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Mühleip A, Flygaard RK, Baradaran R, Haapanen O, Gruhl T, Tobiasson V, Maréchal A, Sharma V, Amunts A. Structural basis of mitochondrial membrane bending by the I-II-III 2-IV 2 supercomplex. Nature 2023; 615:934-938. [PMID: 36949187 PMCID: PMC10060162 DOI: 10.1038/s41586-023-05817-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [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: 06/28/2022] [Accepted: 02/09/2023] [Indexed: 03/24/2023]
Abstract
Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane1. Here we show that a supercomplex containing all four respiratory chain components contributes to membrane curvature induction in ciliates. We report cryo-electron microscopy and cryo-tomography structures of the supercomplex that comprises 150 different proteins and 311 bound lipids, forming a stable 5.8-MDa assembly. Owing to subunit acquisition and extension, complex I associates with a complex IV dimer, generating a wedge-shaped gap that serves as a binding site for complex II. Together with a tilted complex III dimer association, it results in a curved membrane region. Using molecular dynamics simulations, we demonstrate that the divergent supercomplex actively contributes to the membrane curvature induction and tubulation of cristae. Our findings highlight how the evolution of protein subunits of respiratory complexes has led to the I-II-III2-IV2 supercomplex that contributes to the shaping of the bioenergetic membrane, thereby enabling its functional specialization.
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Affiliation(s)
- Alexander Mühleip
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
- School of Infection and Immunity, University of Glasgow, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Rasmus Kock Flygaard
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
- Department of Molecular Biology and Genetics, Danish Research Institute of Translational Neuroscience-DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus C, Denmark
| | - Rozbeh Baradaran
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Outi Haapanen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Thomas Gruhl
- Institute of Structural and Molecular Biology, Birkbeck College, London, UK
| | - Victor Tobiasson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
- MRC Laboratory of Molecular Biology, Cambridge, UK
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD, USA
| | - Amandine Maréchal
- Institute of Structural and Molecular Biology, Birkbeck College, London, UK
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.
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Huang LS, Lümmen P, Berry EA. Crystallographic investigation of the ubiquinone binding site of respiratory Complex II and its inhibitors. Biochim Biophys Acta Proteins Proteom 2021; 1869:140679. [PMID: 34089891 PMCID: PMC8516616 DOI: 10.1016/j.bbapap.2021.140679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/15/2021] [Accepted: 05/24/2021] [Indexed: 01/01/2023]
Abstract
The quinone binding site (Q-site) of Mitochondrial Complex II (succinate-ubiquinone oxidoreductase) is the target for a number of inhibitors useful for elucidating the mechanism of the enzyme. Some of these have been developed as fungicides or pesticides, and species-specific Q-site inhibitors may be useful against human pathogens. We report structures of chicken Complex II with six different Q-site inhibitors bound, at resolutions 2.0-2.4 Å. These structures show the common interactions between the inhibitors and their binding site. In every case a carbonyl or hydroxyl oxygen of the inhibitor is H-bonded to Tyr58 in subunit SdhD and Trp173 in subunit SdhB. Two of the inhibitors H-bond Ser39 in subunit SdhC directly, while two others do so via a water molecule. There is a distinct cavity that accepts the 2-substituent of the carboxylate ring in flutolanil and related inhibitors. A hydrophobic "tail pocket" opens to receive a side-chain of intermediate-length inhibitors. Shorter inhibitors fit entirely within the main binding cleft, while the long hydrophobic side chains of ferulenol and atpenin A5 protrude out of the cleft into the bulk lipid region, as presumably does that of ubiquinone. Comparison of mitochondrial and Escherichia coli Complex II shows a rotation of the membrane-anchor subunits by 7° relative to the iron‑sulfur protein. This rotation alters the geometry of the Q-site and the H-bonding pattern of SdhB:His216 and SdhD:Asp57. This conformational difference, rather than any active-site mutation, may be responsible for the different inhibitor sensitivity of the bacterial enzyme.
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Affiliation(s)
- Li-Shar Huang
- Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 E. Adams Street, Syracuse, N.Y 13210, USA
| | - Peter Lümmen
- Bayer AG, Crop Science Division, Industrial Park Höchst, Frankfurt/Main, Germany
| | - Edward A Berry
- Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 E. Adams Street, Syracuse, N.Y 13210, USA.
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