6zkc Citations

The coupling mechanism of mammalian respiratory complex I.

Science 370 (2020)
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Cited: 92 times
EuropePMC logo PMID: 32972993

Abstract

Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions.

Reviews - 6zkc mentioned but not cited (5)

  1. Analysis of Human Mutations in the Supernumerary Subunits of Complex I. Dang QL, Phan DH, Johnson AN, Pasapuleti M, Alkhaldi HA, Zhang F, Vik SB. Life (Basel) 10 E296 (2020)
  2. Ubiquinone Binding and Reduction by Complex I-Open Questions and Mechanistic Implications. Galemou Yoga E, Schiller J, Zickermann V. Front Chem 9 672851 (2021)
  3. The functional significance of mitochondrial respiratory chain supercomplexes. Kohler A, Barrientos A, Fontanesi F, Ott M. EMBO Rep 24 e57092 (2023)
  4. From the 'black box' to 'domino effect' mechanism: what have we learned from the structures of respiratory complex I. Sazanov LA. Biochem J 480 319-333 (2023)
  5. The Mysterious Multitude: Structural Perspective on the Accessory Subunits of Respiratory Complex I. Padavannil A, Ayala-Hernandez MG, Castellanos-Silva EA, Letts JA. Front Mol Biosci 8 798353 (2021)

Articles - 6zkc mentioned but not cited (7)

  1. Cryo-EM structures of mitochondrial respiratory complex I from Drosophila melanogaster. Agip AA, Chung I, Sanchez-Martinez A, Whitworth AJ, Hirst J. Elife 12 e84424 (2023)
  2. Cryo-electron microscopy reveals how acetogenins inhibit mitochondrial respiratory complex I. Grba DN, Blaza JN, Bridges HR, Agip AA, Yin Z, Murai M, Miyoshi H, Hirst J. J Biol Chem 298 101602 (2022)
  3. Quinone Catalysis Modulates Proton Transfer Reactions in the Membrane Domain of Respiratory Complex I. Kim H, Saura P, Pöverlein MC, Gamiz-Hernandez AP, Kaila VRI. J Am Chem Soc 145 17075-17086 (2023)
  4. Diverse reaction behaviors of artificial ubiquinones in mitochondrial respiratory complex I. Uno S, Masuya T, Zdorevskyi O, Ikunishi R, Shinzawa-Itoh K, Lasham J, Sharma V, Murai M, Miyoshi H. J Biol Chem 298 102075 (2022)
  5. NDUFS3 knockout cancer cells and molecular docking reveal specificity and mode of action of anti-cancer respiratory complex I inhibitors. Kurelac I, Cavina B, Sollazzo M, Miglietta S, Fornasa A, De Luise M, Iorio M, Lama E, Traversa D, Nasiri HR, Ghelli A, Musiani F, Porcelli AM, Iommarini L, Gasparre G. Open Biol 12 220198 (2022)
  6. New Insights on Rotenone Resistance of Complex I Induced by the m.11778G>A/MT-ND4 Mutation Associated with Leber's Hereditary Optic Neuropathy. Musiani F, Rigobello L, Iommarini L, Carelli V, Degli Esposti M, Ghelli AM. Molecules 27 1341 (2022)
  7. Resting mitochondrial complex I from Drosophila melanogaster adopts a helix-locked state. Padavannil A, Murari A, Rhooms SK, Owusu-Ansah E, Letts JA. Elife 12 e84415 (2023)


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  1. Generation of Reactive Oxygen Species by Mitochondria. Hernansanz-Agustín P, Enríquez JA. Antioxidants (Basel) 10 415 (2021)
  2. Structure of respiratory complex I - An emerging blueprint for the mechanism. Kampjut D, Sazanov LA. Curr Opin Struct Biol 74 102350 (2022)
  3. The assembly, regulation and function of the mitochondrial respiratory chain. Vercellino I, Sazanov LA. Nat Rev Mol Cell Biol 23 141-161 (2022)
  4. Mitochondrial Cristae Morphology Reflecting Metabolism, Superoxide Formation, Redox Homeostasis, and Pathology. Ježek P, Jabůrek M, Holendová B, Engstová H, Dlasková A. Antioxid Redox Signal 39 635-683 (2023)
  5. Accessory Subunits of the Matrix Arm of Mitochondrial Complex I with a Focus on Subunit NDUFS4 and Its Role in Complex I Function and Assembly. Kahlhöfer F, Gansen M, Zickermann V. Life (Basel) 11 455 (2021)
  6. Human induced pluripotent stem cells for studying mitochondrial diseases in the heart. Caudal A, Ren L, Tu C, Wu JC. FEBS Lett 596 1735-1745 (2022)
  7. Mitochondria: intracellular sentinels of infections. Brokatzky D, Häcker G. Med Microbiol Immunol 211 161-172 (2022)
  8. Molecular Mechanisms behind Inherited Neurodegeneration of the Optic Nerve. Maresca A, Carelli V. Biomolecules 11 496 (2021)
  9. Evolution of complex I-like respiratory complexes. Yu H, Schut GJ, Haja DK, Adams MWW, Li H. J Biol Chem 296 100740 (2021)
  10. Making the leap from structure to mechanism: are the open states of mammalian complex I identified by cryoEM resting states or catalytic intermediates? Chung I, Grba DN, Wright JJ, Hirst J. Curr Opin Struct Biol 77 102447 (2022)
  11. Organization of the Respiratory Supercomplexes in Cells with Defective Complex III: Structural Features and Metabolic Consequences. Rugolo M, Zanna C, Ghelli AM. Life (Basel) 11 351 (2021)
  12. Tackling Dysfunction of Mitochondrial Bioenergetics in the Brain. Zanfardino P, Doccini S, Santorelli FM, Petruzzella V. Int J Mol Sci 22 8325 (2021)
  13. The biogenesis and regulation of the plant oxidative phosphorylation system. Ghifari AS, Saha S, Murcha MW. Plant Physiol 192 728-747 (2023)
  14. Binding of Natural Inhibitors to Respiratory Complex I. Schiller J, Zickermann V. Pharmaceuticals (Basel) 15 1088 (2022)
  15. Genetic mutations affecting mitochondrial function in cancer drug resistance. Lee C, Park SH, Yoon SK. Genes Genomics 45 261-270 (2023)
  16. Mechanisms of mitochondrial respiratory adaptation. Bennett CF, Latorre-Muro P, Puigserver P. Nat Rev Mol Cell Biol 23 817-835 (2022)
  17. Mitochondrial complex I ROS production and redox signaling in hypoxia. Okoye CN, Koren SA, Wojtovich AP. Redox Biol 67 102926 (2023)
  18. Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient. Kaur D, Khaniya U, Zhang Y, Gunner MR. Front Chem 9 660954 (2021)
  19. Targeting oxidative stress as a preventive and therapeutic approach for cardiovascular disease. Yan Q, Liu S, Sun Y, Chen C, Yang S, Lin M, Long J, Yao J, Lin Y, Yi F, Meng L, Tan Y, Ai Q, Chen N, Yang Y. J Transl Med 21 519 (2023)

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  1. Essential role of accessory subunit LYRM6 in the mechanism of mitochondrial complex I. Galemou Yoga E, Parey K, Djurabekova A, Haapanen O, Siegmund K, Zwicker K, Sharma V, Zickermann V, Angerer H. Nat Commun 11 6008 (2020)
  2. A ferredoxin bridge connects the two arms of plant mitochondrial complex I. Klusch N, Senkler J, Yildiz Ö, Kühlbrandt W, Braun HP. Plant Cell 33 2072-2091 (2021)
  3. ND3 Cys39 in complex I is exposed during mitochondrial respiration. Burger N, James AM, Mulvey JF, Hoogewijs K, Ding S, Fearnley IM, Loureiro-López M, Norman AAI, Arndt S, Mottahedin A, Sauchanka O, Hartley RC, Krieg T, Murphy MP. Cell Chem Biol 29 636-649.e14 (2022)
  4. High-resolution structure and dynamics of mitochondrial complex I-Insights into the proton pumping mechanism. Parey K, Lasham J, Mills DJ, Djurabekova A, Haapanen O, Yoga EG, Xie H, Kühlbrandt W, Sharma V, Vonck J, Zickermann V. Sci Adv 7 eabj3221 (2021)
  5. Structural basis of mammalian respiratory complex I inhibition by medicinal biguanides. Bridges HR, Blaza JN, Yin Z, Chung I, Pollak MN, Hirst J. Science 379 351-357 (2023)
  6. Assembly of The Mitochondrial Complex I Assembly Complex Suggests a Regulatory Role for Deflavination. Giachin G, Jessop M, Bouverot R, Acajjaoui S, Saïdi M, Chretien A, Bacia-Verloop M, Signor L, Mas PJ, Favier A, Borel Meneroud E, Hons M, Hart DJ, Kandiah E, Boeri Erba E, Buisson A, Leonard G, Gutsche I, Soler-Lopez M. Angew Chem Int Ed Engl 60 4689-4697 (2021)
  7. Differences in mitochondrial NADH dehydrogenase activities in trypanosomatids. Čermáková P, Maďarová A, Baráth P, Bellová J, Yurchenko V, Horváth A. Parasitology 148 1161-1170 (2021)
  8. Analysis of the assembly pathway for membrane subunits of Complex I reveals that subunit L (ND5) can assemble last in E. coli. Zhang F, Vik SB. BBA Adv 1 100027 (2021)
  9. Conformational changes in mitochondrial complex I of the thermophilic eukaryote Chaetomium thermophilum. Laube E, Meier-Credo J, Langer JD, Kühlbrandt W. Sci Adv 8 eadc9952 (2022)
  10. Cork-in-bottle mechanism of inhibitor binding to mammalian complex I. Chung I, Serreli R, Cross JB, Di Francesco ME, Marszalek JR, Hirst J. Sci Adv 7 eabg4000 (2021)
  11. Cryo-EM structures define ubiquinone-10 binding to mitochondrial complex I and conformational transitions accompanying Q-site occupancy. Chung I, Wright JJ, Bridges HR, Ivanov BS, Biner O, Pereira CS, Arantes GM, Hirst J. Nat Commun 13 2758 (2022)
  12. Enhancing Spns2/S1P in macrophages alleviates hyperinflammation and prevents immunosuppression in sepsis. Fang C, Ren P, Bian G, Wang J, Bai J, Huang J, Ding Y, Li X, Li M, Hou Z. EMBO Rep 24 e56635 (2023)
  13. Plant-specific features of respiratory supercomplex I + III2 from Vigna radiata. Maldonado M, Fan Z, Abe KM, Letts JA. Nat Plants 9 157-168 (2023)
  14. A Quinol Anion as Catalytic Intermediate Coupling Proton Translocation With Electron Transfer in E. coli Respiratory Complex I. Nuber F, Mérono L, Oppermann S, Schimpf J, Wohlwend D, Friedrich T. Front Chem 9 672969 (2021)
  15. A conserved arginine residue is critical for stabilizing the N2 FeS cluster in mitochondrial complex I. Hameedi MA, Grba DN, Richardson KH, Jones AJY, Song W, Roessler MM, Wright JJ, Hirst J. J Biol Chem 296 100474 (2021)
  16. Dimethylglycine Sodium Salt Alleviates Intrauterine Growth Restriction-Induced Low Growth Performance, Redox Status Imbalance, and Hepatic Mitochondrial Dysfunction in Suckling Piglets. Bai K, Jiang L, Wang T. Front Vet Sci 9 905488 (2022)
  17. Human clinical mutations in mitochondrially encoded subunits of Complex I can be successfully modeled in E. coli. Zhang F, Dang QL, Vik SB. Mitochondrion 64 59-72 (2022)
  18. Membrane-domain mutations in respiratory complex I impede catalysis but do not uncouple proton pumping from ubiquinone reduction. Jarman OD, Hirst J. PNAS Nexus 1 pgac276 (2022)
  19. Paracoccus denitrificans: a genetically tractable model system for studying respiratory complex I. Jarman OD, Biner O, Wright JJ, Hirst J. Sci Rep 11 10143 (2021)
  20. Resolving Chemical Dynamics in Biological Energy Conversion: Long-Range Proton-Coupled Electron Transfer in Respiratory Complex I. Kaila VRI. Acc Chem Res 54 4462-4473 (2021)
  21. Respiratory complex I with charge symmetry in the membrane arm pumps protons. Hoeser F, Tausend H, Götz S, Wohlwend D, Einsle O, Günther S, Friedrich T. Proc Natl Acad Sci U S A 119 e2123090119 (2022)
  22. Structural basis for bacterial energy extraction from atmospheric hydrogen. Grinter R, Kropp A, Venugopal H, Senger M, Badley J, Cabotaje PR, Jia R, Duan Z, Huang P, Stripp ST, Barlow CK, Belousoff M, Shafaat HS, Cook GM, Schittenhelm RB, Vincent KA, Khalid S, Berggren G, Greening C. Nature 615 541-547 (2023)
  23. Structure of Escherichia coli respiratory complex I reconstituted into lipid nanodiscs reveals an uncoupled conformation. Kolata P, Efremov RG. Elife 10 e68710 (2021)
  24. Structure of mycobacterial respiratory complex I. Liang Y, Plourde A, Bueler SA, Liu J, Brzezinski P, Vahidi S, Rubinstein JL. Proc Natl Acad Sci U S A 120 e2214949120 (2023)
  25. Subunits E-F-G of E. coli Complex I can form an active complex when expressed alone, but in time-delayed assembly co-expression of B-CD-E-F-G is optimal. Alkhaldi HA, Vik SB. Biochim Biophys Acta Bioenerg 1863 148593 (2022)
  26. A lethal mitonuclear incompatibility in complex I of natural hybrids. Moran BM, Payne CY, Powell DL, Iverson ENK, Donny AE, Banerjee SM, Langdon QK, Gunn TR, Rodriguez-Soto RA, Madero A, Baczenas JJ, Kleczko KM, Liu F, Matney R, Singhal K, Leib RD, Hernandez-Perez O, Corbett-Detig R, Frydman J, Gifford C, Schartl M, Havird JC, Schumer M. Nature (2024)
  27. A universal coupling mechanism of respiratory complex I. Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov L. Nature 609 808-814 (2022)
  28. An Abundant and Diverse New Family of Electron Bifurcating Enzymes With a Non-canonical Catalytic Mechanism. Schut GJ, Haja DK, Feng X, Poole FL, Li H, Adams MWW. Front Microbiol 13 946711 (2022)
  29. Biochemical consequences of two clinically relevant ND-gene mutations in Escherichia coli respiratory complex I. Nuber F, Schimpf J, di Rago JP, Tribouillard-Tanvier D, Procaccio V, Martin-Negrier ML, Trimouille A, Biner O, von Ballmoos C, Friedrich T. Sci Rep 11 12641 (2021)
  30. Case Reports Case report: A rare variant m.4135T>C in the MT-ND1 gene leads to Leber hereditary optic neuropathy and altered respiratory chain supercomplexes. Rákosníková T, Kelifová S, Štufková H, Lokvencová K, Lišková P, Kousal B, Honzík T, Hansíková H, Martínek V, Tesařová M. Front Genet 14 1182288 (2023)
  31. Cryo-EM structures of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae. Kishikawa JI, Ishikawa M, Masuya T, Murai M, Kitazumi Y, Butler NL, Kato T, Barquera B, Miyoshi H. Nat Commun 13 4082 (2022)
  32. Efficient tagging of endogenous proteins in human cell lines for structural studies by single-particle cryo-EM. Choi W, Wu H, Yserentant K, Huang B, Cheng Y. Proc Natl Acad Sci U S A 120 e2302471120 (2023)
  33. Exploring ND-011992, a quinazoline-type inhibitor targeting quinone reductases and quinol oxidases. Kägi J, Sloan W, Schimpf J, Nasiri HR, Lashley D, Friedrich T. Sci Rep 13 12226 (2023)
  34. Forty years in cryoEM of membrane proteins. Kühlbrandt W. Microscopy (Oxf) 71 i30-i50 (2022)
  35. Functional Dynamics of an Ancient Membrane-Bound Hydrogenase. Mühlbauer ME, Gamiz-Hernandez AP, Kaila VRI. J Am Chem Soc 143 20873-20883 (2021)
  36. Functional Water Wires Catalyze Long-Range Proton Pumping in the Mammalian Respiratory Complex I. Röpke M, Saura P, Riepl D, Pöverlein MC, Kaila VRI. J Am Chem Soc 142 21758-21766 (2020)
  37. Functional basis of electron transport within photosynthetic complex I. Richardson KH, Wright JJ, Šimėnas M, Thiemann J, Esteves AM, McGuire G, Myers WK, Morton JJL, Hippler M, Nowaczyk MM, Hanke GT, Roessler MM. Nat Commun 12 5387 (2021)
  38. H2O2 selectively damages the binuclear iron-sulfur cluster N1b of respiratory complex I. Strotmann L, Harter C, Gerasimova T, Ritter K, Jessen HJ, Wohlwend D, Friedrich T. Sci Rep 13 7652 (2023)
  39. Horizontal proton transfer across the antiporter-like subunits in mitochondrial respiratory complex I. Zdorevskyi O, Djurabekova A, Lasham J, Sharma V. Chem Sci 14 6309-6318 (2023)
  40. Investigation of hydrated channels and proton pathways in a high-resolution cryo-EM structure of mammalian complex I. Grba DN, Chung I, Bridges HR, Agip AA, Hirst J. Sci Adv 9 eadi1359 (2023)
  41. Ion transfer mechanisms in Mrp-type antiporters from high resolution cryoEM and molecular dynamics simulations. Lee Y, Haapanen O, Altmeyer A, Kühlbrandt W, Sharma V, Zickermann V. Nat Commun 13 6091 (2022)
  42. Knockdown of mitochondrial threonyl-tRNA synthetase 2 inhibits lung adenocarcinoma cell proliferation and induces apoptosis. Tian H, Yan H, Zhang Y, Fu Q, Li C, He J, Li H, Zhou Y, Huang Y, Li R. Bioengineered 13 5190-5204 (2022)
  43. Editorial Looking Back to the Future of Mitochondrial Research. Bernardi P. Front Physiol 12 682467 (2021)
  44. Mechanism of rotenone binding to respiratory complex I depends on ligand flexibility. Pereira CS, Teixeira MH, Russell DA, Hirst J, Arantes GM. Sci Rep 13 6738 (2023)
  45. Mitochondrial ferredoxin-like is essential for forming complex I-containing supercomplexes in Arabidopsis. Röhricht H, Przybyla-Toscano J, Forner J, Boussardon C, Keech O, Rouhier N, Meyer EH. Plant Physiol 191 2170-2184 (2023)
  46. Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. Molina-Granada D, González-Vioque E, Dibley MG, Cabrera-Pérez R, Vallbona-Garcia A, Torres-Torronteras J, Sazanov LA, Ryan MT, Cámara Y, Martí R. Commun Biol 5 620 (2022)
  47. Mutation at the entrance of the quinone cavity severely disrupts quinone binding in respiratory complex I. Yi JT, Wang P, Stuchebrukhov AA. Sci Rep 13 20413 (2023)
  48. Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes. Minhas BF, Beck EA, Cheng CC, Catchen J. Sci Rep 13 6939 (2023)
  49. Protein N-myristoylation plays a critical role in the mitochondrial localization of human mitochondrial complex I accessory subunit NDUFB7. Harada H, Moriya K, Kobuchi H, Ishihara N, Utsumi T. Sci Rep 13 22991 (2023)
  50. Protein model refinement for cryo-EM maps using AlphaFold2 and the DAQ score. Terashi G, Wang X, Kihara D. Acta Crystallogr D Struct Biol 79 10-21 (2023)
  51. Quinone binding in respiratory complex I: Going through the eye of a needle. The squeeze-in mechanism of passing the narrow entrance of the quinone site. Dhananjayan N, Wang P, Leontyev I, Stuchebrukhov AA. Photochem Photobiol Sci 21 1-12 (2022)
  52. Redox-dependent loss of flavin by mitochondria complex I is different in brain and heart. Yoval-Sánchez B, Ansari F, James J, Niatsetskaya Z, Sosunov S, Filipenko P, Tikhonova IG, Ten V, Wittig I, Rafikov R, Galkin A. Redox Biol 51 102258 (2022)
  53. Respiratory complex I in mitochondrial membrane catalyzes oversized ubiquinones. Ikunishi R, Otani R, Masuya T, Shinzawa-Itoh K, Shiba T, Murai M, Miyoshi H. J Biol Chem 299 105001 (2023)
  54. Reverse Electron Transfer by Respiratory Complex I Catalyzed in a Modular Proteoliposome System. Wright JJ, Biner O, Chung I, Burger N, Bridges HR, Hirst J. J Am Chem Soc 144 6791-6801 (2022)
  55. Single protonation of the reduced quinone in respiratory complex I drives four-proton pumping. Stuchebrukhov AA, Hayashi T. FEBS Lett 597 237-245 (2023)
  56. Structure of the membrane-bound formate hydrogenlyase complex from Escherichia coli. Steinhilper R, Höff G, Heider J, Murphy BJ. Nat Commun 13 5395 (2022)
  57. Structures of Tetrahymena's respiratory chain reveal the diversity of eukaryotic core metabolism. Zhou L, Maldonado M, Padavannil A, Guo F, Letts JA. Science 376 831-839 (2022)
  58. Structures of Tetrahymena thermophila respiratory megacomplexes on the tubular mitochondrial cristae. Han F, Hu Y, Wu M, He Z, Tian H, Zhou L. Nat Commun 14 2542 (2023)
  59. Supplementation of Dimethylglycine Sodium Salt in Sow Milk Reverses Skeletal Muscle Redox Status Imbalance and Mitochondrial Dysfunction of Intrauterine Growth Restriction Newborns. Bai K, Jiang L, Li Q, Zhang J, Zhang L, Wang T. Antioxidants (Basel) 11 1550 (2022)
  60. The antipsychotic medications aripiprazole, brexpiprazole and cariprazine are off-target respiratory chain complex I inhibitors. Hardy RE, Chung I, Yu Y, Loh SHY, Morone N, Soleilhavoup C, Travaglio M, Serreli R, Panman L, Cain K, Hirst J, Martins LM, MacFarlane M, Pryde KR. Biol Direct 18 43 (2023)
  61. Transgenic NADH dehydrogenase restores oxygen regulation of breathing in mitochondrial complex I-deficient mice. Jiménez-Gómez B, Ortega-Sáenz P, Gao L, González-Rodríguez P, García-Flores P, Chandel N, López-Barneo J. Nat Commun 14 1172 (2023)