
| | - Michal Gorka
- Max-Planck-Institute of Molecular Plant Physiology; Am Mühlenberg 1 14476 Potsdam-Golm Germany
| | - Silke Leimkühler
- University of Potsdam; Institut für Biochemie und Biologie; Karl-Liebknecht-Str. 24-25 14476 Potsdam-Golm Germany
| | - Thorsten Friedrich
- Albert-Ludwigs-Universität, Institut für Biochemie; Albertstr. 21 D-79104 Freiburg Germany
- Spemann Graduate School of Biology and Medicine (SGBM); University of Freiburg; Germany
| |
Collapse
|
11
|
Kalyanaraman B, Cheng G, Zielonka J, Bennett B. Low-Temperature EPR Spectroscopy as a Probe-Free Technique for Monitoring Oxidants Formed in Tumor Cells and Tissues: Implications in Drug Resistance and OXPHOS-Targeted Therapies. Cell Biochem Biophys 2018; 77:89-98. [PMID: 30259334 DOI: 10.1007/s12013-018-0858-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/12/2018] [Indexed: 12/12/2022]
Abstract
Oxidants formed from oxidative and nitrative metabolism include reactive oxygen species (ROS) such as superoxide, hydrogen peroxide/lipid hydroperoxides and reactive nitrogen species (RNS) (e.g., peroxynitrite [ONOO-] and nitrogen dioxide), and reactive halogenated species (e.g., hypochlorous acid [HOCl]). Increasingly, ROS and RNS are implicated in tumorigenesis as well as tumor growth, progression, and metastasis. Recently, ROS were implicated in drug resistance, metabolic reprogramming, and T-cell metabolism in immunotherapy. Mostly, fluorescent probes have been used in cell culture systems. The identity of species is obtained by LC-MS analyses of diagnostic marker products. However, extrapolation of these assays to cancer xenografts is difficult if not impossible. Thus, development of a probe-free assay for monitoring and assessing oxidant formation in tumor cells and tumor xenografts is critical and timely. Here, we describe the use of ex vivo electron paramagnetic resonance (EPR) spectroscopy at cryogenic temperatures as a uniquely useful probe-free technique for assessing intracellular oxidation and oxidants via EPR signals from redox centers, particularly iron-sulfur clusters, in mitochondrial and cytosolic redox proteins. Examples of cancer cells subjected to inhibition of mitochondrial oxidative phosphorylation are presented. This ex vivo methodology can be readily extended to monitor oxidant formation in tumor tissues isolated from mice and humans.
Collapse
Affiliation(s)
- Balaraman Kalyanaraman
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA. .,Free Radical Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA. .,Cancer Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Gang Cheng
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.,Free Radical Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Jacek Zielonka
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.,Free Radical Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.,Cancer Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Brian Bennett
- Department of Physics, Marquette University, 540 N. 15th St., Milwaukee, WI, 53233, USA.
| |
Collapse
|
12
|
Mitochondrial complex I in the post-ischemic heart: reperfusion-mediated oxidative injury and protein cysteine sulfonation. J Mol Cell Cardiol 2018; 121:190-204. [PMID: 30031815 DOI: 10.1016/j.yjmcc.2018.07.244] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 07/17/2018] [Accepted: 07/18/2018] [Indexed: 12/20/2022]
Abstract
A serious consequence of ischemia-reperfusion injury (I/R) is oxidative damage leading to mitochondrial dysfunction. Such I/R-induced mitochondrial dysfunction is observed as impaired state 3 respiration and overproduction of O2-. The cascading ROS can propagate cysteine oxidation on mitochondrial complex I and add insult to injury. Herein we employed LC-MS/MS to identify protein sulfonation of complex I in mitochondria from the infarct region of rat hearts subjected to 30-min of coronary ligation and 24-h of reperfusion in vivo as well as the mitochondria of sham controls. Mitochondrial preparations from the I/R regions had enhanced sulfonation levels on the cysteine ligands of iron‑sulfur clusters, including N3 (C425), N1b (C92), N4 (C226), N2 (C158/C188), and N1a (C134/C139). The 4Fe-4S centers of N3, N1b, N4, and N2 are key redox-active components of complex I, thus sulfonation of metal-binding sites impaired the main electron transfer pathway. The binuclear N1a has a very low redox potential and an antioxidative function. Increased C134/C139 sulfonation by I/R impaired the N1a cluster, potentially contributing to overall O2- generation by the FMN moiety of complex I. MS analysis also revealed I/R-mediated increased sulfonation at the core subunits of 51 kDa (C125, C187, C206, C238, C255, C286), 75 kDa (C367, C554, C564, C727), 49 kDa (C146, C326, C347), and PSST (C188). These results were consistent with the consensus indicating that 51 kDa and 75 kDa are two of major subunits hosting regulatory thiols, and their enhanced sulfonation by I/R predisposed the myocardium to further oxidant stress with impaired ubiquinone reduction. MS analysis further showed I/R-mediated enhanced sulfonation at the supernumerary subunits of 42 kDa (C67, C112, C183, C253), 15 kDa (C43), and 13 kDa (C79). The 42 kDa protein is metazoan-specific, which was reported to stabilize mammalian complex I. C43 of the 15 kDa subunit forms an intramolecular disulfide bond with C56, which was reported to stabilize complex I structure. C79 of the 13 kDa subunit is involved in Zn2+-binding, which was reported functionally important for complex I assembly. C79 sulfonation by I/R was found to impair Zn2+-binding. No significant enhancement of protein sulfonation was observed in mitochondrial complex I from the rat heart subjected to 30-min ischemia alone in vivo despite a decreased state 3 respiration, suggesting that the physiologic conditions of hyperoxygenation during reperfusion mediated an increase in complex I sulfonation and oxidative injury. In conclusion, sulfonation of specific cysteines of complex I mediates I/R-induced mitochondrial dysfunction via impaired ETC activity, increasing •O2- production, and mediating redox dysfunction of complex I.
Collapse
|
13
|
Abstract
Mitochondria are the power stations of the eukaryotic cell, using the energy released by the oxidation of glucose and other sugars to produce ATP. Electrons are transferred from NADH, produced in the citric acid cycle in the mitochondrial matrix, to oxygen by a series of large protein complexes in the inner mitochondrial membrane, which create a transmembrane electrochemical gradient by pumping protons across the membrane. The flow of protons back into the matrix via a proton channel in the ATP synthase leads to conformational changes in the nucleotide binding pockets and the formation of ATP. The three proton pumping complexes of the electron transfer chain are NADH-ubiquinone oxidoreductase or complex I, ubiquinone-cytochrome c oxidoreductase or complex III, and cytochrome c oxidase or complex IV. Succinate dehydrogenase or complex II does not pump protons, but contributes reduced ubiquinone. The structures of complex II, III and IV were determined by x-ray crystallography several decades ago, but complex I and ATP synthase have only recently started to reveal their secrets by advances in x-ray crystallography and cryo-electron microscopy. The complexes I, III and IV occur to a certain extent as supercomplexes in the membrane, the so-called respirasomes. Several hypotheses exist about their function. Recent cryo-electron microscopy structures show the architecture of the respirasome with near-atomic detail. ATP synthase occurs as dimers in the inner mitochondrial membrane, which by their curvature are responsible for the folding of the membrane into cristae and thus for the huge increase in available surface that makes mitochondria the efficient energy plants of the eukaryotic cell.
Collapse
Affiliation(s)
- Joana S Sousa
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Edoardo D'Imprima
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
| |
Collapse
|
14
|
Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part I. [4Fe-4S] + [2Fe-2S] iron-sulfur proteins. J Struct Biol 2017; 200:1-19. [DOI: 10.1016/j.jsb.2017.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/25/2017] [Indexed: 01/08/2023]
|
15
|
Zhang Y, Yang C, Dancis A, Nakamaru-Ogiso E. EPR studies of wild type and mutant Dre2 identify essential [2Fe--2S] and [4Fe--4S] clusters and their cysteine ligands. J Biochem 2016; 161:67-78. [PMID: 27672211 DOI: 10.1093/jb/mvw054] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 08/11/2016] [Indexed: 11/12/2022] Open
Abstract
Yeast Dre2 (anamorsin or CIAPIN1) is an essential component for cytosolic Fe/S cluster biosynthesis. The C-terminal domain contains eight evolutionarily conserved cysteine residues, and we previously demonstrated that the yeast Dre2 overexpressed in Escherichia coli contains one binuclear ([2Fe-2S]) cluster and one tetranuclear ([4Fe-4S]) cluster. In this study, we replaced each conserved cysteine with alanine and analyzed the effects by Electron Paramagnetic Resonance. Although the C311A mutant lacked both signals, our data clearly suggest that the [2Fe-2S] cluster is ligated to Cys252, Cys263, Cys266 and Cys268, whereas the [4Fe-4S] cluster is ligated to Cys311, Cys314, Cys322 and Cys325. By simulation analysis of the C263A and C322A data, we obtained the g-values for the [4Fe-4S] cluster (gx,y,z = 1.830, 1.947 and 2.018) and for the [2Fe-2S] cluster (gx,y,z =1.919, 1.962 and 2.001). We also observed spin-spin interaction between the two clusters, suggesting their close proximity. Chemically reconstituted Dre2 showed air sensitivity of the [4Fe-4S] cluster converting to a [2Fe-2S] cluster. Furthermore, using a yeast shuffle strain, we demonstrated for the first time that each of the Cys Fe-S cluster ligands with the exception of C252 is essential, indicating that both Dre2 clusters are needed for cell viability.
Collapse
Affiliation(s)
- Yan Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Rd, Tianjin 300072, China
| | - Chunyu Yang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Rd, Tianjin 300072, China
| | - Andrew Dancis
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Eiko Nakamaru-Ogiso
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
16
|
Gnandt E, Dörner K, Strampraad MFJ, de Vries S, Friedrich T. The multitude of iron-sulfur clusters in respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1068-1072. [PMID: 26944855 DOI: 10.1016/j.bbabio.2016.02.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/19/2016] [Accepted: 02/26/2016] [Indexed: 12/13/2022]
Abstract
Respiratory complex I couples the electron transfer from NADH to ubiquinone with the translocation of protons across the membrane. Complex I contains one non-covalently bound flavin mononucleotide and, depending on the species, up to ten iron-sulfur (Fe/S) clusters as cofactors. The reason for the presence of the multitude of Fe/S clusters in complex I remained enigmatic for a long time. The question was partly answered by investigations on the evolution of the complex revealing the stepwise construction of the electron transfer domain from several modules. Extension of the ancestral to the modern electron input domain was associated with the acquisition of several Fe/S-proteins. The X-ray structure of the complex showed that the NADH oxidation-site is connected with the quinone-reduction site by a chain of seven Fe/S-clusters. Fast enzyme kinetics revealed that this chain of Fe/S-clusters is used to regulate electron-tunneling rates within the complex. A possible function of the off-pathway cluster N1a is discussed. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
Collapse
Affiliation(s)
- Emmanuel Gnandt
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, Albertstr. 21, 79104 Freiburg i. Br., Germany
| | - Katerina Dörner
- Deutsches Elektronen-Synchrotron DESY, CFEL, Notkestr. 85, Hamburg, Germany
| | - Marc F J Strampraad
- Delft University of Technology, Department of Biotechnology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Simon de Vries
- Delft University of Technology, Department of Biotechnology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Thorsten Friedrich
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, Albertstr. 21, 79104 Freiburg i. Br., Germany.
| |
Collapse
|
17
|
Bennett B, Helbling D, Meng H, Jarzembowski J, Geurts AM, Friederich MW, Van Hove JLK, Lawlor MW, Dimmock DP. Potentially diagnostic electron paramagnetic resonance spectra elucidate the underlying mechanism of mitochondrial dysfunction in the deoxyguanosine kinase deficient rat model of a genetic mitochondrial DNA depletion syndrome. Free Radic Biol Med 2016; 92:141-151. [PMID: 26773591 PMCID: PMC5047058 DOI: 10.1016/j.freeradbiomed.2016.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/04/2016] [Accepted: 01/06/2016] [Indexed: 01/19/2023]
Abstract
A novel rat model for a well-characterized human mitochondrial disease, mitochondrial DNA depletion syndrome with associated deoxyguanosine kinase (DGUOK) deficiency, is described. The rat model recapitulates the pathologic and biochemical signatures of the human disease. The application of electron paramagnetic (spin) resonance (EPR) spectroscopy to the identification and characterization of respiratory chain abnormalities in the mitochondria from freshly frozen tissue of the mitochondrial disease model rat is introduced. EPR is shown to be a sensitive technique for detecting mitochondrial functional abnormalities in situ and, here, is particularly useful in characterizing the redox state changes and oxidative stress that can result from depressed expression and/or diminished specific activity of the distinct respiratory chain complexes. As EPR requires no sample preparation or non-physiological reagents, it provides information on the status of the mitochondrion as it was in the functioning state. On its own, this information is of use in identifying respiratory chain dysfunction; in conjunction with other techniques, the information from EPR shows how the respiratory chain is affected at the molecular level by the dysfunction. It is proposed that EPR has a role in mechanistic pathophysiological studies of mitochondrial disease and could be used to study the impact of new treatment modalities or as an additional diagnostic tool.
Collapse
Affiliation(s)
- Brian Bennett
- National Biomedical EPR Center, Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
| | - Daniel Helbling
- Human Molecular Genetics Center and Division of Genetics, Department of Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
| | - Hui Meng
- Division of Pediatric Pathology, Department of Pathology and Laboratory Medicine, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
| | - Jason Jarzembowski
- Division of Pediatric Pathology, Department of Pathology and Laboratory Medicine, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
| | - Aron M Geurts
- Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
| | - Marisa W Friederich
- Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Mailstop 8400, 13121 East 17th Avenue, Aurora, CO 80045, USA.
| | - Johan L K Van Hove
- Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Mailstop 8400, 13121 East 17th Avenue, Aurora, CO 80045, USA.
| | - Michael W Lawlor
- Division of Pediatric Pathology, Department of Pathology and Laboratory Medicine, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
| | - David P Dimmock
- Human Molecular Genetics Center and Division of Genetics, Department of Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
| |
Collapse
|
18
|
de Vries S, Dörner K, Strampraad MJF, Friedrich T. Die Elektronentunnelraten im Atmungskettenkomplex I sind auf eine effiziente Energiewandlung abgestimmt. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410967] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
19
|
de Vries S, Dörner K, Strampraad MJF, Friedrich T. Electron tunneling rates in respiratory complex I are tuned for efficient energy conversion. Angew Chem Int Ed Engl 2015; 54:2844-8. [PMID: 25600069 PMCID: PMC4506566 DOI: 10.1002/anie.201410967] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Indexed: 12/13/2022]
Abstract
Respiratory complex I converts the free energy of ubiquinone reduction by NADH into a proton motive force, a redox reaction catalyzed by flavin mononucleotide(FMN) and a chain of seven iron–sulfur centers. Electron transfer rates between the centers were determined by ultrafast freeze-quenching and analysis by EPR and UV/Vis spectroscopy. The complex rapidly oxidizes three NADH molecules. The electron-tunneling rate between the most distant centers in the middle of the chain depends on the redox state of center N2 at the end of the chain, and is sixfold slower when N2 is reduced. The conformational changes that accompany reduction of N2 decrease the electronic coupling of the longest electron-tunneling step. The chain of iron–sulfur centers is not just a simple electron-conducting wire; it regulates the electron-tunneling rate synchronizing it with conformation-mediated proton pumping, enabling efficient energy conversion. Synchronization of rates is a principle means of enhancing the specificity of enzymatic reactions.
Collapse
Affiliation(s)
- Simon de Vries
- Department of Biotechnology, Institution Delft University of Technology, Julianalaan 67, 2628 BC, Delft (The Netherlands).
| | | | | | | |
Collapse
|
20
|
Friedrich T. On the mechanism of respiratory complex I. J Bioenerg Biomembr 2014; 46:255-68. [PMID: 25022766 DOI: 10.1007/s10863-014-9566-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 07/03/2014] [Indexed: 02/08/2023]
Abstract
The energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, couples the transfer of electrons from NADH to ubiquinone with the translocation of protons across the membrane. Electron microscopy and X-ray crystallography revealed the two-part structure of the enzyme complex. A peripheral arm extending into the aqueous phase catalyzes the electron transfer reaction. Accordingly, this arm contains the redox-active cofactors, namely one flavin mononucleotide (FMN) and up to ten iron-sulfur (Fe/S) clusters. A membrane arm embedded in the lipid bilayer catalyzes proton translocation by a yet unknown mechanism. The binding site of the substrate (ubi) quinone is located at the interface of the two arms. The oxidation of one NADH is coupled with the translocation of four protons across the membrane. In this review, the binding of the substrates, the intramolecular electron transfer, the role of individual Fe/S clusters and the mechanism of proton translocation are discussed in the light of recent data obtained from our laboratory.
Collapse
Affiliation(s)
- Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität, Albertstr. 21, 79104, Freiburg, Germany,
| |
Collapse
|
21
|
Sato M, Torres-Bacete J, Sinha PK, Matsuno-Yagi A, Yagi T. Essential regions in the membrane domain of bacterial complex I (NDH-1): the machinery for proton translocation. J Bioenerg Biomembr 2014; 46:279-87. [PMID: 24973951 DOI: 10.1007/s10863-014-9558-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 06/18/2014] [Indexed: 01/09/2023]
Abstract
The proton-translocating NADH-quinone oxidoreductase (complex I/NDH-1) is the first and largest enzyme of the respiratory chain which has a central role in cellular energy production and is implicated in many human neurodegenerative diseases and aging. It is believed that the peripheral domain of complex I/NDH-1 transfers the electron from NADH to Quinone (Q) and the redox energy couples the proton translocation in the membrane domain. To investigate the mechanism of the proton translocation, in a series of works we have systematically studied all membrane subunits in the Escherichia coli NDH-1 by site-directed mutagenesis. In this mini-review, we have summarized our strategy and results of the mutagenesis by depicting residues essential for proton translocation, along with those for subunit connection. It is suggested that clues to understanding the driving forces of proton translocation lie in the similarities and differences of the membrane subunits, highlighting the communication of essential charged residues among the subunits. A possible proton translocation mechanism with all membrane subunits operating in unison is described.
Collapse
Affiliation(s)
- Motoaki Sato
- Department of Molecular and Experimental Medicine, MEM-256, The Scripps Research Institute, La Jolla, CA, 92037, USA,
| | | | | | | | | |
Collapse
|
22
|
Berggren G, Garcia-Serres R, Brazzolotto X, Clemancey M, Gambarelli S, Atta M, Latour JM, Hernández HL, Subramanian S, Johnson MK, Fontecave M. An EPR/HYSCORE, Mössbauer, and resonance Raman study of the hydrogenase maturation enzyme HydF: a model for N-coordination to [4Fe-4S] clusters. J Biol Inorg Chem 2014; 19:75-84. [PMID: 24240692 PMCID: PMC4439245 DOI: 10.1007/s00775-013-1062-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 10/30/2013] [Indexed: 10/26/2022]
Abstract
The biosynthesis of the organometallic H cluster of [Fe-Fe] hydrogenase requires three accessory proteins, two of which (HydE and HydG) belong to the radical S-adenosylmethionine enzyme superfamily. The third, HydF, is an Fe-S protein with GTPase activity. The [4Fe-4S] cluster of HydF is bound to the polypeptide chain through only the three, conserved, cysteine residues present in the binding sequence motif CysXHisX(46-53)HisCysXXCys. However, the involvement of the two highly conserved histidines as a fourth ligand for the cluster coordination is controversial. In this study, we set out to characterize further the [4Fe-4S] cluster of HydF using Mössbauer, EPR, hyperfine sublevel correlation (HYSCORE), and resonance Raman spectroscopy in order to investigate the influence of nitrogen ligands on the spectroscopic properties of [4Fe-4S](2+/+) clusters. Our results show that Mössbauer, resonance Raman, and EPR spectroscopy are not able to readily discriminate between the imidazole-coordinated [4Fe-4S] cluster and the non-imidazole-bound [4Fe-4S] cluster with an exchangeable fourth ligand that is present in wild-type HydF. HYSCORE spectroscopy, on the other hand, detects the presence of an imidazole/histidine ligand on the cluster on the basis of the appearance of a specific spectral pattern in the strongly coupled region, with a coupling constant of approximately 6 MHz. We also discovered that a His-tagged version of HydF, with a hexahistidine tag at the N-terminus, has a [4Fe-4S] cluster coordinated by one histidine from the tag. This observation strongly indicates that care has to be taken in the analysis of data obtained on tagged forms of metalloproteins.
Collapse
Affiliation(s)
- Gustav Berggren
- Laboratoire de Chimie et Biologie des Métaux, Équipe «Biocatalyse», Institut de Recherches en Technologies et Sciences pour le Vivant, iRTSV-LCBM/Biocat, UMR 5249 CEA/CNRS/UJF, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Ricardo Garcia-Serres
- Laboratoire de Chimie et Biologie des Métaux, Équipe “Physicochimie des Métaux en Biologie”, Institut de Recherches en Technologies et Sciences pour le Vivant, iRTSV-LCBM/pmb, UMR 5249 CEA/CNRS/UJF, CEA/Grenoble, Grenoble, France
| | - Xavier Brazzolotto
- Laboratoire de Chimie et Biologie des Métaux, Équipe «Biocatalyse», Institut de Recherches en Technologies et Sciences pour le Vivant, iRTSV-LCBM/Biocat, UMR 5249 CEA/CNRS/UJF, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Martin Clemancey
- Laboratoire de Chimie et Biologie des Métaux, Équipe “Physicochimie des Métaux en Biologie”, Institut de Recherches en Technologies et Sciences pour le Vivant, iRTSV-LCBM/pmb, UMR 5249 CEA/CNRS/UJF, CEA/Grenoble, Grenoble, France
| | - Serge Gambarelli
- Laboratoire “Résonance Magnétique”, Université Joseph Fourier, Grenoble 1/CEA/Institut Nanoscience et Cryogénie/SCIB, UMR-E3, Grenoble, France
| | - Mohamed Atta
- Laboratoire de Chimie et Biologie des Métaux, Équipe «Biocatalyse», Institut de Recherches en Technologies et Sciences pour le Vivant, iRTSV-LCBM/Biocat, UMR 5249 CEA/CNRS/UJF, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Jean-Marc Latour
- Laboratoire de Chimie et Biologie des Métaux, Équipe “Physicochimie des Métaux en Biologie”, Institut de Recherches en Technologies et Sciences pour le Vivant, iRTSV-LCBM/pmb, UMR 5249 CEA/CNRS/UJF, CEA/Grenoble, Grenoble, France
| | - Heather L. Hernández
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA
| | - Sowmya Subramanian
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA
| | - Michael K. Johnson
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA
| | - Marc Fontecave
- Laboratoire de Chimie et Biologie des Métaux, Équipe «Biocatalyse», Institut de Recherches en Technologies et Sciences pour le Vivant, iRTSV-LCBM/Biocat, UMR 5249 CEA/CNRS/UJF, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
- Collége de France, 11 place Marcellin-Berthelot, Paris, France
| |
Collapse
|
23
|
Sato M, Sinha PK, Torres-Bacete J, Matsuno-Yagi A, Yagi T. Energy transducing roles of antiporter-like subunits in Escherichia coli NDH-1 with main focus on subunit NuoN (ND2). J Biol Chem 2013; 288:24705-16. [PMID: 23864658 DOI: 10.1074/jbc.m113.482968] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The proton-translocating NADH-quinone oxidoreductase (complex I/NDH-1) contains a peripheral and a membrane domain. Three antiporter-like subunits in the membrane domain, NuoL, NuoM, and NuoN (ND5, ND4 and ND2, respectively), are structurally similar. We analyzed the role of NuoN in Escherichia coli NDH-1. The lysine residue at position 395 in NuoN (NLys(395)) is conserved in NuoL (LLys(399)) but is replaced by glutamic acid (MGlu(407)) in NuoM. Our mutation study on NLys(395) suggests that this residue participates in the proton translocation. Furthermore, we found that MGlu(407) is also essential and most likely interacts with conserved LArg(175). Glutamic acids, NGlu(133), MGlu(144), and LGlu(144), are corresponding residues. Unlike mutants of MGlu(144) and LGlu(144), mutation of NGlu(133) scarcely affected the energy-transducing activities. However, a double mutant of NGlu(133) and nearby KGlu(72) showed significant inhibition of these activities. This suggests that NGlu(133) bears a functional role similar to LGlu(144) and MGlu(144) but its mutation can be partially compensated by the nearby carboxyl residue. Conserved prolines located at loops of discontinuous transmembrane helices of NuoL, NuoM, and NuoN were shown to play a similar role in the energy-transducing activity. It seems likely that NuoL, NuoM, and NuoN pump protons by a similar mechanism. Our data also revealed that NLys(158) is one of the key interaction points with helix HL in NuoL. A truncation study indicated that the C-terminal amphipathic segments of NTM14 interacts with the Mβ sheet located on the opposite side of helix HL. Taken together, the mechanism of H(+) translocation in NDH-1 is discussed.
Collapse
Affiliation(s)
- Motoaki Sato
- Department of Molecular and Experimental Medicine, MEM-256, The Scripps Research Institute, La Jolla, California 92037, USA
| | | | | | | | | |
Collapse
|
24
|
Narayanan M, Gabrieli DJ, Leung SA, Elguindy MM, Glaser CA, Saju N, Sinha SC, Nakamaru-Ogiso E. Semiquinone and cluster N6 signals in His-tagged proton-translocating NADH:ubiquinone oxidoreductase (complex I) from Escherichia coli. J Biol Chem 2013; 288:14310-14319. [PMID: 23543743 DOI: 10.1074/jbc.m113.467803] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
NADH:ubiquinone oxidoreductase (complex I) pumps protons across the membrane using downhill redox energy. The Escherichia coli complex I consists of 13 different subunits named NuoA-N coded by the nuo operon. Due to the low abundance of the protein and some difficulty with the genetic manipulation of its large ~15-kb operon, purification of E. coli complex I has been technically challenging. Here, we generated a new strain in which a polyhistidine sequence was inserted upstream of nuoE in the operon. This allowed us to prepare large amounts of highly pure and active complex I by efficient affinity purification. The purified complex I contained 0.94 ± 0.1 mol of FMN, 29.0 ± 0.37 mol of iron, and 1.99 ± 0.07 mol of ubiquinone/1 mol of complex I. The extinction coefficient of isolated complex I was 495 mM(-1) cm(-1) at 274 nm and 50.3 mM(-1) cm(-1) at 410 nm. NADH:ferricyanide activity was 219 ± 9.7 μmol/min/mg by using HEPES-Bis-Tris propane, pH 7.5. Detailed EPR analyses revealed two additional iron-sulfur cluster signals, N6a and N6b, in addition to previously assigned signals. Furthermore, we found small but significant semiquinone signal(s), which have been reported only for bovine complex I. The line width was ~12 G, indicating its neutral semiquinone form. More than 90% of the semiquinone signal originated from the single entity with P½ (half-saturation power level) = 1.85 milliwatts. The semiquinone signal(s) decreased by 60% when with asimicin, a potent complex I inhibitor. The functional role of semiquinone and the EPR assignment of clusters N6a/N6b are discussed.
Collapse
Affiliation(s)
- Madhavan Narayanan
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - David J Gabrieli
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Steven A Leung
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Mahmoud M Elguindy
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Carl A Glaser
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Nitha Saju
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Subhash C Sinha
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Eiko Nakamaru-Ogiso
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104.
| |
Collapse
|
25
|
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.
Collapse
Affiliation(s)
- Marina Verkhovskaya
- Helsinki Bioenergetics Group, Institute of Biotechnology, PO Box 65 (Viikinkaari 1) FIN-00014 University of Helsinki, Finland.
| | | |
Collapse
|
26
|
Sinha PK, Nakamaru-Ogiso E, Torres-Bacete J, Sato M, Castro-Guerrero N, Ohnishi T, Matsuno-Yagi A, Yagi T. Electron transfer in subunit NuoI (TYKY) of Escherichia coli NADH:quinone oxidoreductase (NDH-1). J Biol Chem 2012; 287:17363-17373. [PMID: 22474289 DOI: 10.1074/jbc.m111.329649] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial proton-translocating NADH:quinone oxidoreductase (NDH-1) consists of a peripheral and a membrane domain. The peripheral domain catalyzes the electron transfer from NADH to quinone through a chain of seven iron-sulfur (Fe/S) clusters. Subunit NuoI in the peripheral domain contains two [4Fe-4S] clusters (N6a and N6b) and plays a role in bridging the electron transfer from cluster N5 to the terminal cluster N2. We constructed mutants for eight individual Cys-coordinating Fe/S clusters. With the exception of C63S, all mutants had damaged architecture of NDH-1, suggesting that Cys-coordinating Fe/S clusters help maintain the NDH-1 structure. Studies of three mutants (C63S-coordinating N6a, P110A located near N6a, and P71A in the vicinity of N6b) were carried out using EPR measurement. These three mutations did not affect the EPR signals from [2Fe-2S] clusters and retained electron transfer activities. Signals at g(z) = 2.09 disappeared in C63S and P110A but not in P71A. Considering our data together with the available information, g(z,x) = 2.09, 1.88 signals are assigned to cluster N6a. It is of interest that, in terms of g(z,x) values, cluster N6a is similar to cluster N4. In addition, we investigated the residues (Ile-94 and Ile-100) that are predicted to serve as electron wires between N6a and N6b and between N6b and N2, respectively. Replacement of Ile-100 and Ile-94 with Ala/Gly did not affect the electron transfer activity significantly. It is concluded that conserved Ile-100 and Ile-94 are not essential for the electron transfer.
Collapse
Affiliation(s)
- Prem Kumar Sinha
- Department of Molecular and Experimental Medicine, MEM-256, The Scripps Research Institute, La Jolla, California 92037
| | - Eiko Nakamaru-Ogiso
- Johnson Research Foundation, Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Jesus Torres-Bacete
- Department of Molecular and Experimental Medicine, MEM-256, The Scripps Research Institute, La Jolla, California 92037
| | - Motoaki Sato
- Department of Molecular and Experimental Medicine, MEM-256, The Scripps Research Institute, La Jolla, California 92037
| | - Norma Castro-Guerrero
- Department of Molecular and Experimental Medicine, MEM-256, The Scripps Research Institute, La Jolla, California 92037
| | - Tomoko Ohnishi
- Johnson Research Foundation, Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Akemi Matsuno-Yagi
- Department of Molecular and Experimental Medicine, MEM-256, The Scripps Research Institute, La Jolla, California 92037
| | - Takao Yagi
- Department of Molecular and Experimental Medicine, MEM-256, The Scripps Research Institute, La Jolla, California 92037.
| |
Collapse
|
27
|
Bridges HR, Bill E, Hirst J. Mössbauer spectroscopy on respiratory complex I: the iron-sulfur cluster ensemble in the NADH-reduced enzyme is partially oxidized. Biochemistry 2011; 51:149-58. [PMID: 22122402 PMCID: PMC3254188 DOI: 10.1021/bi201644x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
In mitochondria, complex I (NADH:quinone oxidoreductase)
couples
electron transfer to proton translocation across an energy-transducing
membrane. It contains a flavin mononucleotide to oxidize NADH, and
an unusually long series of iron–sulfur (FeS) clusters that
transfer the electrons to quinone. Understanding electron transfer
in complex I requires spectroscopic and structural data to be combined
to reveal the properties of individual clusters and of the ensemble.
EPR studies on complex I from Bos taurus have established
that five clusters (positions 1, 2, 3, 5, and 7 along the seven-cluster
chain extending from the flavin) are (at least partially) reduced
by NADH. The other three clusters, positions 4 and 6 plus a cluster
on the other side of the flavin, are not observed in EPR spectra from
the NADH-reduced enzyme: they may remain oxidized, have unusual or
coupled spin states, or their EPR signals may be too fast relaxing.
Here, we use Mössbauer spectroscopy on 57Fe-labeled
complex I from the mitochondria of Yarrowia lipolytica to show that the cluster ensemble is only partially reduced in the
NADH-reduced enzyme. The three EPR-silent clusters are oxidized, and
only the terminal 4Fe cluster (position 7) is fully reduced. Together
with the EPR analyses, our results reveal an alternating profile of
higher and lower potential clusters between the two active sites in
complex I; they are not consistent with the consensus picture of a
set of isopotential clusters. The implications for intramolecular
electron transfer along the extended chain of cofactors in complex
I are discussed.
Collapse
Affiliation(s)
- Hannah R Bridges
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Cambridge, CB2 0XY, UK
| | | | | |
Collapse
|
28
|
Gadicherla AK, Stowe DF, Antholine WE, Yang M, Camara AKS. Damage to mitochondrial complex I during cardiac ischemia reperfusion injury is reduced indirectly by anti-anginal drug ranolazine. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:419-29. [PMID: 22178605 DOI: 10.1016/j.bbabio.2011.11.021] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 11/23/2011] [Accepted: 11/30/2011] [Indexed: 12/19/2022]
Abstract
Ranolazine, an anti-anginal drug, is a late Na(+) channel current blocker that is also believed to attenuate fatty acid oxidation and mitochondrial respiratory complex I activity, especially during ischemia. In this study, we investigated if ranolazine's protective effect against cardiac ischemia/reperfusion (IR) injury is mediated at the mitochondrial level and specifically if respiratory complex I (NADH Ubiquinone oxidoreductase) function is protected. We treated isolated and perfused guinea pig hearts with ranolazine just before 30 min ischemia and then isolated cardiac mitochondria at the end of 30 min ischemia and/or 30 min ischemia followed by 10 min reperfusion. We utilized spectrophotometric and histochemical techniques to assay complex I activity, Western blot analysis for complex I subunit NDUFA9, electron paramagnetic resonance for activity of complex I Fe-S clusters, enzyme linked immuno sorbent assay (ELISA) for determination of protein acetylation, native gel histochemical staining for respiratory supercomplex assemblies, and high pressure liquid chromatography for cardiolipin integrity; cardiac function was measured during IR. Ranolazine treated hearts showed higher complex I activity and greater detectable complex I protein levels compared to untreated IR hearts. Ranolazine treatment also led to more normalized electron transfer via Fe-S centers, supercomplex assembly and cardiolipin integrity. These improvements in complex I structure and function with ranolazine were associated with improved cardiac function after IR. However, these protective effects of ranolazine are not mediated by a direct action on mitochondria, but rather indirectly via cytosolic mechanisms that lead to less oxidation and better structural integrity of complex I.
Collapse
Affiliation(s)
- Ashish K Gadicherla
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | | | | | | |
Collapse
|
29
|
Belevich G, Knuuti J, Verkhovsky MI, Wikström M, Verkhovskaya M. Probing the mechanistic role of the long α-helix in subunit L of respiratory Complex I from Escherichia coli by site-directed mutagenesis. Mol Microbiol 2011; 82:1086-95. [PMID: 22060017 PMCID: PMC3274701 DOI: 10.1111/j.1365-2958.2011.07883.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The C-terminus of the NuoL subunit of Complex I includes a long amphipathic α-helix positioned parallel to the membrane, which has been considered to function as a piston in the proton pumping machinery. Here, we have introduced three types of mutations into the nuoL gene to test the piston-like function. First, NuoL was truncated at its C- and N-termini, which resulted in low production of a fragile Complex I with negligible activity. Second, we mutated three partially conserved residues of the amphipathic α-helix: Asp and Lys residues and a Pro were substituted for acidic, basic or neutral residues. All these variants exhibited almost a wild-type phenotype. Third, several substitutions and insertions were made to reduce rigidity of the amphipathic α-helix, and/or to change its geometry. Most insertions/substitutions resulted in a normal growth phenotype, albeit often with reduced stability of Complex I. In contrast, insertion of six to seven amino acids at a site of the long α-helix between NuoL and M resulted in substantial loss of proton pumping efficiency. The implications of these results for the proton pumping mechanism of Complex I are discussed.
Collapse
Affiliation(s)
- Galina Belevich
- Helsinki Bioenergetics Group, Institute of Biotechnology, FIN-00014, University of Helsinki, Helsinki, Finland
| | | | | | | | | |
Collapse
|
30
|
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]
|
31
|
Genova ML, Lenaz G. New developments on the functions of coenzyme Q in mitochondria. Biofactors 2011; 37:330-54. [PMID: 21989973 DOI: 10.1002/biof.168] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 04/06/2011] [Indexed: 12/12/2022]
Abstract
The notion of a mobile pool of coenzyme Q (CoQ) in the lipid bilayer has changed with the discovery of respiratory supramolecular units, in particular the supercomplex comprising complexes I and III; in this model, the electron transfer is thought to be mediated by tunneling or microdiffusion, with a clear kinetic advantage on the transfer based on random collisions. The CoQ pool, however, has a fundamental function in establishing a dissociation equilibrium with bound quinone, besides being required for electron transfer from other dehydrogenases to complex III. The mechanism of CoQ reduction by complex I is analyzed regarding recent developments on the crystallographic structure of the enzyme, also in relation to the capacity of complex I to generate superoxide. Although the mechanism of the Q-cycle is well established for complex III, involvement of CoQ in proton translocation by complex I is still debated. Some additional roles of CoQ are also examined, such as the antioxidant effect of its reduced form and the capacity to bind the permeability transition pore and the mitochondrial uncoupling proteins. Finally, a working hypothesis is advanced on the establishment of a vicious circle of oxidative stress and supercomplex disorganization in pathological states, as in neurodegeneration and cancer.
Collapse
|
32
|
Torres-Bacete J, Sinha PK, Matsuno-Yagi A, Yagi T. Structural contribution of C-terminal segments of NuoL (ND5) and NuoM (ND4) subunits of complex I from Escherichia coli. J Biol Chem 2011; 286:34007-14. [PMID: 21835926 DOI: 10.1074/jbc.m111.260968] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The proton-translocating NADH-quinone oxidoreductase (complex I/NDH-1) is a multisubunit enzymatic complex. It has a characteristic L-shaped form with two domains, a hydrophilic peripheral domain and a hydrophobic membrane domain. The membrane domain contains three antiporter-like subunits (NuoL, NuoM, and NuoN, Escherichia coli naming) that are considered to be involved in the proton translocation. Deletion of either NuoL or NuoM resulted in an incomplete assembly of NDH-1 and a total loss of the NADH-quinone oxidoreductase activity. We have truncated the C terminus segments of NuoM and NuoL by introducing STOP codons at different locations using site-directed mutagenesis of chromosomal DNA. Our results suggest an important structural role for the C-terminal segments of both subunits. The data further advocate that the elimination of the last transmembrane helix (TM14) of NuoM and the TM16 (at least C-terminal seven residues) or together with the HL helix and the TM15 of the NuoL subunit lead to reduced stability of the membrane arm and therefore of the whole NDH-1 complex. A region of NuoL critical for stability of NDH-1 architecture has been discussed.
Collapse
Affiliation(s)
- Jesus Torres-Bacete
- Department of Molecular and Experimental Medicine, MEM-256, The Scripps Research Institute, La Jolla, California 92037, USA
| | | | | | | |
Collapse
|
33
|
Myers CR, Antholine WE, Myers JM. The pro-oxidant chromium(VI) inhibits mitochondrial complex I, complex II, and aconitase in the bronchial epithelium: EPR markers for Fe-S proteins. Free Radic Biol Med 2010; 49:1903-15. [PMID: 20883776 PMCID: PMC3005768 DOI: 10.1016/j.freeradbiomed.2010.09.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 08/27/2010] [Accepted: 09/20/2010] [Indexed: 11/26/2022]
Abstract
Hexavalent chromium (Cr(VI)) compounds (e.g., chromates) are strong oxidants that readily enter cells, where they are reduced to reactive Cr species that also facilitate reactive oxygen species generation. Recent studies demonstrated inhibition and oxidation of the thioredoxin system, with greater effects on mitochondrial thioredoxin (Trx2). This implies that Cr(VI)-induced oxidant stress may be especially directed at the mitochondria. Examination of other redox-sensitive mitochondrial functions showed that Cr(VI) treatments that cause Trx2 oxidation in human bronchial epithelial cells also result in pronounced and irreversible inhibition of aconitase, a TCA cycle enzyme that has an iron-sulfur (Fe-S) center that is labile with respect to certain oxidants. The activities of electron transport complexes I and II were also inhibited, whereas complex III was not. Electron paramagnetic resonance (EPR) studies of samples at liquid helium temperature (10K) showed a strong signal at g=1.94 that is consistent with the inhibition of electron flow through complex I and/or II. A signal at g=2.02 was also observed, which is consistent with oxidation of the Fe-S center of aconitase. The g=1.94 signal was particularly intense and remained after extracellular Cr(VI) was removed, whereas the g=2.02 signal declined in intensity after Cr(VI) was removed. A similar inhibition of these activities and analogous EPR findings were noted in bovine airways treated ex vivo with Cr(VI). Overall, the data support the hypothesis that Cr(VI) exposure has deleterious effects on a number of redox-sensitive core mitochondrial proteins. The g=1.94 signal could prove to be an important biomarker for oxidative damage resulting from Cr(VI) exposure. The EPR spectra simultaneously showed signals for Cr(V) and Cr(III), which verify Cr(VI) exposure and its intracellular reductive activation.
Collapse
Affiliation(s)
- Charles R Myers
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | | | | |
Collapse
|
34
|
Ohnishi T, Nakamaru-Ogiso E, Ohnishi ST. A new hypothesis on the simultaneous direct and indirect proton pump mechanisms in NADH-quinone oxidoreductase (complex I). FEBS Lett 2010; 584:4131-7. [PMID: 20816962 DOI: 10.1016/j.febslet.2010.08.039] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 08/21/2010] [Accepted: 08/29/2010] [Indexed: 02/07/2023]
Abstract
Recently, Sazanov's group reported the X-ray structure of whole complex I [Nature, 465, 441 (2010)], which presented a strong clue for a "piston-like" structure as a key element in an "indirect" proton pump. We have studied the NuoL subunit which has a high sequence similarity to Na(+)/H(+) antiporters, as do the NuoM and N subunits. We constructed 27 site-directed NuoL mutants. Our data suggest that the H(+)/e(-) stoichiometry seems to have decreased from (4H(+)/2e(-)) in the wild-type to approximately (3H(+)/2e(-)) in NuoL mutants. We propose a revised hypothesis that each of the "direct" and the "indirect" proton pumps transports 2H(+) per 2e(-).
Collapse
Affiliation(s)
- Tomoko Ohnishi
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6059, USA.
| | | | | |
Collapse
|
35
|
Nakamaru-Ogiso E, Kao MC, Chen H, Sinha SC, Yagi T, Ohnishi T. The membrane subunit NuoL(ND5) is involved in the indirect proton pumping mechanism of Escherichia coli complex I. J Biol Chem 2010; 285:39070-8. [PMID: 20826797 DOI: 10.1074/jbc.m110.157826] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Complex I pumps protons across the membrane by using downhill redox energy. Here, to investigate the proton pumping mechanism by complex I, we focused on the largest transmembrane subunit NuoL (Escherichia coli ND5 homolog). NuoL/ND5 is believed to have H(+) translocation site(s), because of a high sequence similarity to multi-subunit Na(+)/H(+) antiporters. We mutated thirteen highly conserved residues between NuoL/ND5 and MrpA of Na(+)/H(+) antiporters in the chromosomal nuoL gene. The dNADH oxidase activities in mutant membranes were mostly at the control level or modestly reduced, except mutants of Glu-144, Lys-229, and Lys-399. In contrast, the peripheral dNADH-K(3)Fe(CN)(6) reductase activities basically remained unchanged in all the NuoL mutants, suggesting that the peripheral arm of complex I was not affected by point mutations in NuoL. The proton pumping efficiency (the ratio of H(+)/e(-)), however, was decreased in most NuoL mutants by 30-50%, while the IC(50) values for asimicin (a potent complex I inhibitor) remained unchanged. This suggests that the H(+)/e(-) stoichiometry has changed from 4H(+)/2e(-) to 3H(+) or 2H(+)/2e(-) without affecting the direct coupling site. Furthermore, 50 μm of 5-(N-ethyl-N-isopropyl)-amiloride (EIPA), a specific inhibitor for Na(+)/H(+) antiporters, caused a 38 ± 5% decrease in the initial H(+) pump activity in the wild type, while no change was observed in D178N, D303A, and D400A mutants where the H(+) pumping efficiency had already been significantly decreased. The electron transfer activities were basically unaffected by EIPA in both control and mutants. Taken together, our data strongly indicate that the NuoL subunit is involved in the indirect coupling mechanism.
Collapse
Affiliation(s)
- Eiko Nakamaru-Ogiso
- Johnson Research Foundation, Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | | | | | | | | | | |
Collapse
|
36
|
Medvedev ES, Couch VA, Stuchebrukhov AA. Determination of the intrinsic redox potentials of FeS centers of respiratory complex I from experimental titration curves. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1665-71. [PMID: 20513348 DOI: 10.1016/j.bbabio.2010.05.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Revised: 05/17/2010] [Accepted: 05/24/2010] [Indexed: 11/19/2022]
Abstract
Recently, Euro et al. [Biochem. 47, 3185 (2008) ] have reported titration data for seven of nine FeS redox centers of complex I from Escherichiacoli. There is a significant uncertainty in the assignment of the titration data. Four of the titration curves were assigned to N1a, N1b, N6b, and N2 centers; one curve either to N3 or N7; one more either to N4 or N5; and the last one denoted Nx could not be assigned at all. In addition, the assignment of the titration data to the N6b/N6a pair is also uncertain. In this paper, using our calculated interaction energies [Couch et al. BBA 1787, 1266 (2009)], we perform statistical analysis of these data, considering a variety of possible assignments, find the best fit, and determine the intrinsic redox potentials of the centers. The intrinsic potentials could be determined with an uncertainty of less than +/-10 mV at a 95% confidence level for best fit assignments. We also find that the best agreement between theoretical and experimental titration curves is obtained with the N6b-N2 interaction equal to 71+/-14 or 96+/-26 mV depending on the N6b/N6a titration data assignment, which is stronger than was expected and may indicate a close distance of the N2 center to the membrane surface.
Collapse
Affiliation(s)
- Emile S Medvedev
- Institute of Problems of Chemical Physics, Russian Academy of Sciences, 142432 Chernogolovka, Russia
| | | | | |
Collapse
|
37
|
Ransac S, Arnarez C, Mazat JP. The flitting of electrons in complex I: a stochastic approach. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:641-8. [PMID: 20230777 DOI: 10.1016/j.bbabio.2010.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2009] [Revised: 02/19/2010] [Accepted: 03/06/2010] [Indexed: 12/12/2022]
Abstract
A stochastic approach based on the Gillespie algorithm is particularly well adapted to describe the time course of the redox reactions that occur inside the respiratory chain complexes because they involve the motion of single electrons between the individual unique redox centres of a given complex. We use this approach to describe the molecular functioning of the peripheral arm of complex I based on its known crystallographic structure and the rate constants of electron tunnelling derived from the Moser and Dutton phenomenological equations. There are several possible electrons pathways but we show that most of them take the route defined by the successive sites and redox centres: NADH+ site-FMN-N3-N1b-N4-N5-N6a-N6b-N2-Q site. However, the electrons do not go directly from NADH towards the ubiquinone molecule. They frequently jump back and forth between neighbouring redox centres with the result that the net flux of electrons through complex I (i.e. net number of electrons reducing a ubiquinone) is far smaller than the number of redox reactions which actually occur. While most of the redox centres are reduced in our simulations the degree of reduction can vary according to the individual midpoint potentials. The high turnover number observed in our simulation seems to indicate that, in the whole complex I, one or several slower step(s) follow(s) the redox reactions involved in the peripheral arm. It also appears that the residence time of FMNH* and SQ* (possible producers of ROS) is low (around 4% and between 1.6% and 5% respectively according to the values of the midpoint potentials). We did not find any evidence for a role of N7 which remains mainly reduced in our simulations. The role of N1a is complex and depends upon its midpoint potential. In all cases its presence slightly decreases the life time of the flavosemiquinone species. These simulations demonstrate the interest of this type of model which links the molecular physico-chemistry of the individual redox reactions to the more global level of the reaction, as is observed experimentally.
Collapse
Affiliation(s)
- Stéphane Ransac
- Université de Bordeaux 2, Mitochondrial physiopathology laboratory, INSERM U688, Bordeaux, France
| | | | | |
Collapse
|
38
|
Roessler MM, King MS, Robinson AJ, Armstrong FA, Harmer J, Hirst J. Direct assignment of EPR spectra to structurally defined iron-sulfur clusters in complex I by double electron-electron resonance. Proc Natl Acad Sci U S A 2010; 107:1930-5. [PMID: 20133838 PMCID: PMC2808219 DOI: 10.1073/pnas.0908050107] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In oxidative phosphorylation, complex I (NADH:quinone oxidoreductase) couples electron transfer to proton translocation across an energy-transducing membrane. Complex I contains a flavin mononucleotide to oxidize NADH, and an unusually long series of iron-sulfur (FeS) clusters, in several subunits, to transfer the electrons to quinone. Understanding coupled electron transfer in complex I requires a detailed knowledge of the properties of individual clusters and of the cluster ensemble, and so it requires the correlation of spectroscopic and structural data: This has proved a challenging task. EPR studies on complex I from Bos taurus have established that EPR signals N1b, N2 and N3 arise, respectively, from the 2Fe cluster in the 75 kDa subunit, and from 4Fe clusters in the PSST and 51 kDa subunits (positions 2, 7, and 1 along the seven-cluster chain extending from the flavin). The other clusters have either evaded detection or definitive signal assignments have not been established. Here, we combine double electron-electron resonance (DEER) spectroscopy on B. taurus complex I with the structure of the hydrophilic domain of Thermus thermophilus complex I. By considering the magnetic moments of the clusters and the orientation selectivity of the DEER experiment explicitly, signal N4 is assigned to the first 4Fe cluster in the TYKY subunit (position 5), and N5 to the all-cysteine ligated 4Fe cluster in the 75 kDa subunit (position 3). The implications of our assignment for the mechanisms of electron transfer and energy transduction by complex I are discussed.
Collapse
Affiliation(s)
- Maxie M. Roessler
- Center for Advanced Electron Spin Resonance, and
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, United Kingdom; and
| | - Martin S. King
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/Medical Research Council Building, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Alan J. Robinson
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/Medical Research Council Building, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Fraser A. Armstrong
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, United Kingdom; and
| | | | - Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/Medical Research Council Building, Hills Road, Cambridge, CB2 0XY, United Kingdom
| |
Collapse
|
39
|
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.
Collapse
|
40
|
Abstract
NADH:ubiquinone oxidoreductase (complex I) is an entry point for electrons into the respiratory chain in many eukaryotes. It couples NADH oxidation and ubiquinone reduction to proton translocation across the mitochondrial inner membrane. Because complex I deficiencies occur in a wide range of neuromuscular diseases, including Parkinson's disease, there is a clear need for model eukaryotic systems to facilitate structural, functional and mutational studies. In the present study, we describe the purification and characterization of the complexes I from two yeast species, Pichia pastoris and Pichia angusta. They are obligate aerobes which grow to very high cell densities on simple medium, as yeast-like, spheroidal cells. Both Pichia enzymes catalyse inhibitor-sensitive NADH:ubiquinone oxidoreduction, display EPR spectra which match closely to those from other eukaryotic complexes I, and show patterns characteristic of complex I in SDS/PAGE analysis. Mass spectrometry was used to identify several canonical complex I subunits. Purified P. pastoris complex I has a particularly high specific activity, and incorporating it into liposomes demonstrates that NADH oxidation is coupled to the generation of a protonmotive force. Interestingly, the rate of NADH-induced superoxide production by the Pichia enzymes is more than twice as high as that of the Bos taurus enzyme. Our results both resolve previous disagreement about whether Pichia species encode complex I, furthering understanding of the evolution of complex I within dikarya, and they provide two new, robust and highly active model systems for study of the structure and catalytic mechanism of eukaryotic complexes I.
Collapse
|
41
|
Abstract
Based on explicit definitions of biomolecular EPR spectroscopy and of the metallome, this tutorial review positions EPR in the field of metallomics as a unique method to study native, integrated systems of metallobiomolecular coordination complexes subject to external stimuli. The specific techniques of whole-system bioEPR spectroscopy are described and their historic, recent, and anticipated applications are discussed.
Collapse
Affiliation(s)
- Wilfred R Hagen
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628BC Delft, The Netherlands.
| |
Collapse
|
42
|
Couch VA, Medvedev ES, Stuchebrukhov AA. Electrostatics of the FeS clusters in respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:1266-71. [PMID: 19445896 DOI: 10.1016/j.bbabio.2009.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Revised: 04/29/2009] [Accepted: 05/07/2009] [Indexed: 10/20/2022]
Abstract
Respiratory complex I couples the transfer of electrons from NADH to ubiquinone and the translocation of protons across the mitochondrial membrane. A detailed understanding of the midpoint reduction potentials (E(m)) of each redox center and the factors which influence those potentials are critical in the elucidation of the mechanism of electron transfer in this enzyme. We present accurate electrostatic interaction energies for the iron-sulfur (FeS) clusters of complex I to facilitate the development of models and the interpretation of experiments in connection to electron transfer (ET) in this enzyme. To calculate redox titration curves for the FeS clusters it is necessary to include interactions between clusters, which in turn can be used to refine E(m) values and validate spectroscopic assignments of each cluster. Calculated titration curves for clusters N4, N5, and N6a are discussed. Furthermore, we present some initial findings on the electrostatics of the redox centers of complex I under the influence of externally applied membrane potentials. A means of determining the location of the FeS cofactors within the holo-complex based on electrostatic arguments is proposed. A simple electrostatic model of the protein/membrane system is examined to illustrate the viability of our hypothesis.
Collapse
Affiliation(s)
- Vernon A Couch
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | | | | |
Collapse
|
43
|
Maly T, Zwicker K, Cernescu A, Brandt U, Prisner TF. New pulsed EPR methods and their application to characterize mitochondrial complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:584-92. [PMID: 19366602 DOI: 10.1016/j.bbabio.2009.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Revised: 02/04/2009] [Accepted: 02/05/2009] [Indexed: 10/21/2022]
Abstract
Electron Paramagnetic Resonance (EPR) spectroscopy is the method of choice to study paramagnetic cofactors that often play an important role as active centers in electron transfer processes in biological systems. However, in many cases more than one paramagnetic species is contributing to the observed EPR spectrum, making the analysis of individual contributions difficult and in some cases impossible. With time-domain techniques it is possible to exploit differences in the relaxation behavior of different paramagnetic species to distinguish between them and separate their individual spectral contribution. Here we give an overview of the use of pulsed EPR spectroscopy to study the iron-sulfur clusters of NADH:ubiquinone oxidoreductase (complex I). While FeS cluster N1 can be studied individually at a temperature of 30 K, this is not possible for FeS cluster N2 due to its severe spectral overlap with cluster N1. In this case Relaxation Filtered Hyperfine (REFINE) spectroscopy can be used to separate the overlapping spectra based on differences in their relaxation behavior.
Collapse
Affiliation(s)
- Thorsten Maly
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | | | | |
Collapse
|
44
|
Zickermann V, Kerscher S, Zwicker K, Tocilescu MA, Radermacher M, Brandt U. Architecture of complex I and its implications for electron transfer and proton pumping. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:574-83. [PMID: 19366614 DOI: 10.1016/j.bbabio.2009.01.012] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Revised: 01/15/2009] [Accepted: 01/15/2009] [Indexed: 11/27/2022]
Abstract
Proton pumping NADH:ubiquinone oxidoreductase (complex I) is the largest and remains by far the least understood enzyme complex of the respiratory chain. It consists of a peripheral arm harbouring all known redox active prosthetic groups and a membrane arm with a yet unknown number of proton translocation sites. The ubiquinone reduction site close to iron-sulfur cluster N2 at the interface of the 49-kDa and PSST subunits has been mapped by extensive site directed mutagenesis. Independent lines of evidence identified electron transfer events during reduction of ubiquinone to be associated with the potential drop that generates the full driving force for proton translocation with a 4H(+)/2e(-) stoichiometry. Electron microscopic analysis of immuno-labelled native enzyme and of a subcomplex lacking the electron input module indicated a distance of 35-60 A of cluster N2 to the membrane surface. Resolution of the membrane arm into subcomplexes showed that even the distal part harbours subunits that are prime candidates to participate in proton translocation because they are homologous to sodium/proton antiporters and contain conserved charged residues in predicted transmembrane helices. The mechanism of redox linked proton translocation by complex I is largely unknown but has to include steps where energy is transmitted over extremely long distances. In this review we compile the available structural information on complex I and discuss implications for complex I function.
Collapse
Affiliation(s)
- Volker Zickermann
- Goethe-Universität, Fachbereich Medizin, Molekulare Bioenergetik, ZBC, Theodor-Stern-Kai 7, Haus 26, D-60590 Frankfurt am Main, Germany
| | | | | | | | | | | |
Collapse
|
45
|
|
46
|
Challenges in elucidating structure and mechanism of proton pumping NADH:ubiquinone oxidoreductase (complex I). J Bioenerg Biomembr 2008; 40:475-83. [PMID: 18982432 DOI: 10.1007/s10863-008-9171-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Accepted: 08/01/2008] [Indexed: 12/11/2022]
Abstract
Proton pumping NADH:ubiquinone oxidoreductase (complex I) is the most complicated and least understood enzyme of the respiratory chain. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulfur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST- and 49-kDa subunits of complex I. An access path for ubiquinone and different partially overlapping inhibitor binding regions were defined within this pocket by site directed mutagenesis. A combination of biochemical and single particle analysis studies suggests that the ubiquinone reduction site is located well above the membrane domain. Therefore, direct coupling mechanisms seem unlikely and the redox energy must be converted into a conformational change that drives proton pumping across the membrane arm. It is not known which of the subunits and how many are involved in proton translocation. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. The physiological role of this phenomenon is yet unclear but it could contribute to the regulation of complex I activity in-vivo.
Collapse
|
47
|
Nakamaru-Ogiso E, Matsuno-Yagi A, Yoshikawa S, Yagi T, Ohnishi T. Iron-sulfur cluster N5 is coordinated by an HXXXCXXCXXXXXC motif in the NuoG subunit of Escherichia coli NADH:quinone oxidoreductase (complex I). J Biol Chem 2008; 283:25979-87. [PMID: 18603533 DOI: 10.1074/jbc.m804015200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
NADH:quinone oxidoreductase (complex I) plays a central role in cellular energy metabolism, and its dysfunction is found in numerous human mitochondrial diseases. Although the understanding of its structure and function has been limited, the x-ray crystal structure of the hydrophilic part of Thermus thermophilus complex I recently became available. It revealed the localization of all redox centers, including 9 iron-sulfur clusters and their coordinating ligands, and confirmed the predictions mostly made by Ohnishi et al. (Ohnishi, T., and Nakamaru-Ogiso, E. (2008) Biochim. Biophys. Acta 1777, 703-710) based on various EPR studies. Recently, Yakovlev et al. (Yakovlev, G., Reda, T., and Hirst, J. (2007) Proc. Natl. Acad. Sci. U. S. A. 104, 12720-12725) claimed that the EPR signals from clusters N4, N5, and N6b were misassigned. Here we identified and characterized cluster N5 in the Escherichia coli complex I whose EPR signals had never been detected by any group. Using homologous recombination, we constructed mutant strains of H101A, H101C, H101A/C114A, and cluster N5 knock-out. Although mutant NuoEFG subcomplexes were dissociated from complex I, we successfully recovered these mutant NuoCDEFG subcomplexes by expressing the His-tagged NuoCD subunit, which had a high affinity to NuoG. The W221A mutant was used as a control subcomplex carrying wild-type clusters. By lowering temperatures to around 3 K, we finally succeeded in detecting cluster N5 signals in the control for the first time. However, no cluster N5 signals were found in any of the N5 mutants, whereas EPR signals from all other clusters were detected. These data confirmed that, contrary to the misassignment claim, cluster N5 has a unique coordination with His(Cys)(3) ligands in NuoG.
Collapse
Affiliation(s)
- Eiko Nakamaru-Ogiso
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | | | | | | | | |
Collapse
|