6rdb Citations

Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F1-Fo coupling.

Abstract

F1Fo-adenosine triphosphate (ATP) synthases make the energy of the proton-motive force available for energy-consuming processes in the cell. We determined the single-particle cryo-electron microscopy structure of active dimeric ATP synthase from mitochondria of Polytomella sp. at a resolution of 2.7 to 2.8 angstroms. Separation of 13 well-defined rotary substates by three-dimensional classification provides a detailed picture of the molecular motions that accompany c-ring rotation and result in ATP synthesis. Crucially, the F1 head rotates along with the central stalk and c-ring rotor for the first ~30° of each 120° primary rotary step to facilitate flexible coupling of the stoichiometrically mismatched F1 and Fo subcomplexes. Flexibility is mediated primarily by the interdomain hinge of the conserved OSCP subunit. A conserved metal ion in the proton access channel may synchronize c-ring protonation with rotation.

Reviews citing this publication (28)

  1. The mitochondrial permeability transition: Recent progress and open questions. Bernardi P, Carraro M, Lippe G. FEBS J 289 7051-7074 (2022)
  2. Structure and Mechanisms of F-Type ATP Synthases. Kühlbrandt W. Annu Rev Biochem 88 515-549 (2019)
  3. Visualizing and trapping transient oligomers in amyloid assembly pathways. Cawood EE, Karamanos TK, Wilson AJ, Radford SE. Biophys Chem 268 106505 (2021)
  4. Molecular and Supramolecular Structure of the Mitochondrial Oxidative Phosphorylation System: Implications for Pathology. Nesci S, Trombetti F, Pagliarani A, Ventrella V, Algieri C, Tioli G, Lenaz G. Life (Basel) 11 242 (2021)
  5. ATP synthase: Evolution, energetics, and membrane interactions. Nirody JA, Budin I, Rangamani P. J Gen Physiol 152 e201912475 (2020)
  6. Redesigned and reversed: architectural and functional oddities of the trypanosomal ATP synthase. Gahura O, Hierro-Yap C, Zíková A. Parasitology 148 1151-1160 (2021)
  7. The mystery of massive mitochondrial complexes: the apicomplexan respiratory chain. Maclean AE, Hayward JA, Huet D, van Dooren GG, Sheiner L. Trends Parasitol 38 1041-1052 (2022)
  8. Therapeutic use of extracellular mitochondria in CNS injury and disease. Nakamura Y, Park JH, Hayakawa K. Exp Neurol 324 113114 (2020)
  9. Extracellular Mitochondria Signals in CNS Disorders. Park JH, Hayakawa K. Front Cell Dev Biol 9 642853 (2021)
  10. Rotational Mechanism of FO Motor in the F-Type ATP Synthase Driven by the Proton Motive Force. Kubo S, Takada S. Front Microbiol 13 872565 (2022)
  11. The biogenesis and regulation of the plant oxidative phosphorylation system. Ghifari AS, Saha S, Murcha MW. Plant Physiol 192 728-747 (2023)
  12. The importance of the membrane for biophysical measurements. Chorev DS, Robinson CV. Nat Chem Biol 16 1285-1292 (2020)
  13. The new role of F1Fo ATP synthase in mitochondria-mediated neurodegeneration and neuroprotection. Mnatsakanyan N, Jonas EA. Exp Neurol 332 113400 (2020)
  14. ATP synthase FOF1 structure, function, and structure-based drug design. Vlasov AV, Osipov SD, Bondarev NA, Uversky VN, Borshchevskiy VI, Yanyushin MF, Manukhov IV, Rogachev AV, Vlasova AD, Ilyinsky NS, Kuklin AI, Dencher NA, Gordeliy VI. Cell Mol Life Sci 79 179 (2022)
  15. Cryo-EM Analyses Permit Visualization of Structural Polymorphism of Biological Macromolecules. Chang WH, Huang SH, Lin HH, Chung SC, Tu IP. Front Bioinform 1 788308 (2021)
  16. CryoEM Reveals the Complexity and Diversity of ATP Synthases. Courbon GM, Rubinstein JL. Front Microbiol 13 864006 (2022)
  17. Directed proton transfer from Fo to F1 extends the multifaceted proton functions in ATP synthase. Nesterov SV, Yaguzhinsky LS. Biophys Rev 15 859-873 (2023)
  18. F1FO ATP synthase molecular motor mechanisms. Frasch WD, Bukhari ZA, Yanagisawa S. Front Microbiol 13 965620 (2022)
  19. F1·Fo ATP Synthase/ATPase: Contemporary View on Unidirectional Catalysis. Zharova TV, Grivennikova VG, Borisov VB. Int J Mol Sci 24 5417 (2023)
  20. From the Structural and (Dys)Function of ATP Synthase to Deficiency in Age-Related Diseases. Garone C, Pietra A, Nesci S. Life (Basel) 12 401 (2022)
  21. Identity, structure, and function of the mitochondrial permeability transition pore: controversies, consensus, recent advances, and future directions. Bernardi P, Gerle C, Halestrap AP, Jonas EA, Karch J, Mnatsakanyan N, Pavlov E, Sheu SS, Soukas AA. Cell Death Differ 30 1869-1885 (2023)
  22. Membranes under the Magnetic Lens: A Dive into the Diverse World of Membrane Protein Structures Using Cryo-EM. Piper SJ, Johnson RM, Wootten D, Sexton PM. Chem Rev 122 13989-14017 (2022)
  23. Mitochondrial OXPHOS Biogenesis: Co-Regulation of Protein Synthesis, Import, and Assembly Pathways. Tang JX, Thompson K, Taylor RW, Oláhová M. Int J Mol Sci 21 (2020)
  24. Reversible binding of divalent cations to Ductin protein assemblies-A putative new regulatory mechanism of membrane traffic processes. Sebők-Nagy K, Blastyák A, Juhász G, Páli T. Front Mol Biosci 10 1195010 (2023)
  25. Rotary mechanism of V/A-ATPases-how is ATP hydrolysis converted into a mechanical step rotation in rotary ATPases? Yokoyama K. Front Mol Biosci 10 1176114 (2023)
  26. Rotor subunits adaptations in ATP synthases from photosynthetic organisms. Cheuk A, Meier T. Biochem Soc Trans 49 541-550 (2021)
  27. The ATPase Inhibitory Factor 1 is a Tissue-Specific Physiological Regulator of the Structure and Function of Mitochondrial ATP Synthase: A Closer Look Into Neuronal Function. Domínguez-Zorita S, Romero-Carramiñana I, Cuezva JM, Esparza-Moltó PB. Front Physiol 13 868820 (2022)
  28. Understanding a protein fold: The physics, chemistry, and biology of α-helical coiled coils. Woolfson DN. J Biol Chem 299 104579 (2023)

Articles citing this publication (49)

  1. Cryo-EM structure of the entire mammalian F-type ATP synthase. Pinke G, Zhou L, Sazanov LA. Nat Struct Mol Biol 27 1077-1085 (2020)
  2. Cryo-EM reveals distinct conformations of E. coli ATP synthase on exposure to ATP. Sobti M, Ishmukhametov R, Bouwer JC, Ayer A, Suarna C, Smith NJ, Christie M, Stocker R, Duncan TM, Stewart AG. Elife 8 e43864 (2019)
  3. Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization. Flygaard RK, Mühleip A, Tobiasson V, Amunts A. Nat Commun 11 5342 (2020)
  4. 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)
  5. Interface mobility between monomers in dimeric bovine ATP synthase participates in the ultrastructure of inner mitochondrial membranes. Spikes TE, Montgomery MG, Walker JE. Proc Natl Acad Sci U S A 118 e2021012118 (2021)
  6. Structure of V-ATPase from the mammalian brain. Abbas YM, Wu D, Bueler SA, Robinson CV, Rubinstein JL. Science 367 1240-1246 (2020)
  7. Assembly of Spinach Chloroplast ATP Synthase Rotor Ring Protein-Lipid Complex. Novitskaia O, Buslaev P, Gushchin I. Front Mol Biosci 6 135 (2019)
  8. Structure of the dimeric ATP synthase from bovine mitochondria. Spikes TE, Montgomery MG, Walker JE. Proc Natl Acad Sci U S A 117 23519-23526 (2020)
  9. The mitochondrial chaperone TRAP1 regulates F-ATP synthase channel formation. Cannino G, Urbani A, Gaspari M, Varano M, Negro A, Filippi A, Ciscato F, Masgras I, Gerle C, Tibaldi E, Brunati AM, Colombo G, Lippe G, Bernardi P, Rasola A. Cell Death Differ 29 2335-2346 (2022)
  10. Characterization of a highly diverged mitochondrial ATP synthase Fo subunit in Trypanosoma brucei. Dewar CE, Oeljeklaus S, Wenger C, Warscheid B, Schneider A. J Biol Chem 298 101829 (2022)
  11. CryoFold: determining protein structures and data-guided ensembles from cryo-EM density maps. Shekhar M, Terashi G, Gupta C, Sarkar D, Debussche G, Sisco NJ, Nguyen J, Mondal A, Vant J, Fromme P, Van Horn WD, Tajkhorshid E, Kihara D, Dill K, Perez A, Singharoy A. Matter 4 3195-3216 (2021)
  12. The mitochondrial permeability transition pore activates the mitochondrial unfolded protein response and promotes aging. Angeli S, Foulger A, Chamoli M, Peiris TH, Gerencser A, Shahmirzadi AA, Andersen J, Lithgow G. Elife 10 e63453 (2021)
  13. ATP Synthase K+- and H+-Fluxes Drive ATP Synthesis and Enable Mitochondrial K+-"Uniporter" Function: I. Characterization of Ion Fluxes. Juhaszova M, Kobrinsky E, Zorov DB, Nuss HB, Yaniv Y, Fishbein KW, de Cabo R, Montoliu L, Gabelli SB, Aon MA, Cortassa S, Sollott SJ. Function (Oxf) 3 zqab065 (2022)
  14. Changes within the central stalk of E. coli F1Fo ATP synthase observed after addition of ATP. Sobti M, Zeng YC, Walshe JL, Brown SHJ, Ishmukhametov R, Stewart AG. Commun Biol 6 26 (2023)
  15. Computational Design of Inhibitors Targeting the Catalytic β Subunit of Escherichia coli FOF1-ATP Synthase. Avila-Barrientos LP, Cofas-Vargas LF, Agüero-Chapin G, Hernández-García E, Ruiz-Carmona S, Valdez-Cruz NA, Trujillo-Roldán M, Weber J, Ruiz-Blanco YB, Barril X, García-Hernández E. Antibiotics (Basel) 11 557 (2022)
  16. Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of Vo complex. Roh SH, Shekhar M, Pintilie G, Chipot C, Wilkens S, Singharoy A, Chiu W. Sci Adv 6 (2020)
  17. FO-F1 coupling and symmetry mismatch in ATP synthase resolved in every FO rotation step. Kubo S, Niina T, Takada S. Biophys J 122 2898-2909 (2023)
  18. Protein folding and unfolding: proline cis-trans isomerization at the c subunits of F1 FO -ATPase might open a high conductance ion channel. Nesci S. Proteins 90 2001-2005 (2022)
  19. pH-dependent 11° F1FO ATP synthase sub-steps reveal insight into the FO torque generating mechanism. Yanagisawa S, Frasch WD. Elife 10 e70016 (2021)
  20. An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases. Gahura O, Mühleip A, Hierro-Yap C, Panicucci B, Jain M, Hollaus D, Slapničková M, Zíková A, Amunts A. Nat Commun 13 5989 (2022)
  21. Direct observation of stepping rotation of V-ATPase reveals rigid component in coupling between Vo and V1 motors. Otomo A, Iida T, Okuni Y, Ueno H, Murata T, Iino R. Proc Natl Acad Sci U S A 119 e2210204119 (2022)
  22. Elucidating Events within the Black Box of Enzyme Catalysis in Energy Metabolism: Insights into the Molecular Mechanism of ATP Hydrolysis by F1-ATPase. Nath S. Biomolecules 13 1596 (2023)
  23. Mitochondrial ATP synthase inhibitory factor 1 interacts with the p53-cyclophilin D complex and promotes opening of the permeability transition pore. Guo L. J Biol Chem 298 101858 (2022)
  24. Protonic Capacitor: Elucidating the biological significance of mitochondrial cristae formation. Lee JW. Sci Rep 10 10304 (2020)
  25. Structural ensemble of a glutamate transporter homologue in lipid nanodisc environment. Arkhipova V, Guskov A, Slotboom DJ. Nat Commun 11 998 (2020)
  26. Structure of a mitochondrial ATP synthase with bound native cardiolipin. Mühleip A, McComas SE, Amunts A. Elife 8 (2019)
  27. Sustained Oligomycin Sensitivity Conferring Protein Expression in Cardiomyocytes Protects Against Cardiac hypertrophy Induced by Pressure Overload via Improving Mitochondrial Function. Guo Y, Zhang K, Gao X, Zhou Z, Liu Z, Yang K, Huang K, Yang Q, Long Q. Hum Gene Ther 31 1178-1189 (2020)
  28. The catalytic dwell in ATPases is not crucial for movement against applied torque. Bai C, Asadi M, Warshel A. Nat Chem 12 1187-1192 (2020)
  29. The persistent homology of mitochondrial ATP synthases. Sinha SD, Wideman JG. iScience 26 106700 (2023)
  30. Top-Down Identification and Sequence Analysis of Small Membrane Proteins Using MALDI-MS/MS. Meier-Credo J, Preiss L, Wüllenweber I, Resemann A, Nordmann C, Zabret J, Suckau D, Michel H, Nowaczyk MM, Meier T, Langer JD. J Am Soc Mass Spectrom 33 1293-1302 (2022)
  31. Withania somnifera mitochondrial atp4 gene editing alters the ATP synthase b subunit, independent of salt stress. Ramadan AM, Al-Ghamdi KM, Alghamdi AJ, Amer M, Ibrahim MIM, Atef A. Saudi J Biol Sci 30 103817 (2023)
  32. ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria. Mühleip A, Kock Flygaard R, Ovciarikova J, Lacombe A, Fernandes P, Sheiner L, Amunts A. Nat Commun 12 120 (2021)
  33. CGL160-mediated recruitment of the coupling factor CF1 is required for efficient thylakoid ATP synthase assembly, photosynthesis, and chloroplast development in Arabidopsis. Reiter B, Rosenhammer L, Marino G, Geimer S, Leister D, Rühle T. Plant Cell 35 488-509 (2023)
  34. CHCHD2 Thr61Ile mutation impairs F1F0-ATPase assembly in in vitro and in vivo models of Parkinson's disease. Chen X, Lin Y, Zhang Z, Tang Y, Ye P, Dai W, Zhang W, Liu H, Peng G, Huang S, Qiu J, Guo W, Zhu X, Wu Z, Kuang Y, Xu P, Zhou M. Neural Regen Res 19 196-204 (2024)
  35. Common Patterns of Hydrolysis Initiation in P-loop Fold Nucleoside Triphosphatases. Kozlova MI, Shalaeva DN, Dibrova DV, Mulkidjanian AY. Biomolecules 12 1345 (2022)
  36. Cryo-EM structures provide insight into how E. coli F1Fo ATP synthase accommodates symmetry mismatch. Sobti M, Walshe JL, Wu D, Ishmukhametov R, Zeng YC, Robinson CV, Berry RM, Stewart AG. Nat Commun 11 2615 (2020)
  37. Determinants of Directionality and Efficiency of the ATP Synthase Fo Motor at Atomic Resolution. Marciniak A, Chodnicki P, Hossain KA, Slabonska J, Czub J. J Phys Chem Lett 13 387-392 (2022)
  38. Forty years in cryoEM of membrane proteins. Kühlbrandt W. Microscopy (Oxf) 71 i30-i50 (2022)
  39. Mechanical inhibition of isolated Vo from V/A-ATPase for proton conductance. Kishikawa JI, Nakanishi A, Furuta A, Kato T, Namba K, Tamakoshi M, Mitsuoka K, Yokoyama K. Elife 9 (2020)
  40. Mitochondrial surface coating with artificial lipid membrane improves the transfer efficacy. Nakano T, Nakamura Y, Park JH, Tanaka M, Hayakawa K. Commun Biol 5 745 (2022)
  41. Molecular basis of diseases induced by the mitochondrial DNA mutation m.9032T>C. Baranowska E, Niedzwiecka K, Panja C, Charles C, Dautant A, di Rago JP, Tribouillard-Tanvier D, Kucharczyk R. Hum Mol Genet 32 1313-1323 (2023)
  42. Structural and Functional Analysis of SsaV Cytoplasmic Domain and Variable Linker States in the Context of the InvA-SsaV Chimeric Protein. Xu J, Wang J, Liu A, Zhang Y, Gao X. Microbiol Spectr 9 e0125121 (2021)
  43. Structural basis for power stroke vs. Brownian ratchet mechanisms of motor proteins. Hwang W, Karplus M. Proc. Natl. Acad. Sci. U.S.A. 116 19777-19785 (2019)
  44. Structure of ATP synthase under strain during catalysis. Guo H, Rubinstein JL. Nat Commun 13 2232 (2022)
  45. The Ancestral Shape of the Access Proton Path of Mitochondrial ATP Synthases Revealed by a Split Subunit-a. Wong JE, Zíková A, Gahura O. Mol Biol Evol 40 msad146 (2023)
  46. The OPR Protein MTHI1 Controls the Expression of Two Different Subunits of ATP Synthase CFo in Chlamydomonas reinhardtii. Ozawa SI, Cavaiuolo M, Jarrige D, Kuras R, Rutgers M, Eberhard S, Drapier D, Wollman FA, Choquet Y. Plant Cell 32 1179-1203 (2020)
  47. The pathogenic m.8993 T > G mutation in mitochondrial ATP6 gene prevents proton release from the subunit c-ring rotor of ATP synthase. Su X, Dautant A, Rak M, Godard F, Ezkurdia N, Bouhier M, Bietenhader M, Mueller DM, Kucharczyk R, di Rago JP, Tribouillard-Tanvier D. Hum Mol Genet 30 381-392 (2021)
  48. The resolution revolution in cryoEM requires high-quality sample preparation: a rapid pipeline to a high-resolution map of yeast fatty acid synthase. Joppe M, D'Imprima E, Salustros N, Paithankar KS, Vonck J, Grininger M, Kühlbrandt W. IUCrJ 7 220-227 (2020)
  49. Threshold of heteroplasmic truncating MT-ATP6 mutation in reprogramming, Notch hyperactivation and motor neuron metabolism. Kenvin S, Torregrosa-Muñumer R, Reidelbach M, Pennonen J, Turkia JJ, Rannila E, Kvist J, Sainio MT, Huber N, Herukka SK, Haapasalo A, Auranen M, Trokovic R, Sharma V, Ylikallio E, Tyynismaa H. Hum Mol Genet 31 958-974 (2022)