1
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Djurabekova A, Lasham J, Zdorevskyi O, Zickermann V, Sharma V. Long-range electron proton coupling in respiratory complex I - insights from molecular simulations of the quinone chamber and antiporter-like subunits. Biochem J 2024; 481:499-514. [PMID: 38572757 DOI: 10.1042/bcj20240009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 04/05/2024]
Abstract
Respiratory complex I is a redox-driven proton pump. Several high-resolution structures of complex I have been determined providing important information about the putative proton transfer paths and conformational transitions that may occur during catalysis. However, how redox energy is coupled to the pumping of protons remains unclear. In this article, we review biochemical, structural and molecular simulation data on complex I and discuss several coupling models, including the key unresolved mechanistic questions. Focusing both on the quinone-reductase domain as well as the proton-pumping membrane-bound domain of complex I, we discuss a molecular mechanism of proton pumping that satisfies most experimental and theoretical constraints. We suggest that protonation reactions play an important role not only in catalysis, but also in the physiologically-relevant active/deactive transition of complex I.
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Affiliation(s)
| | - Jonathan Lasham
- Department of Physics, University of Helsinki, Helsinki, Finland
| | | | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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2
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Méndez D, Tellería F, Monroy-Cárdenas M, Montecino-Garrido H, Mansilla S, Castro L, Trostchansky A, Muñoz-Córdova F, Zickermann V, Schiller J, Alfaro S, Caballero J, Araya-Maturana R, Fuentes E. Linking triphenylphosphonium cation to a bicyclic hydroquinone improves their antiplatelet effect via the regulation of mitochondrial function. Redox Biol 2024; 72:103142. [PMID: 38581860 PMCID: PMC11002875 DOI: 10.1016/j.redox.2024.103142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/11/2024] [Accepted: 03/28/2024] [Indexed: 04/08/2024] Open
Abstract
Platelets are the critical target for preventing and treating pathological thrombus formation. However, despite current antiplatelet therapy, cardiovascular mortality remains high, and cardiovascular events continue in prescribed patients. In this study, first results were obtained with ortho-carbonyl hydroquinones as antiplatelet agents; we found that linking triphenylphosphonium cation to a bicyclic ortho-carbonyl hydroquinone moiety by a short alkyl chain significantly improved their antiplatelet effect by affecting the mitochondrial functioning. The mechanism of action involves uncoupling OXPHOS, which leads to an increase in mitochondrial ROS production and a decrease in the mitochondrial membrane potential and OCR. This alteration disrupts the energy production by mitochondrial function necessary for the platelet activation process. These effects are responsive to the complete structure of the compounds and not to isolated parts of the compounds tested. The results obtained in this research can be used as the basis for developing new antiplatelet agents that target mitochondria.
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Affiliation(s)
- Diego Méndez
- Thrombosis and Healthy Aging Research Center, MIBI: Interdisciplinary Group on Mitochondrial Targeting and Bioenergetics, Medical Technology School, Department of Clinical Biochemistry and Immunohematology, Faculty of Health Sciences, Universidad de Talca, Talca, Chile
| | - Francisca Tellería
- Thrombosis and Healthy Aging Research Center, MIBI: Interdisciplinary Group on Mitochondrial Targeting and Bioenergetics, Medical Technology School, Department of Clinical Biochemistry and Immunohematology, Faculty of Health Sciences, Universidad de Talca, Talca, Chile
| | - Matías Monroy-Cárdenas
- Instituto de Química de Recursos Naturales, MIBI: Interdisciplinary Group on Mitochondrial Targeting and Bioenergetics, Universidad de Talca, Talca, 3460000, Chile
| | - Héctor Montecino-Garrido
- Thrombosis and Healthy Aging Research Center, MIBI: Interdisciplinary Group on Mitochondrial Targeting and Bioenergetics, Medical Technology School, Department of Clinical Biochemistry and Immunohematology, Faculty of Health Sciences, Universidad de Talca, Talca, Chile
| | - Santiago Mansilla
- Departamento de Métodos Cuantitativos and Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, 11800, Uruguay
| | - Laura Castro
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, 11800, Uruguay
| | - Andrés Trostchansky
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, 11800, Uruguay
| | | | - Volker Zickermann
- Institute of Biochemistry II, Goethe University Medical School, Germany
| | - Jonathan Schiller
- Institute of Biochemistry II, Goethe University Medical School, Germany
| | - Sergio Alfaro
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile
| | - Julio Caballero
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile
| | - Ramiro Araya-Maturana
- Instituto de Química de Recursos Naturales, MIBI: Interdisciplinary Group on Mitochondrial Targeting and Bioenergetics, Universidad de Talca, Talca, 3460000, Chile.
| | - Eduardo Fuentes
- Thrombosis and Healthy Aging Research Center, MIBI: Interdisciplinary Group on Mitochondrial Targeting and Bioenergetics, Medical Technology School, Department of Clinical Biochemistry and Immunohematology, Faculty of Health Sciences, Universidad de Talca, Talca, Chile.
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3
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Lasham J, Djurabekova A, Zickermann V, Vonck J, Sharma V. Role of Protonation States in the Stability of Molecular Dynamics Simulations of High-Resolution Membrane Protein Structures. J Phys Chem B 2024; 128:2304-2316. [PMID: 38430110 DOI: 10.1021/acs.jpcb.3c07421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Classical molecular dynamics (MD) simulations provide unmatched spatial and time resolution of protein structure and function. However, the accuracy of MD simulations often depends on the quality of force field parameters and the time scale of sampling. Another limitation of conventional MD simulations is that the protonation states of titratable amino acid residues remain fixed during simulations, even though protonation state changes coupled to conformational dynamics are central to protein function. Due to the uncertainty in selecting protonation states, classical MD simulations are sometimes performed with all amino acids modeled in their standard charged states at pH 7. Here, we performed and analyzed classical MD simulations on high-resolution cryo-EM structures of two large membrane proteins that transfer protons by catalyzing protonation/deprotonation reactions. In simulations performed with titratable amino acids modeled in their standard protonation (charged) states, the structure diverges far from its starting conformation. In comparison, MD simulations performed with predetermined protonation states of amino acid residues reproduce the structural conformation, protein hydration, and protein-water and protein-protein interactions of the structure much better. The results support the notion that it is crucial to perform basic protonation state calculations, especially on structures where protonation changes play an important functional role, prior to the launch of any conventional MD simulations. Furthermore, the combined approach of fast protonation state prediction and MD simulations can provide valuable information about the charge states of amino acids in the cryo-EM sample. Even though accurate prediction of protonation states in proteinaceous environments currently remains a challenge, we introduce an approach of combining pKa prediction with cryo-EM density map analysis that helps in improving not only the protonation state predictions but also the atomic modeling of density data.
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Affiliation(s)
- Jonathan Lasham
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Amina Djurabekova
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Vivek Sharma
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
- HiLIFE Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
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4
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Laube E, Schiller J, Zickermann V, Vonck J. Using cryo-EM to understand the assembly pathway of respiratory complex I. Acta Crystallogr D Struct Biol 2024; 80:159-173. [PMID: 38372588 PMCID: PMC10910544 DOI: 10.1107/s205979832400086x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/23/2024] [Indexed: 02/20/2024] Open
Abstract
Complex I (proton-pumping NADH:ubiquinone oxidoreductase) is the first component of the mitochondrial respiratory chain. In recent years, high-resolution cryo-EM studies of complex I from various species have greatly enhanced the understanding of the structure and function of this important membrane-protein complex. Less well studied is the structural basis of complex I biogenesis. The assembly of this complex of more than 40 subunits, encoded by nuclear or mitochondrial DNA, is an intricate process that requires at least 20 different assembly factors in humans. These are proteins that are transiently associated with building blocks of the complex and are involved in the assembly process, but are not part of mature complex I. Although the assembly pathways have been studied extensively, there is limited information on the structure and molecular function of the assembly factors. Here, the insights that have been gained into the assembly process using cryo-EM are reviewed.
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Affiliation(s)
- Eike Laube
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Jonathan Schiller
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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5
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Schiller J, Laube E, Wittig I, Kühlbrandt W, Vonck J, Zickermann V. Insights into complex I assembly: Function of NDUFAF1 and a link with cardiolipin remodeling. Sci Adv 2022; 8:eadd3855. [PMID: 36383672 PMCID: PMC9668296 DOI: 10.1126/sciadv.add3855] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/14/2022] [Indexed: 06/02/2023]
Abstract
Respiratory complex I is a ~1-MDa proton pump in mitochondria. Its structure has been revealed in great detail, but the structural basis of its assembly, in humans involving at least 15 assembly factors, is essentially unknown. We determined cryo-electron microscopy structures of assembly intermediates associated with assembly factor NDUFAF1 in a yeast model system. Subunits ND2 and NDUFC2 together with assembly factors NDUFAF1 and CIA84 form the nucleation point of the NDUFAF1-dependent assembly pathway. Unexpectedly, the cardiolipin remodeling enzyme tafazzin is an integral component of this core complex. In a later intermediate, all 12 subunits of the proximal proton pump module have assembled. NDUFAF1 locks the central ND3 subunit in an assembly-competent conformation, and major rearrangements of central subunits are required for complex I maturation.
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Affiliation(s)
- Jonathan Schiller
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Center for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Eike Laube
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Ilka Wittig
- Functional Proteomics, Institute for Cardiovascular Physiology, Goethe University, 60590 Frankfurt am Main, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Center for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
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6
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Lee Y, Haapanen O, Altmeyer A, Kühlbrandt W, Sharma V, Zickermann V. Ion transfer mechanisms in Mrp-type antiporters from high resolution cryoEM and molecular dynamics simulations. Nat Commun 2022; 13:6091. [PMID: 36241630 PMCID: PMC9568556 DOI: 10.1038/s41467-022-33640-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 09/23/2022] [Indexed: 12/24/2022] Open
Abstract
Multiple resistance and pH adaptation (Mrp) cation/proton antiporters are essential for growth of a variety of halophilic and alkaliphilic bacteria under stress conditions. Mrp-type antiporters are closely related to the membrane domain of respiratory complex I. We determined the structure of the Mrp antiporter from Bacillus pseudofirmus by electron cryo-microscopy at 2.2 Å resolution. The structure resolves more than 99% of the sidechains of the seven membrane subunits MrpA to MrpG plus 360 water molecules, including ~70 in putative ion translocation pathways. Molecular dynamics simulations based on the high-resolution structure revealed details of the antiport mechanism. We find that switching the position of a histidine residue between three hydrated pathways in the MrpA subunit is critical for proton transfer that drives gated trans-membrane sodium translocation. Several lines of evidence indicate that the same histidine-switch mechanism operates in respiratory complex I.
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Affiliation(s)
- Yongchan Lee
- grid.419494.50000 0001 1018 9466Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany ,grid.268441.d0000 0001 1033 6139Present Address: Graduate School of Medical Life Science, Yokohama City University, 230-0045 Kanagawa, Japan
| | - Outi Haapanen
- grid.7737.40000 0004 0410 2071Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Anton Altmeyer
- grid.7839.50000 0004 1936 9721Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany ,grid.7839.50000 0004 1936 9721Centre for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Werner Kühlbrandt
- grid.419494.50000 0001 1018 9466Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Vivek Sharma
- grid.7737.40000 0004 0410 2071Department of Physics, University of Helsinki, 00014 Helsinki, Finland ,grid.7737.40000 0004 0410 2071HiLIFE Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Volker Zickermann
- grid.7839.50000 0004 1936 9721Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany ,grid.7839.50000 0004 1936 9721Centre for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
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7
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Djurabekova A, Galemou Yoga E, Nyman A, Pirttikoski A, Zickermann V, Haapanen O, Sharma V. Docking and molecular simulations reveal a quinone binding site on the surface of respiratory complex I. FEBS Lett 2022; 596:1133-1146. [PMID: 35363885 DOI: 10.1002/1873-3468.14346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/11/2022] [Accepted: 03/24/2022] [Indexed: 11/07/2022]
Abstract
The first component of the mitochondrial electron transport chain is respiratory complex I. Several high-resolution structures of complex I from different species have been resolved. However, despite these significant achievements, the mechanism of redox-coupled proton pumping remains elusive. Here, we combined atomistic docking, molecular dynamics simulations and site-directed mutagenesis on respiratory complex I from Yarrowia lipolytica to identify a quinone (Q) binding site on its surface near the horizontal amphipathic helices of ND1 and NDUFS7 subunits. The surface-bound Q makes stable interactions with conserved charged and polar residues, including the highly conserved Arg72 from the NDUFS7 subunit. The binding and dynamics of a Q molecule at the surface-binding site raises interesting possibilities about the mechanism of complex I, which are discussed.
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Affiliation(s)
| | - Etienne Galemou Yoga
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Aino Nyman
- Department of Physics, University of Helsinki, Finland
| | | | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Outi Haapanen
- Department of Physics, University of Helsinki, Finland
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Finland.,HiLIFE Institute of Biotechnology, University of Helsinki, Finland
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8
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Parey K, Lasham J, Mills DJ, Djurabekova A, Haapanen O, Yoga EG, Xie H, Kühlbrandt W, Sharma V, Vonck J, Zickermann V. High-resolution structure and dynamics of mitochondrial complex I-Insights into the proton pumping mechanism. Sci Adv 2021; 7:eabj3221. [PMID: 34767441 PMCID: PMC8589321 DOI: 10.1126/sciadv.abj3221] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/24/2021] [Indexed: 05/23/2023]
Abstract
Mitochondrial NADH:ubiquinone oxidoreductase (complex I) is a 1-MDa membrane protein complex with a central role in energy metabolism. Redox-driven proton translocation by complex I contributes substantially to the proton motive force that drives ATP synthase. Several structures of complex I from bacteria and mitochondria have been determined, but its catalytic mechanism has remained controversial. We here present the cryo-EM structure of complex I from Yarrowia lipolytica at 2.1-Å resolution, which reveals the positions of more than 1600 protein-bound water molecules, of which ~100 are located in putative proton translocation pathways. Another structure of the same complex under steady-state activity conditions at 3.4-Å resolution indicates conformational transitions that we associate with proton injection into the central hydrophilic axis. By combining high-resolution structural data with site-directed mutagenesis and large-scale molecular dynamic simulations, we define details of the proton translocation pathways and offer insights into the redox-coupled proton pumping mechanism of complex I.
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Affiliation(s)
- Kristian Parey
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Jonathan Lasham
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Deryck J. Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Amina Djurabekova
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Outi Haapanen
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Etienne Galemou Yoga
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Hao Xie
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Vivek Sharma
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
- HiLIFE Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
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9
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Galemou Yoga E, Schiller J, Zickermann V. Ubiquinone Binding and Reduction by Complex I-Open Questions and Mechanistic Implications. Front Chem 2021; 9:672851. [PMID: 33996767 PMCID: PMC8119997 DOI: 10.3389/fchem.2021.672851] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
NADH: ubiquinone oxidoreductase (complex I) is the first enzyme complex of the respiratory chain. Complex I is a redox-driven proton pump that contributes to the proton motive force that drives ATP synthase. The structure of complex I has been analyzed by x-ray crystallography and electron cryo-microscopy and is now well-described. The ubiquinone (Q) reduction site of complex I is buried in the peripheral arm and a tunnel-like structure is thought to provide access for the hydrophobic substrate from the membrane. Several intermediate binding positions for Q in the tunnel were identified in molecular simulations. Structural data showed the binding of native Q molecules and short chain analogs and inhibitors in the access pathway and in the Q reduction site, respectively. We here review the current knowledge on the interaction of complex I with Q and discuss recent hypothetical models for the coupling mechanism.
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Affiliation(s)
- Etienne Galemou Yoga
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt, Germany.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt, Germany
| | - Jonathan Schiller
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt, Germany.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt, Germany
| | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt, Germany.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt, Germany
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10
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Scherr J, Tang Z, Küllmer M, Balser S, Scholz AS, Winter A, Parey K, Rittner A, Grininger M, Zickermann V, Rhinow D, Terfort A, Turchanin A. Smart Molecular Nanosheets for Advanced Preparation of Biological Samples in Electron Cryo-Microscopy. ACS Nano 2020; 14:9972-9978. [PMID: 32589396 DOI: 10.1021/acsnano.0c03052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Transmission electron cryo-microscopy (cryoEM) of vitrified biological specimens is a powerful tool for structural biology. Current preparation of vitrified biological samples starts off with sample isolation and purification, followed by the fixation in a freestanding layer of amorphous ice. Here, we demonstrate that ultrathin (∼10 nm) smart molecular nanosheets having specific biorecognition sites embedded in a biorepulsive layer covalently bound to a mechanically stable carbon nanomembrane allow for a much simpler isolation and structural analysis. We characterize in detail the engineering of these nanosheets and their biorecognition properties employing complementary methods such as X-ray photoelectron and infrared spectroscopy, atomic force microscopy as well as surface plasmon resonance measurements. The desired functionality of the developed nanosheets is demonstrated by in situ selection of a His-tagged protein from a mixture and its subsequent structural analysis by cryoEM.
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Affiliation(s)
- Julian Scherr
- Department of Chemistry, University of Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Zian Tang
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Lessingstr. 10, 07743 Jena, Germany
| | - Maria Küllmer
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Lessingstr. 10, 07743 Jena, Germany
| | - Sebastian Balser
- Department of Chemistry, University of Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Alexander Stefan Scholz
- Department of Chemistry, University of Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Andreas Winter
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Lessingstr. 10, 07743 Jena, Germany
| | - Kristian Parey
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt, Germany
| | - Alexander Rittner
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, University of Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, University of Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Volker Zickermann
- Institute of Biochemistry II, Medical School, University of Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Daniel Rhinow
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt, Germany
| | - Andreas Terfort
- Department of Chemistry, University of Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Andrey Turchanin
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Lessingstr. 10, 07743 Jena, Germany
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11
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Parey K, Wirth C, Vonck J, Zickermann V. Respiratory complex I - structure, mechanism and evolution. Curr Opin Struct Biol 2020; 63:1-9. [PMID: 32058886 DOI: 10.1016/j.sbi.2020.01.004] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/10/2020] [Indexed: 02/07/2023]
Abstract
Respiratory complex I is an intricate multi-subunit membrane protein with a central function in aerobic energy metabolism. During the last years, structures of mitochondrial complex I and respiratory supercomplexes were determined by cryo-EM at increasing resolution. Structural and computational studies have shed light on the dynamics of proton translocation pathways, the interaction of complex I with lipids and the unusual access pathway of ubiquinone to the active site. Recent advances in understanding complex I function include characterization of specific conformational changes that are critical for proton pumping. Cryo-EM structures of the NADH dehydrogenase-like (NDH) complex of photosynthesis and a bacterial membrane bound hydrogenase (MBH) have provided a broader perspective on the complex I superfamily.
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Affiliation(s)
- Kristian Parey
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany; Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany; Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Christophe Wirth
- Institute of Biochemistry and Molecular Biology, ZBMZ, Medical Faculty, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
| | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany; Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany.
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12
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Parey K, Haapanen O, Sharma V, Köfeler H, Züllig T, Prinz S, Siegmund K, Wittig I, Mills DJ, Vonck J, Kühlbrandt W, Zickermann V. High-resolution cryo-EM structures of respiratory complex I: Mechanism, assembly, and disease. Sci Adv 2019; 5:eaax9484. [PMID: 31844670 PMCID: PMC6905873 DOI: 10.1126/sciadv.aax9484] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/22/2019] [Indexed: 05/23/2023]
Abstract
Respiratory complex I is a redox-driven proton pump, accounting for a large part of the electrochemical gradient that powers mitochondrial adenosine triphosphate synthesis. Complex I dysfunction is associated with severe human diseases. Assembly of the one-megadalton complex I in the inner mitochondrial membrane requires assembly factors and chaperones. We have determined the structure of complex I from the aerobic yeast Yarrowia lipolytica by electron cryo-microscopy at 3.2-Å resolution. A ubiquinone molecule was identified in the access path to the active site. The electron cryo-microscopy structure indicated an unusual lipid-protein arrangement at the junction of membrane and matrix arms that was confirmed by molecular simulations. The structure of a complex I mutant and an assembly intermediate provide detailed molecular insights into the cause of a hereditary complex I-linked disease and complex I assembly in the inner mitochondrial membrane.
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Affiliation(s)
- Kristian Parey
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Outi Haapanen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Harald Köfeler
- Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Thomas Züllig
- Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Simone Prinz
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Karin Siegmund
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Ilka Wittig
- Functional Proteomics, SFB815 Core Unit, Medical School, Goethe University, Frankfurt am Main, Germany
| | - Deryck J. Mills
- 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
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
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13
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Scherr J, Neuhaus A, Parey K, Klusch N, Murphy BJ, Zickermann V, Kühlbrandt W, Terfort A, Rhinow D. Noncovalent Functionalization of Carbon Substrates with Hydrogels Improves Structural Analysis of Vitrified Proteins by Electron Cryo-Microscopy. ACS Nano 2019; 13:7185-7190. [PMID: 31117383 DOI: 10.1021/acsnano.9b02651] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In electron cryo-microscopy, structure determination of protein molecules is frequently hampered by adsorption of the particles to the support film material, typically amorphous carbon. Here, we report that pyrene derivatives with one or two polyglycerol (PG) side chains bind to the amorphous carbon films, forming a biorepulsive hydrogel layer so that the number of protein particles in the vitreous ice drastically increases. This approach could be extended by adding a hydrogel-functionalized carbon nanotube network (HyCaNet, the hydrogel again being formed from the PG-pyrene derivatives), which stabilized the protein-containing thin ice films during imaging with the electron beam. The stabilization resulted in reduced particle motion by up to 70%. These substrates were instrumental for determining the structure of a large membrane protein complex.
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Affiliation(s)
- Julian Scherr
- Department of Chemistry, Institute of Inorganic and Analytical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt , Germany
| | - Alexander Neuhaus
- Department of Structural Biology , Max Planck Institute of Biophysics , Max-von-Laue-Str. 3 , 60438 Frankfurt , Germany
| | - Kristian Parey
- Department of Structural Biology , Max Planck Institute of Biophysics , Max-von-Laue-Str. 3 , 60438 Frankfurt , Germany
| | - Niklas Klusch
- Department of Structural Biology , Max Planck Institute of Biophysics , Max-von-Laue-Str. 3 , 60438 Frankfurt , Germany
| | - Bonnie J Murphy
- Department of Structural Biology , Max Planck Institute of Biophysics , Max-von-Laue-Str. 3 , 60438 Frankfurt , Germany
| | - Volker Zickermann
- Structural Bioenergetics Group , Institute of Biochemistry II, Medical School , Max-von-Laue-Str. 9 , 60438 Frankfurt , Germany
| | - Werner Kühlbrandt
- Department of Structural Biology , Max Planck Institute of Biophysics , Max-von-Laue-Str. 3 , 60438 Frankfurt , Germany
| | - Andreas Terfort
- Department of Chemistry, Institute of Inorganic and Analytical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt , Germany
| | - Daniel Rhinow
- Department of Structural Biology , Max Planck Institute of Biophysics , Max-von-Laue-Str. 3 , 60438 Frankfurt , Germany
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14
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Parey K, Brandt U, Xie H, Mills DJ, Siegmund K, Vonck J, Kühlbrandt W, Zickermann V. Cryo-EM structure of respiratory complex I at work. eLife 2018; 7:39213. [PMID: 30277212 PMCID: PMC6168287 DOI: 10.7554/elife.39213] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/30/2018] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial complex I has a key role in cellular energy metabolism, generating a major portion of the proton motive force that drives aerobic ATP synthesis. The hydrophilic arm of the L-shaped ~1 MDa membrane protein complex transfers electrons from NADH to ubiquinone, providing the energy to drive proton pumping at distant sites in the membrane arm. The critical steps of energy conversion are associated with the redox chemistry of ubiquinone. We report the cryo-EM structure of complete mitochondrial complex I from the aerobic yeast Yarrowia lipolytica both in the deactive form and after capturing the enzyme during steady-state activity. The site of ubiquinone binding observed during turnover supports a two-state stabilization change mechanism for complex I.
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Affiliation(s)
- Kristian Parey
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Ulrich Brandt
- Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, The Netherlands.,Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Frankfurt, Germany
| | - Hao Xie
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Deryck J Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Karin Siegmund
- Medical School, Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt, Germany.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany.,Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Frankfurt, Germany
| | - Volker Zickermann
- Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Frankfurt, Germany.,Medical School, Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt, Germany.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
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15
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Angerer H, Schönborn S, Gorka J, Bahr U, Karas M, Wittig I, Heidler J, Hoffmann J, Morgner N, Zickermann V. Acyl modification and binding of mitochondrial ACP to multiprotein complexes. Biochim Biophys Acta Mol Cell Res 2017; 1864:1913-1920. [PMID: 28802701 DOI: 10.1016/j.bbamcr.2017.08.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 08/03/2017] [Accepted: 08/08/2017] [Indexed: 01/06/2023]
Abstract
The mitochondrial acyl carrier protein (ACPM/NDUFAB1) is a central element of the mitochondrial fatty acid synthesis type II machinery. Originally ACPM was detected as a subunit of respiratory complex I but the reason for the association with the large enzyme complex remained elusive. Complex I from the aerobic yeast Yarrowia lipolytica comprises two different ACPMs, ACPM1 and ACPM2. They are anchored to the protein complex by LYR (leucine-tyrosine-arginine) motif containing protein (LYRM) subunits LYRM3 (NDUFB9) and LYRM6 (NDUFA6). The ACPM1-LYRM6 and ACPM2-LYRM3 modules are essential for complex I activity and assembly/stability, respectively. We show that in addition to the complex I bound fraction, ACPM1 is present as a free matrix protein and in complex with the soluble LYRM4(ISD11)/NFS1 complex implicated in Fe-S cluster biogenesis. We show that the presence of a long acyl chain bound to the phosphopantetheine cofactor is important for docking ACPMs to protein complexes and we propose that association of ACPMs and LYRMs is universally based on a new protein-protein interaction motif.
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Affiliation(s)
- Heike Angerer
- Goethe University Frankfurt, Medical School, Institute of Biochemistry II, Structural Bioenergetics Group, Max-von-Laue Str. 9, 60438 Frankfurt, Germany.
| | - Stefan Schönborn
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Jan Gorka
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Ute Bahr
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Michael Karas
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Ilka Wittig
- Functional Proteomics, SFB 815 core unit, Goethe-University Frankfurt, Medical School, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Juliana Heidler
- Functional Proteomics, SFB 815 core unit, Goethe-University Frankfurt, Medical School, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Jan Hoffmann
- Goethe University Frankfurt, Institute of Physical and Theoretical Chemistry, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Nina Morgner
- Goethe University Frankfurt, Institute of Physical and Theoretical Chemistry, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Volker Zickermann
- Goethe University Frankfurt, Medical School, Institute of Biochemistry II, Structural Bioenergetics Group, Max-von-Laue Str. 9, 60438 Frankfurt, Germany; Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Germany.
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16
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Scherr J, Parey K, Klusch N, Murphy BJ, Balser S, Neuhaus A, Zickermann V, Kühlbrandt W, Terfort A, Rhinow D. Self-Perforated Hydrogel Nanomembranes Facilitate Structural Analysis of Proteins by Electron Cryo-Microscopy. ACS Nano 2017; 11:6467-6473. [PMID: 28598595 DOI: 10.1021/acsnano.7b03099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We developed a method to improve specimen preparation for electron cryo-microscopy of membrane proteins. The method features a perforated hydrogel nanomembrane that stabilizes the thin film of aqueous buffer spanning the holes of holey carbon films, while at the same time preventing the depletion of protein molecules from these holes. The membrane is obtained by cross-linking of thiolated polyglycerol dendrimer films on gold, which self-perforate upon transfer to holey carbon substrates, forming a sub-micron-sized hydrogel network. The perforated nanomembrane improves the distribution of the protein molecules in the ice considerably. This facilitates data acquisition as demonstrated with two eukaryotic membrane protein complexes.
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Affiliation(s)
- Julian Scherr
- Department of Chemistry, Institute of Inorganic and Analytical Chemistry, Goethe-University , Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Kristian Parey
- Department of Structural Biology, Max Planck Institute of Biophysics , Max-von-Laue-Str. 3, 60438 Frankfurt, Germany
| | - Niklas Klusch
- Department of Structural Biology, Max Planck Institute of Biophysics , Max-von-Laue-Str. 3, 60438 Frankfurt, Germany
| | - Bonnie J Murphy
- Department of Structural Biology, Max Planck Institute of Biophysics , Max-von-Laue-Str. 3, 60438 Frankfurt, Germany
| | - Sebastian Balser
- Department of Chemistry, Institute of Inorganic and Analytical Chemistry, Goethe-University , Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Alexander Neuhaus
- Department of Structural Biology, Max Planck Institute of Biophysics , Max-von-Laue-Str. 3, 60438 Frankfurt, Germany
| | - Volker Zickermann
- Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe-University Frankfurt , Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics , Max-von-Laue-Str. 3, 60438 Frankfurt, Germany
| | - Andreas Terfort
- Department of Chemistry, Institute of Inorganic and Analytical Chemistry, Goethe-University , Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Daniel Rhinow
- Department of Structural Biology, Max Planck Institute of Biophysics , Max-von-Laue-Str. 3, 60438 Frankfurt, Germany
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17
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Krishnathas R, Bonke E, Dröse S, Zickermann V, Nasiri HR. Identification of 4- N-[2-(4-phenoxyphenyl)ethyl]quinazoline-4,6-diamine as a novel, highly potent and specific inhibitor of mitochondrial complex I. Medchemcomm 2017; 8:657-661. [PMID: 30108783 DOI: 10.1039/c6md00655h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 02/17/2017] [Indexed: 12/21/2022]
Abstract
By probing the quinone substrate binding site of mitochondrial complex I with a focused set of quinazoline-based compounds, we identified substitution patterns as being critical for the observed inhibition. The structure activity relationship study also resulted in the discovery of the quinazoline 4-N-[2-(4-phenoxyphenyl)ethyl]quinazoline-4,6-diamine (EVP4593) as a highly potent inhibitor of the multisubunit membrane protein. EVP4593 specifically and effectively reduces the mitochondrial complex I-dependent respiration with no effect on the respiratory chain complexes II-IV. Similar to established Q-site inhibitors, EVP4593 elicits the release of reactive oxygen species at the flavin site of mitochondrial complex I. Recently, EVP4593 was nominated as a lead compound for the treatment of Huntingtons disease. Our results challenge the postulated primary mode-of-action of EVP4593 as an inhibitor of NF-κB pathway activation and/or store-operated calcium influx.
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Affiliation(s)
- Robin Krishnathas
- Johann Wolfgang Goethe-University Frankfurt , Max-von-Laue-Straße 7 , D-60438 Frankfurt am Main , Germany .
| | - Erik Bonke
- Department of Anaesthesiology , Intensive-Care Medicine and Pain Therapy , University Hospital Frankfurt , 60590 Frankfurt am Main , Germany
| | - Stefan Dröse
- Department of Anaesthesiology , Intensive-Care Medicine and Pain Therapy , University Hospital Frankfurt , 60590 Frankfurt am Main , Germany
| | - Volker Zickermann
- Structural Bioenergetics Group , Institute of Biochemistry II , Medical School , Goethe-University , 60438 Frankfurt am Main , Germany.,Cluster of Excellence Frankfurt "Macromolecular Complexes," , Goethe-University , 60438 Frankfurt am Main , Germany
| | - Hamid R Nasiri
- Johann Wolfgang Goethe-University Frankfurt , Max-von-Laue-Straße 7 , D-60438 Frankfurt am Main , Germany .
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18
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Kahlhöfer F, Kmita K, Wittig I, Zwicker K, Zickermann V. Accessory subunit NUYM (NDUFS4) is required for stability of the electron input module and activity of mitochondrial complex I. Biochim Biophys Acta Bioenerg 2016; 1858:175-181. [PMID: 27871794 DOI: 10.1016/j.bbabio.2016.11.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 11/15/2016] [Accepted: 11/17/2016] [Indexed: 11/18/2022]
Abstract
Mitochondrial complex I is an intricate 1MDa membrane protein complex with a central role in aerobic energy metabolism. The minimal form of complex I consists of fourteen central subunits that are conserved from bacteria to man. In addition, eukaryotic complex I comprises some 30 accessory subunits of largely unknown function. The gene for the accessory NDUFS4 subunit of human complex I is a hot spot for fatal pathogenic mutations in humans. We have deleted the gene for the orthologous NUYM subunit in the aerobic yeast Yarrowia lipolytica, an established model system to study eukaryotic complex I and complex I linked diseases. We observed assembly of complex I which lacked only subunit NUYM and retained weak interaction with assembly factor N7BML (human NDUFAF2). Absence of NUYM caused distortion of iron sulfur clusters of the electron input domain leading to decreased complex I activity and increased release of reactive oxygen species. We conclude that NUYM has an important stabilizing function for the electron input module of complex I and is essential for proper complex I function.
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Affiliation(s)
- Flora Kahlhöfer
- Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe-University Frankfurt am Main, Germany
| | - Katarzyna Kmita
- Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe-University Frankfurt am Main, Germany
| | - Ilka Wittig
- Functional Proteomics, Institute of Biochemistry I, Medical School, Goethe-University Frankfurt am Main, Germany; Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University Frankfurt am Main, Germany
| | - Klaus Zwicker
- Institute of Biochemistry I, Medical School, Goethe University Frankfurt am Main, Germany
| | - Volker Zickermann
- Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe-University Frankfurt am Main, Germany; Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University Frankfurt am Main, Germany.
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19
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Wirth C, Zickermann V, Kmita K, Brandt U, Hunte C. Crystal structure of mitochondrial respiratory complex I. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316099435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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20
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Hahn A, Parey K, Bublitz M, Mills DJ, Zickermann V, Vonck J, Kühlbrandt W, Meier T. Structure of a Complete ATP Synthase Dimer Reveals the Molecular Basis of Inner Mitochondrial Membrane Morphology. Mol Cell 2016; 63:445-56. [PMID: 27373333 PMCID: PMC4980432 DOI: 10.1016/j.molcel.2016.05.037] [Citation(s) in RCA: 199] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 04/21/2016] [Accepted: 05/26/2016] [Indexed: 11/28/2022]
Abstract
We determined the structure of a complete, dimeric F1Fo-ATP synthase from yeast Yarrowia lipolytica mitochondria by a combination of cryo-EM and X-ray crystallography. The final structure resolves 58 of the 60 dimer subunits. Horizontal helices of subunit a in Fo wrap around the c-ring rotor, and a total of six vertical helices assigned to subunits a, b, f, i, and 8 span the membrane. Subunit 8 (A6L in human) is an evolutionary derivative of the bacterial b subunit. On the lumenal membrane surface, subunit f establishes direct contact between the two monomers. Comparison with a cryo-EM map of the F1Fo monomer identifies subunits e and g at the lateral dimer interface. They do not form dimer contacts but enable dimer formation by inducing a strong membrane curvature of ∼100°. Our structure explains the structural basis of cristae formation in mitochondria, a landmark signature of eukaryotic cell morphology. Cryo-EM structure of a yeast F1Fo-ATP synthase dimer Inhibitor-free X-ray structure of the F1 head and rotor complex Mechanism of ATP generation by rotary catalysis Structural basis of cristae formation in the inner mitochondrial membrane
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Affiliation(s)
- Alexander Hahn
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Kristian Parey
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Maike Bublitz
- Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Deryck J Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Volker Zickermann
- Institute of Biochemistry II, Medical School, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany.
| | - Thomas Meier
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany.
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21
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Wirth C, Brandt U, Hunte C, Zickermann V. Structure and function of mitochondrial complex I. Biochim Biophys Acta 2016; 1857:902-14. [PMID: 26921811 DOI: 10.1016/j.bbabio.2016.02.013] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 12/13/2022]
Abstract
Proton-pumping NADH:ubiquinone oxidoreductase (complex I) is the largest and most complicated enzyme of the respiratory chain. Fourteen central subunits represent the minimal form of complex I and can be assigned to functional modules for NADH oxidation, ubiquinone reduction, and proton pumping. In addition, the mitochondrial enzyme comprises some 30 accessory subunits surrounding the central subunits that are not directly associated with energy conservation. Complex I is known to release deleterious oxygen radicals (ROS) and its dysfunction has been linked to a number of hereditary and degenerative diseases. We here review recent progress in structure determination, and in understanding the role of accessory subunits and functional analysis of mitochondrial complex I. For the central subunits, structures provide insight into the arrangement of functional modules including the substrate binding sites, redox-centers and putative proton channels and pump sites. Only for two of the accessory subunits, detailed structures are available. Nevertheless, many of them could be localized in the overall structure of complex I, but most of these assignments have to be considered tentative. Strikingly, redox reactions and proton pumping machinery are spatially completely separated and the site of reduction for the hydrophobic substrate ubiquinone is found deeply buried in the hydrophilic domain of the complex. The X-ray structure of complex I from Yarrowia lipolytica provides clues supporting the previously proposed two-state stabilization change mechanism, in which ubiquinone redox chemistry induces conformational states and thereby drives proton pumping. The same structural rearrangements may explain the active/deactive transition of complex I implying an integrated mechanistic model for energy conversion and regulation. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
- Christophe Wirth
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
| | - Ulrich Brandt
- Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Center, Nijmegen, The Netherlands; Cluster of Excellence Frankfurt "Macromolecular Complexes, Goethe-University, Germany
| | - Carola Hunte
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany.
| | - Volker Zickermann
- Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe-University, Frankfurt am Main, Germany; Cluster of Excellence Frankfurt "Macromolecular Complexes, Goethe-University, Germany.
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22
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Zickermann V, Wirth C, Nasiri H, Siegmund K, Schwalbe H, Hunte C, Brandt U. Structural biology. Mechanistic insight from the crystal structure of mitochondrial complex I. Science 2015; 347:44-9. [PMID: 25554780 DOI: 10.1126/science.1259859] [Citation(s) in RCA: 309] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Proton-pumping complex I of the mitochondrial respiratory chain is among the largest and most complicated membrane protein complexes. The enzyme contributes substantially to oxidative energy conversion in eukaryotic cells. Its malfunctions are implicated in many hereditary and degenerative disorders. We report the x-ray structure of mitochondrial complex I at a resolution of 3.6 to 3.9 angstroms, describing in detail the central subunits that execute the bioenergetic function. A continuous axis of basic and acidic residues running centrally through the membrane arm connects the ubiquinone reduction site in the hydrophilic arm to four putative proton-pumping units. The binding position for a substrate analogous inhibitor and blockage of the predicted ubiquinone binding site provide a model for the "deactive" form of the enzyme. The proposed transition into the active form is based on a concerted structural rearrangement at the ubiquinone reduction site, providing support for a two-state stabilization-change mechanism of proton pumping.
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Affiliation(s)
- Volker Zickermann
- Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe-University, 60438 Frankfurt am Main, Germany. Cluster of Excellence Frankfurt "Macromolecular Complexes," Goethe-University, 60438 Frankfurt am Main, Germany.
| | - Christophe Wirth
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Hamid Nasiri
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK. Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, 60438 Frankfurt am Main, Germany
| | - Karin Siegmund
- Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe-University, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Cluster of Excellence Frankfurt "Macromolecular Complexes," Goethe-University, 60438 Frankfurt am Main, Germany. Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, 60438 Frankfurt am Main, Germany
| | - Carola Hunte
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Ulrich Brandt
- Cluster of Excellence Frankfurt "Macromolecular Complexes," Goethe-University, 60438 Frankfurt am Main, Germany. Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Center, 6525 GA Nijmegen, Netherlands.
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Ruzzenente B, Metodiev MD, Wredenberg A, Bratic A, Park CB, Cámara Y, Milenkovic D, Zickermann V, Wibom R, Hultenby K, Erdjument-Bromage H, Tempst P, Brandt U, Stewart JB, Gustafsson CM, Larsson NG. LRPPRC is necessary for polyadenylation and coordination of translation of mitochondrial mRNAs. EMBO J 2011; 31:443-56. [PMID: 22045337 DOI: 10.1038/emboj.2011.392] [Citation(s) in RCA: 234] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 09/30/2011] [Indexed: 11/09/2022] Open
Abstract
Regulation of mtDNA expression is critical for maintaining cellular energy homeostasis and may, in principle, occur at many different levels. The leucine-rich pentatricopeptide repeat containing (LRPPRC) protein regulates mitochondrial mRNA stability and an amino-acid substitution of this protein causes the French-Canadian type of Leigh syndrome (LSFC), a neurodegenerative disorder characterized by complex IV deficiency. We have generated conditional Lrpprc knockout mice and show here that the gene is essential for embryonic development. Tissue-specific disruption of Lrpprc in heart causes mitochondrial cardiomyopathy with drastic reduction in steady-state levels of most mitochondrial mRNAs. LRPPRC forms an RNA-dependent protein complex that is necessary for maintaining a pool of non-translated mRNAs in mammalian mitochondria. Loss of LRPPRC does not only decrease mRNA stability, but also leads to loss of mRNA polyadenylation and the appearance of aberrant mitochondrial translation. The translation pattern without the presence of LRPPRC is misregulated with excessive translation of some transcripts and no translation of others. Our findings point to the existence of an elaborate machinery that regulates mammalian mtDNA expression at the post-transcriptional level.
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Affiliation(s)
- Benedetta Ruzzenente
- Department of Mitochondrial Genetics, Max Planck Institute for Biology of Ageing, Cologne, Germany
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24
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Dröse S, Krack S, Sokolova L, Zwicker K, Barth HD, Morgner N, Heide H, Steger M, Nübel E, Zickermann V, Kerscher S, Brutschy B, Radermacher M, Brandt U. Functional dissection of the proton pumping modules of mitochondrial complex I. PLoS Biol 2011; 9:e1001128. [PMID: 21886480 PMCID: PMC3160329 DOI: 10.1371/journal.pbio.1001128] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 07/13/2011] [Indexed: 12/28/2022] Open
Abstract
A catalytically active subcomplex of respiratory chain complex I lacks 14 of its 42 subunits yet retains half of its proton-pumping capacity, indicating that its membrane arm has two pump modules. Mitochondrial complex I, the largest and most complicated proton pump of the respiratory chain, links the electron transfer from NADH to ubiquinone to the pumping of four protons from the matrix into the intermembrane space. In humans, defects in complex I are involved in a wide range of degenerative disorders. Recent progress in the X-ray structural analysis of prokaryotic and eukaryotic complex I confirmed that the redox reactions are confined entirely to the hydrophilic peripheral arm of the L-shaped molecule and take place at a remarkable distance from the membrane domain. While this clearly implies that the proton pumping within the membrane arm of complex I is driven indirectly via long-range conformational coupling, the molecular mechanism and the number, identity, and localization of the pump-sites remains unclear. Here, we report that upon deletion of the gene for a small accessory subunit of the Yarrowia complex I, a stable subcomplex (nb8mΔ) is formed that lacks the distal part of the membrane domain as revealed by single particle analysis. The analysis of the subunit composition of holo and subcomplex by three complementary proteomic approaches revealed that two (ND4 and ND5) of the three subunits with homology to bacterial Mrp-type Na+/H+ antiporters that have been discussed as prime candidates for harbouring the proton pumps were missing in nb8mΔ. Nevertheless, nb8mΔ still pumps protons at half the stoichiometry of the complete enzyme. Our results provide evidence that the membrane arm of complex I harbours two functionally distinct pump modules that are connected in series by the long helical transmission element recently identified by X-ray structural analysis. Mitochondria—the power plants of eukaryotic cells—produce energy in the form of ATP. More than one-third of this energy production is driven by a gradient of protons across the mitochondrial membrane created by the pumping action of a very large enzyme called complex I. Defects in complex I are implicated in numerous pathological processes like neurodegeneration and biological aging. Recent X-ray structural analyses revealed that complex I is an L-shaped molecule with one arm integrated into the membrane and the other sticking into the aqueous interior of the mitochondrion; the chemical reactions of the enzyme take place in this hydrophilic arm, clearly separated from proton pumping that must occur somewhere in the membrane arm. To assign the pump function to structural domains, we created a stable subcomplex of complex I by deleting the gene encoding one of its small subunits in a yeast called Yarrowia lipolytica. This subcomplex lacked half of the membrane arm; it was still catalytically active but it pumped only half the number of protons as the full complex. This indicates that complex I has two functionally distinct pump modules operating in its membrane arm.
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Affiliation(s)
- Stefan Dröse
- Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt “Macromolecular Complexes,” Center for Membrane Proteomics, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Stephanie Krack
- Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt “Macromolecular Complexes,” Center for Membrane Proteomics, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Lucie Sokolova
- Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt “Macromolecular Complexes,” Center for Membrane Proteomics, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
- Institute of Physical and Theoretical Chemistry, Cluster of Excellence Frankfurt “Macromolecular Complexes,” Centre for Membrane Proteomics, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Klaus Zwicker
- Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt “Macromolecular Complexes,” Center for Membrane Proteomics, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Hans-Dieter Barth
- Institute of Physical and Theoretical Chemistry, Cluster of Excellence Frankfurt “Macromolecular Complexes,” Centre for Membrane Proteomics, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Cluster of Excellence Frankfurt “Macromolecular Complexes,” Centre for Membrane Proteomics, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Heinrich Heide
- Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt “Macromolecular Complexes,” Center for Membrane Proteomics, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Mirco Steger
- Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt “Macromolecular Complexes,” Center for Membrane Proteomics, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Esther Nübel
- Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt “Macromolecular Complexes,” Center for Membrane Proteomics, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Volker Zickermann
- Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt “Macromolecular Complexes,” Center for Membrane Proteomics, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Stefan Kerscher
- Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt “Macromolecular Complexes,” Center for Membrane Proteomics, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Bernhard Brutschy
- Institute of Physical and Theoretical Chemistry, Cluster of Excellence Frankfurt “Macromolecular Complexes,” Centre for Membrane Proteomics, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Michael Radermacher
- University of Vermont, College of Medicine, Department of Molecular Physiology and Biophysics, Burlington, Vermont, United States of America
| | - Ulrich Brandt
- Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt “Macromolecular Complexes,” Center for Membrane Proteomics, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
- * E-mail:
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Ladig R, Sommer MS, Hahn A, Leisegang MS, Papasotiriou DG, Ibrahim M, Elkehal R, Karas M, Zickermann V, Gutensohn M, Brandt U, Klösgen RB, Schleiff E. A high-definition native polyacrylamide gel electrophoresis system for the analysis of membrane complexes. Plant J 2011; 67:181-94. [PMID: 21418111 DOI: 10.1111/j.1365-313x.2011.04577.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Native polyacrylamide gel electrophoresis (PAGE) is an important technique for the analysis of membrane protein complexes. A major breakthrough was the development of blue native (BN-) and high resolution clear native (hrCN-) PAGE techniques. Although these techniques are very powerful, they could not be applied to all systems with the same resolution. We have developed an alternative protocol for the analysis of membrane protein complexes of plant chloroplasts and cyanobacteria, which we termed histidine- and deoxycholate-based native (HDN-) PAGE. We compared the capacity of HDN-, BN- and hrCN-PAGE to resolve the well-studied respiratory chain complexes in mitochondria of bovine heart muscle and Yarrowia lipolytica, as well as thylakoid localized complexes of Medicago sativa, Pisum sativum and Anabaena sp. PCC7120. Moreover, we determined the assembly/composition of the Anabaena sp. PCC7120 thylakoids and envelope membranes by HDN-PAGE. The analysis of isolated chloroplast envelope complexes by HDN-PAGE permitted us to resolve complexes such as the translocon of the outer envelope migrating at approximately 700 kDa or of the inner envelope of about 230 and 400 kDa with high resolution. By immunodecoration and mass spectrometry of these complexes we present new insights into the assembly/composition of these translocation machineries. The HDN-PAGE technique thus provides an important tool for future analyses of membrane complexes such as protein translocons.
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Affiliation(s)
- Roman Ladig
- Institute of Biology - Plant Physiology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, D-06120 Halle/Saale, Germany
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26
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Radermacher M, Ruiz T, Fowler DJ, Yu L, Dröse S, Krack S, Kerscher S, Zickermann V, Brandt U. 3D Reconstruction of a Subcomplex of NADH-ubiquinone-oxidoreductase (Complex I) from Yarrowia lipolytica. Microsc Microanal 2011; 17:90-91. [PMID: 22267954 PMCID: PMC3261754 DOI: 10.1017/s1431927611001334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.
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Affiliation(s)
- M Radermacher
- University of Vermont, College of Medicine, Dept. Molecular Physiology and Biophysics, 149 Beaumont Ave, Burlington, VT, USA
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27
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Tocilescu MA, Zickermann V, Zwicker K, Brandt U. Quinone binding and reduction by respiratory complex I. Biochimica et Biophysica Acta (BBA) - Bioenergetics 2010; 1797:1883-90. [DOI: 10.1016/j.bbabio.2010.05.009] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Revised: 05/08/2010] [Accepted: 05/10/2010] [Indexed: 12/12/2022]
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28
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Affiliation(s)
- Carola Hunte
- Institute for Biochemistry and Molecular Biology, Centre for Biological Signalling Studies (BIOSS), University of Freiburg, D-79104 Freiburg, Germany
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29
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Zickermann V, Angerer H, Ding MG, Nübel E, Brandt U. Small single transmembrane domain (STMD) proteins organize the hydrophobic subunits of large membrane protein complexes. FEBS Lett 2010; 584:2516-25. [PMID: 20398659 DOI: 10.1016/j.febslet.2010.04.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 03/30/2010] [Accepted: 04/09/2010] [Indexed: 11/24/2022]
Abstract
The large membrane protein complexes of mitochondrial oxidative phosphorylation are composed of central subunits that are essential for their bioenergetic core function and accessory subunits that may assist in regulation, assembly or stabilization. Although sequence conservation is low, a significant proportion of the accessory subunits is characterized by a common single transmembrane (STMD) topology. The STMD signature is also found in subunits of other membrane protein complexes. We hypothesize that the general function of STMD subunits is to organize the hydrophobic subunits of large membrane protein complexes in specialized environments like the inner mitochondrial membrane.
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Affiliation(s)
- Volker Zickermann
- Goethe-Universität, Fachbereich Medizin, Molekulare Bioenergetik, Cluster of Excellence Frankfurt "Macromolecular Complexes", Frankfurt am Main, Germany
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30
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Zickermann V, Wumaier Z, Wrzesniewska B, Hunte C, Schägger H. Native immunoblotting of blue native gels to identify conformation-specific antibodies. Proteomics 2010; 10:159-63. [PMID: 19882660 DOI: 10.1002/pmic.200900468] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A large repertoire of immunological methods permits monitoring the interaction of antibodies with their specific antigen. However, recognition of a protein by a conformation-specific antibody represents a challenge because native conditions must be kept throughout the assay. Native immunoblotting of blue native gels conserves the native state by using Tween 20 instead of methanol for the obligatory destaining of the blot membrane. We validate the new technique with a set of monoclonal antibodies against respiratory NADH:ubiquinone oxidoreductase.
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Affiliation(s)
- Volker Zickermann
- Goethe-Universität, Fachbereich Medizin, Molekulare Bioenergetik, Cluster of Excellence Frankfurt, Macromolecular Complexes, Center for Membrane Proteomics, Frankfurt am Main, Germany.
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31
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Clason T, Ruiz T, Schägger H, Peng G, Zickermann V, Brandt U, Michel H, Radermacher M. The structure of eukaryotic and prokaryotic complex I. J Struct Biol 2010; 169:81-8. [PMID: 19732833 PMCID: PMC3144259 DOI: 10.1016/j.jsb.2009.08.017] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Revised: 08/28/2009] [Accepted: 08/29/2009] [Indexed: 10/20/2022]
Abstract
The structures of the NADH dehydrogenases from Bos taurus and Aquifex aeolicus have been determined by 3D electron microscopy, and have been analyzed in comparison with the previously determined structure of Complex I from Yarrowia lipolytica. The results show a clearly preserved domain structure in the peripheral arm of complex I, which is similar in the bacterial and eukaryotic complex. The membrane arms of both eukaryotic complexes show a similar shape but also significant differences in distinctive domains. One of the major protuberances observed in Y. lipolytica complex I appears missing in the bovine complex, while a protuberance not found in Y. lipolytica connects in bovine complex I a domain of the peripheral arm to the membrane arm. The structural similarities of the peripheral arm agree with the common functional principle of all complex Is. The differences seen in the membrane arm may indicate differences in the regulatory mechanism of the enzyme in different species.
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Affiliation(s)
- T. Clason
- University of Vermont, College of Medicine, Department Molecular Physiology and Biophysics, Burlington, VT 05405, USA
| | - T. Ruiz
- University of Vermont, College of Medicine, Department Molecular Physiology and Biophysics, Burlington, VT 05405, USA
| | - H. Schägger
- Goethe-Universität, Fachbereich Medizin, Molekulare Bioenergetik, D-60590 Frankfurt/Main, Germany
| | - G. Peng
- Max Planck Institute of Biophysics, Department of Molecular Membrane Biology, D-60438 Frankfurt/Main, Germany
| | - V. Zickermann
- Goethe-Universität, Fachbereich Medizin, Molekulare Bioenergetik, D-60590 Frankfurt/Main, Germany
| | - U. Brandt
- Goethe-Universität, Fachbereich Medizin, Molekulare Bioenergetik, D-60590 Frankfurt/Main, Germany
| | - H. Michel
- Max Planck Institute of Biophysics, Department of Molecular Membrane Biology, D-60438 Frankfurt/Main, Germany
| | - M. Radermacher
- University of Vermont, College of Medicine, Department Molecular Physiology and Biophysics, Burlington, VT 05405, USA
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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. Biochim Biophys Acta 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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Affiliation(s)
- Volker Zickermann
- Goethe-Universität, Fachbereich Medizin, Molekulare Bioenergetik, ZBC, Theodor-Stern-Kai 7, Haus 26, D-60590 Frankfurt am Main, Germany
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33
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Morgner N, Zickermann V, Kerscher S, Wittig I, Abdrakhmanova A, Barth HD, Brutschy B, Brandt U. Subunit mass fingerprinting of mitochondrial complex I. Biochimica et Biophysica Acta (BBA) - Bioenergetics 2008; 1777:1384-91. [DOI: 10.1016/j.bbabio.2008.08.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Revised: 07/31/2008] [Accepted: 08/03/2008] [Indexed: 11/29/2022]
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Abstract
Most reducing equivalents extracted from foodstuffs during oxidative metabolism are fed into the respiratory chains of aerobic bacteria and mitochondria by NADH:quinone oxidoreductases. Three families of enzymes can perform this task and differ remarkably in their complexity and role in energy conversion. Alternative or NDH-2-type NADH dehydrogenases are simple one subunit flavoenzymes that completely dissipate the redox energy of the NADH/quinone couple. Sodium-pumping NADH dehydrogenases (Nqr) that are only found in procaryotes contain several flavins and are integral membrane protein complexes composed of six different subunits. Proton-pumping NADH dehydrogenases (NDH-1 or complex I) are highly complicated membrane protein complexes, composed of up to 45 different subunits, that are found in bacteria and mitochondria. This review gives an overview of the origin, structural and functional properties and physiological significance of these three types of NADH dehydrogenase.
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Affiliation(s)
- Stefan Kerscher
- Molecular Bioenergetics Group, Centre of Excellence Macromolecular Complexes, Johann Wolfgang Goethe-Universität, 60590, Frankfurt am Main, Germany
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35
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Clason T, Zickermann V, Ruiz T, Brandt U, Radermacher M. Direct localization of the 51 and 24 kDa subunits of mitochondrial complex I by three-dimensional difference imaging. J Struct Biol 2007; 159:433-42. [PMID: 17591445 PMCID: PMC2700006 DOI: 10.1016/j.jsb.2007.05.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2007] [Revised: 04/27/2007] [Accepted: 05/02/2007] [Indexed: 11/30/2022]
Abstract
Complex I is the largest complex in the respiratory chain, and the least understood. We have determined the 3D structure of complex I from Yarrowia lipolytica lacking the flavoprotein part of the N-module, which consists of the 51 kDa (NUBM) and the 24 kDa (NUHM) subunits. The reconstruction was determined by 3D electron microscopy of single particles. A comparison to our earlier reconstruction of the complete Y. lipolytica complex I clearly assigns the two flavoprotein subunits to an outer lobe of the peripheral arm of complex I. Localizing the two subunits allowed us to fit the X-ray structure of the hydrophilic fragment of complex I from Thermus thermophilus. The fit that is most consistent with previous immuno-electron microscopic data predicts that the ubiquinone reducing catalytic center resides in the second peripheral lobe, while the 75 kDa subunit is placed near the previously seen connection between the peripheral arm and the membrane arm protrusions.
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Affiliation(s)
- Todd Clason
- University of Vermont, College of Medicine, Department Molecular Physiology and Biophysics, Burlington, VT 05405, USA
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36
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Zickermann V, Zwicker K, Tocilescu MA, Kerscher S, Brandt U. Characterization of a subcomplex of mitochondrial NADH:ubiquinone oxidoreductase (complex I) lacking the flavoprotein part of the N-module. Biochim Biophys Acta 2007; 1767:393-400. [PMID: 17448440 DOI: 10.1016/j.bbabio.2007.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Revised: 03/02/2007] [Accepted: 03/05/2007] [Indexed: 11/19/2022]
Abstract
Mitochondrial NADH:ubiquinone oxidoreductase is the largest and most complicated proton pump of the respiratory chain. Here we report the preparation and characterization of a subcomplex of complex I selectively lacking the flavoprotein part of the N-module. Removing the 51-kDa and the 24-kDa subunit resulted in loss of catalytic activity. The redox centers of the subcomplex could be reduced neither by NADH nor NADPH demonstrating that physiological electron input into complex I occurred exclusively via the N-module and that the NADPH binding site in the 39-kDa subunit and further potential nucleotide binding sites are isolated from the electron transfer pathway within the enzyme. Taking advantage of the selective removal of two of the eight iron-sulfur clusters of complex I and providing additional evidence by redox titration and site-directed mutagenesis, we could for the first time unambiguously assign cluster N1 of fungal complex I to mammalian cluster N1b.
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Affiliation(s)
- Volker Zickermann
- Johann Wolfgang Goethe-Universität, Fachbereich Medizin, Molekulare Bioenergetik, Centre of Excellence Frankfurt Macromolecular Complexes, D-60590 Frankfurt am Main, Germany
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37
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Abdrakhmanova A, Zwicker K, Kerscher S, Zickermann V, Brandt U. Tight binding of NADPH to the 39-kDa subunit of complex I is not required for catalytic activity but stabilizes the multiprotein complex. Biochim Biophys Acta 2006; 1757:1676-82. [PMID: 17046710 DOI: 10.1016/j.bbabio.2006.09.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Revised: 09/08/2006] [Accepted: 09/11/2006] [Indexed: 11/18/2022]
Abstract
In addition to the 14 central subunits, respiratory chain complex I from the aerobic yeast Yarrowia lipolytica contains at least 24 accessory subunits, most of which are poorly characterized. Here we investigated the role of the accessory 39-kDa subunit which belongs to the heterogeneous short-chain dehydrogenase/reductase (SDR) enzyme family and contains non-covalently bound NADPH. Deleting the chromosomal copy of the gene that codes for the 39-kDa subunit drastically impaired complex I assembly in Y. lipolytica. We introduced several site-directed mutations into the nucleotide binding motif that severely reduced NADPH binding. This effect was most pronounced when the arginine at the end of the second beta-strand of the NADPH binding Rossman fold was replaced by leucine or aspartate. Mutations affecting nucleotide binding had only minor or moderate effects on specific catalytic activity in mitochondrial membranes but clearly destabilized complex I. One mutant exhibited a temperature sensitive phenotype and significant amounts of three different subcomplexes were observed even at more permissive temperature. We concluded that the 39-kDa subunit of Y. lipolytica plays a critical role in complex I assembly and stability and that the bound NADPH serves to stabilize the subunit and complex I as a whole rather than serving a catalytic function.
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Affiliation(s)
- Albina Abdrakhmanova
- Universität Frankfurt, Zentrum der Biologischen Chemie, Molekulare Bioenergetik, Theodor-Stern-Kai 7, Haus 26, D-60590 Frankfurt am Main, Germany
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38
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Marshall D, Fisher N, Grigic L, Zickermann V, Brandt U, Shannon RJ, Hirst J, Lawrence R, Rich PR. ATR-FTIR redox difference spectroscopy of Yarrowia lipolytica and bovine complex I. Biochemistry 2006; 45:5458-67. [PMID: 16634627 DOI: 10.1021/bi052561e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
ATR-FTIR spectroscopy in combination with electrochemistry has been applied to the redox centers of Yarrowia lipolytica complex I. The redox spectra show broad similarities with previously published data on Escherichia coli complex I and with new data here on bovine complex I. The spectra are dominated by amide I/II protein backbone changes. Comparisons with redox IR spectra of small model ferredoxins demonstrate that these amide I/II changes arise primarily from characteristic structural changes local to the iron-sulfur centers, rather than from global structural alterations as has been suggested previously. Bands arising from the substrate ubiquinone were evident, as was a characteristic 1405 cm(-)(1) band of the reduced form of the FMN cofactor. Other signals are likely to arise from perturbations or protonation changes of a carboxylic amino acid, histidine, and possibly several other specific amino acids. Redox difference spectra of center N2, together with substrate ubiquinone, were isolated from those of the other iron-sulfur centers by selective redox potentiometry. Its redox-linked amide I/II changes were typical of those in other 4Fe-4S iron sulfur proteins. Contrary to published data on bacterial complex I, no center N2 redox-linked protonation changes of carboxylic amino acids or tyrosine were evident, and other residues that could provide its redox-linked protonation site are discussed. Features of the substrate ubiquinone associated with the center N2 spectrum were particularly clear, with firm assignments possible for bands from both oxidized and reduced forms. This is the first report of IR properties of ubiquinone in complex I, and the data could be used to estimate a stoichiometry of 0.2-0.4 per complex I.
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Affiliation(s)
- Douglas Marshall
- Glynn Laboratory of Bioenergetics, Department of Biology, University College London, UK
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Radermacher M, Ruiz T, Clason T, Benjamin S, Brandt U, Zickermann V. The three-dimensional structure of complex I from Yarrowia lipolytica: a highly dynamic enzyme. J Struct Biol 2006; 154:269-79. [PMID: 16621601 PMCID: PMC1764498 DOI: 10.1016/j.jsb.2006.02.011] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2005] [Revised: 02/24/2006] [Accepted: 02/24/2006] [Indexed: 10/24/2022]
Abstract
The structure of complex I from Yarrowia lipolytica was determined by three-dimensional electron microscopy. A random conical data set was collected from deep stain embedded particles. More than 14000 image pairs were analyzed. Through extensive classification combined with three-dimensional reconstruction, it was possible for the first time to show a much more detailed substructure of the complex. The peripheral arm is subdivided in at least six domains. The membrane arm shows two major protrusions on its matrix facing side and exhibits a channel like feature on the side facing the cytoplasm. Structures resembling a tether connecting the subunits near the catalytic center with the protrusions of the membrane arm provide a second connection between matrix and membrane domain.
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Affiliation(s)
- M Radermacher
- University of Vermont, College of Medicine, Department of Molecular Physiology and Biophysics, Burlington, VT, USA.
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Maly T, Grgic L, Zwicker K, Zickermann V, Brandt U, Prisner T. Cluster N1 of complex I from Yarrowia lipolytica studied by pulsed EPR spectroscopy. J Biol Inorg Chem 2006; 11:343-50. [PMID: 16502321 DOI: 10.1007/s00775-006-0081-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2005] [Accepted: 01/16/2006] [Indexed: 11/27/2022]
Abstract
After reduction with nicotinamide adenine dinucleotide (NADH), NADH:ubiquinone oxidoreductase (complex I) of the strictly aerobic yeast Yarrowia lipolytica shows clear signals from five different paramagnetic iron-sulfur (FeS) clusters (N1-N5) which can be detected using electron paramagnetic resonance (EPR) spectroscopy. The ligand environment and the assignment of several FeS clusters to specific binding motifs found in several subunits of the complex are still under debate. In order to characterize the hyperfine interaction of the surrounding nuclei with FeS cluster N1, one- and two-dimensional electron spin echo envelope modulation experiments were performed at a temperature of 30 K. At this temperature only cluster N1 contributes to the overall signal in a pulsed EPR experiment. The hyperfine and quadrupole tensors of a nitrogen nucleus and the isotropic and dipolar hyperfine couplings of two sets of protons could be determined by numerical simulation of the one- and two-dimensional spectra. The values obtained are in perfect agreement with a ferredoxin-like binding structure by four cysteine amino acid residues and allow the assignment of the nitrogen couplings to a backbone nitrogen nucleus and the proton couplings to the beta-protons of the bound cysteine residues.
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Affiliation(s)
- T Maly
- Institut für Physikalische und Theoretische Chemie and Center for Biological Magnetic Resonance, Johann-Wolfgang-Goethe-Universität Frankfurt, 60439, Frankfurt am Main, Germany
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Brandt U, Abdrakhmanova A, Zickermann V, Galkin A, Dröse S, Zwicker K, Kerscher S. Structure-function relationships in mitochondrial complex I of the strictly aerobic yeast Yarrowia lipolytica. Biochem Soc Trans 2005; 33:840-4. [PMID: 16042611 DOI: 10.1042/bst0330840] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The obligate aerobic yeast Yarrowia lipolytica has been established as a powerful model system for the analysis of mitochondrial complex I. Using a combination of genomic and proteomic approaches, a total of 37 subunits was identified. Several of the accessory subunits are predicted to be STMD (single transmembrane domain) proteins. Site-directed mutagenesis of Y. lipolytica complex I has provided strong evidence that a significant part of the ubiquinone reducing catalytic core resides in the 49 kDa and PSST subunits and can be modelled using X-ray structures of distantly related enzymes, i.e. water-soluble [NiFe] hydrogenases from Desulfovibrio spp. Iron-sulphur cluster N2, which is related to the hydrogenase proximal cluster, is directly involved in quinone reduction. Mutagenesis of His226 and Arg141 of the 49 kDa subunit provided detailed insight into the structure-function relationships around cluster N2. Overall, our findings suggest that proton pumping by complex I employs long-range conformational interactions and ubiquinone intermediates play a critical role in this mechanism.
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Affiliation(s)
- U Brandt
- Universität Frankfurt, Zentrum der Biologischen Chemie, Molekulare Bioenergetik, Theodor-Stern-Kai 7, Haus 26, D-60590 Frankfurt am Main, Germany.
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42
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Abdrakhmanova A, Zickermann V, Bostina M, Radermacher M, Schägger H, Kerscher S, Brandt U. Subunit composition of mitochondrial complex I from the yeast Yarrowia lipolytica. Biochim Biophys Acta 2004; 1658:148-56. [PMID: 15282186 DOI: 10.1016/j.bbabio.2004.04.019] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2004] [Revised: 04/29/2004] [Accepted: 04/29/2004] [Indexed: 12/15/2022]
Abstract
Here we present a first assessment of the subunit inventory of mitochondrial complex I from the obligate aerobic yeast Yarrowia lipolytica. A total of 37 subunits were identified. In addition to the seven central, nuclear coded, and the seven mitochondrially coded subunits, 23 accessory subunits were found based on 2D electrophoretic and mass spectroscopic analysis in combination with sequence information from the Y. lipolytica genome. Nineteen of the 23 accessory subunits are clearly conserved between Y. lipolytica and mammals. The remaining four accessory subunits include NUWM, which has no apparent homologue in any other organism and is predicted to contain a single transmembrane domain bounded by highly charged extramembraneous domains. This structural organization is shared among a group of 7 subunits in the Y. lipolytica and 14 subunits in the mammalian enzyme. Because only five of these subunits display significant evolutionary conservation, their as yet unknown function is proposed to be structure- rather than sequence-specific. The NUWM subunit could be assigned to a hydrophobic subcomplex obtained by fragmentation and sucrose gradient centrifugation. Its position within the membrane arm was determined by electron microscopic single particle analysis of Y. lipolytica complex I decorated with a NUWM-specific monoclonal antibody.
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Affiliation(s)
- Albina Abdrakhmanova
- Fachbereich Medizin, Institut für Biochemie I, ZBC, Universität Frankfurt, Theodor-Stern-Kai 7, Haus 25B, D-60590 Frankfurt am Main, Germany
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Waletko A, Zwicker K, Abdrakhmanova A, Zickermann V, Brandt U, Kerscher S. Histidine 129 in the 75-kDa subunit of mitochondrial complex I from Yarrowia lipolytica is not a ligand for [Fe4S4] cluster N5 but is required for catalytic activity. J Biol Chem 2004; 280:5622-5. [PMID: 15572358 DOI: 10.1074/jbc.m411488200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Respiratory chain complex I contains 8-9 iron-sulfur clusters. In several cases, the assignment of these clusters to subunits and binding motifs is still ambiguous. To test the proposed ligation of the tetranuclear iron-sulfur cluster N5 of respiratory chain complex I, we replaced the conserved histidine 129 in the 75-kDa subunit from Yarrowia lipolytica with alanine. In the mutant strain, reduced amounts of fully assembled but destabilized complex I could be detected. Deamino-NADH: ubiquinone oxidoreductase activity was abolished completely by the mutation. However, EPR spectroscopic analysis of mutant complex I exhibited an unchanged cluster N5 signal, excluding histidine 129 as a cluster N5 ligand.
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Affiliation(s)
- Antje Waletko
- Universität Frankfurt, Fachbereich Medizin, Institut für Biochemie I, F-60590 Frankfurt am Main, Germany
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Zickermann V, Bostina M, Hunte C, Ruiz T, Radermacher M, Brandt U. Functional implications from an unexpected position of the 49-kDa subunit of NADH:ubiquinone oxidoreductase. J Biol Chem 2003; 278:29072-8. [PMID: 12754256 DOI: 10.1074/jbc.m302713200] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Membrane-bound complex I (NADH:ubiquinone oxidoreductase) of the respiratory chain is considered the main site of mitochondrial radical formation and plays a major role in many mitochondrial pathologies. Structural information is scarce for complex I, and its molecular mechanism is not known. Recently, the 49-kDa subunit has been identified as part of the "catalytic core" conferring ubiquinone reduction by complex I. We found that the position of the 49-kDa subunit is clearly separated from the membrane part of complex I, suggesting an indirect mechanism of proton translocation. This contradicts all hypothetical mechanisms discussed in the field that link proton translocation directly to redox events and suggests an indirect mechanism of proton pumping by redox-driven conformational energy transfer.
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Affiliation(s)
- Volker Zickermann
- Universität Frankfurt, Fachbereich Medizin, Institut für Biochemie I, D-60590 Frankfurt am Main, Germany
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Abstract
The modular evolutionary origin of NADH:ubiquinone oxidoreductase (complex I) provides useful insights into its functional organization. Iron-sulfur cluster N2 and the PSST and 49 kDa subunits were identified as key players in ubiquinone reduction and proton pumping. Structural studies indicate that this 'catalytic core' region of complex I is clearly separated from the membrane. Complex I from Escherichia coli and Klebsiella pneumoniae was shown to pump sodium ions rather than protons. These new insights into structure and function of complex I strongly suggest that proton or sodium pumping in complex I is achieved by conformational energy transfer rather than by a directly linked redox pump.
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Affiliation(s)
- Ulrich Brandt
- Universität Frankfurt, Fachbereich Medizin, Institut für Biochemie I, Theodor-Stern-Kai 7, Haus 25B, D-60590 Frankfurt am Main, Germany.
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Peng G, Fritzsch G, Zickermann V, Schägger H, Mentele R, Lottspeich F, Bostina M, Radermacher M, Huber R, Stetter KO, Michel H. Isolation, characterization and electron microscopic single particle analysis of the NADH:ubiquinone oxidoreductase (complex I) from the hyperthermophilic eubacterium Aquifex aeolicus. Biochemistry 2003; 42:3032-9. [PMID: 12627969 DOI: 10.1021/bi026876v] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The proton-translocating NADH:ubiquinone oxidoreductase (complex I) has been purified from Aquifex aeolicus, a hyperthermophilic eubacterium of known genome sequence. The purified detergent solubilized enzyme is highly active above 50 degrees C. The specific activity for electron transfer from NADH to decylubiquinone is 29 U/mg at 80 degrees C. The A. aeolicus complex I is completely sensitive to rotenone and 2-n-decyl-quinazoline-4-yl-amine. SDS polyacrylamide gel electrophoresis shows that it may contain up to 14 subunits. N-terminal amino acid sequencing of the bands indicates the presence of a stable subcomplex, which is composed of subunits E, F, and G. The isolated complex is highly stable and active in a temperature range from 50 to 90 degrees C, with a half-life of about 10 h at 80 degrees C. The activity shows a linear Arrhenius plot at 50-85 degrees C with an activation energy at 31.92 J/mol K. Single particle electron microscopy shows that the A. aeolicus complex I has the typical L-shape. However, visual inspection of averaged images reveals many more details in the external arm of the complex than has been observed for complex I from other sources. In addition, the angle (90 degrees ) between the cytoplasmic peripheral arm and the membrane intrinsic arm of the complex appears to be invariant.
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Affiliation(s)
- Guohong Peng
- Max-Planck-Institut für Biophysik, Frankfurt a. M., Germany
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Kerscher S, Dröse S, Zwicker K, Zickermann V, Brandt U. Yarrowia lipolytica, a yeast genetic system to study mitochondrial complex I. Biochim Biophys Acta 2002; 1555:83-91. [PMID: 12206896 DOI: 10.1016/s0005-2728(02)00259-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The obligate aerobic yeast Yarrowia lipolytica is introduced as a powerful new model for the structural and functional analysis of mitochondrial complex I. A brief introduction into the biology and the genetics of this nonconventional yeast is given and the relevant genetic tools that have been developed in recent years are summarized. The respiratory chain of Y. lipolytica contains complexes I-IV, one "alternative" NADH-dehydrogenase (NDH2) and a non-heme alternative oxidase (AOX). Because the NADH binding site of NDH2 faces the mitochondrial intermembrane space rather than the matrix, complex I is an essential enzyme in Y. lipolytica. Nevertheless, complex I deletion strains could be generated by attaching the targeting sequence of a matrix protein, thereby redirecting NDH2 to the matrix side. Deletion strains for several complex I subunits have been constructed that can be complemented by shuttle plasmids carrying the deleted gene. Attachment of a hexa-histidine tag to the NUGM (30 kDa) subunit allows fast and efficient purification of complex I from Y. lipolytica by affinity-chromatography. The purified complex has lost most of its NADH:ubiquinone oxidoreductase activity, but is almost fully reactivated by adding 400-500 molecules of phosphatidylcholine per complex I. The established set of genetic tools has proven useful for the site-directed mutagenesis of individual subunits of Y. lipolytica complex I. Characterization of a number of mutations already allowed for the identification of several functionally important amino acids, demonstrating the usefulness of this approach.
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Affiliation(s)
- Stefan Kerscher
- Universitätsklinikum Frankfurt, Institut für Biochemie I, Zentrum der Biologischen Chemie, Theodor-Stern-Kai 7, Haus 25 B, D-60590 Frankfurt am Main, Germany
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Kerscher S, Kashani-Poor N, Zwicker K, Zickermann V, Brandt U. Exploring the catalytic core of complex I by Yarrowia lipolytica yeast genetics. J Bioenerg Biomembr 2001; 33:187-96. [PMID: 11695828 DOI: 10.1023/a:1010726818165] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We have developed Yarrowia lipolytica as a model system to study mitochondrial complex I that combines the application of fast and convenient yeast genetics with efficient structural and functional analysis of its very stable complex I isolated by his-tag affinity purification with high yield. Guided by a structural model based on homologies between complex I and [NiFe] hydrogenases mutational analysis revealed that the 49 kDa subunit plays a central functional role in complex I. We propose that critical parts of the catalytic core of complex I have evolved from the hydrogen reactive site of [NiFe] hydrogenases and that iron-sulfur cluster N2 resides at the interface between the 49 kDa and PSST subunits. These findings are in full agreement with the "semiquinone switch" mechanism according to which coupling of electron and proton transfer in complex I is achieved by a single integrated pump comprising cluster N2, the binding site for substrate ubiquinone, and a tightly bound quinone or quinoid group.
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Affiliation(s)
- S Kerscher
- Universitätsklinikum Frankfurt, Institut für Biochemie I, Zentrum der Biologischen Chemie, Frankfurt am Main, Germany
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Kashani-Poor N, Kerscher S, Zickermann V, Brandt U. Efficient large scale purification of his-tagged proton translocating NADH:ubiquinone oxidoreductase (complex I) from the strictly aerobic yeast Yarrowia lipolytica. Biochim Biophys Acta 2001; 1504:363-70. [PMID: 11245800 DOI: 10.1016/s0005-2728(00)00266-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Proton translocating NADH:ubiquinone oxidoreductase (complex I) is the largest membrane bound multiprotein complex of the respiratory chain and the only one for which no molecular structure is available so far. Thus, information on the mechanism of this central enzyme of aerobic energy metabolism is still very limited. As a new approach to analyze complex I, we have recently established the strictly aerobic yeast Yarrowia lipolytica as a model system that offers a complete set of convenient genetic tools and contains a complex I that is stable after isolation. For crystallization of complex I and to obtain its molecular structure it is a prerequisite to prepare large amounts of highly pure enzyme. Here we present the construction of his-tagged complex I that for the first time allows efficient affinity purification. Our protocol recovers almost 40% of complex I present in Yarrowia mitochondrial membranes. Overall, 40-80 mg highly pure and homogeneous complex I can be obtained from 10 l of an overnight Y. lipolytica culture. After reconstitution into asolectin proteoliposomes, the purified enzyme exhibits full NADH:ubiquinone oxidoreductase activity, is fully sensitive to inhibition by quinone analogue inhibitors and capable of generating a proton-motive force.
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Affiliation(s)
- N Kashani-Poor
- Universitätsklinikum Frankfurt, Institut für Biochemie I, ZBC, Theodor-Stern-Kai 7, Haus 25B, D-60590, Frankfurt am Main, Germany
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Kurki S, Zickermann V, Kervinen M, Hassinen I, Finel M. Mutagenesis of three conserved Glu residues in a bacterial homologue of the ND1 subunit of complex I affects ubiquinone reduction kinetics but not inhibition by dicyclohexylcarbodiimide. Biochemistry 2000; 39:13496-502. [PMID: 11063586 DOI: 10.1021/bi001134s] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Steady-state kinetics of the H(+)-translocating NADH:ubiquinone reductase (complex I) were analyzed in membrane samples from bovine mitochondria and the soil bacterium Paracoccus denitrificans. In both enzymes the calculated K(m) values, in the membrane lipid phase, for four different ubiquinone analogues were in the millimolar range. Both the structure and size of the hydrophobic side chain of the acceptor affected its affinity for complex I. The ND1 subunit of bovine complex I is a mitochondrially encoded protein that binds the inhibitor dicyclohexylcarbodiimide (DCCD) covalently [Yagi and Hatefi (1988) J. Biol. Chem. 263, 16150-16155]. The NQO8 subunit of P. denitrificans complex I is a homologue of ND1, and within it three conserved Glu residues that could bind DCCD, E158, E212, and E247, were changed to either Asp or Gln and in the case of E212 also to Val. The DCCD sensitivity of the resulting mutants was, however, unaffected by the mutations. On the other hand, the ubiquinone reductase activity of the mutants was altered, and the mutations changed the interactions of complex I with short-chain ubiquinones. The implications of the results for the location of the ubiquinone reduction site in this enzyme are discussed.
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Affiliation(s)
- S Kurki
- Helsinki Bioenergetics Group, Department of Medical Chemistry, Institute of Biomedical Sciences and Biocentrum Helsinki, University of Helsinki, Helsinki, Finland
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