预印本 / 版本 1

A Supercomplex Incorporating Both Electron Transport Chain and ATP Synthase

本文是预印本,尚未经过同行评审认证。

作者

    Yiqi Hu, 
    Yiqi Hu
    • Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
    Jonathan Wong, 
    Jonathan Wong
    • Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
    • Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
    Erik Endres, 
    Erik Endres
    • Department of Physics, University of Helsinki, Helsinki, Finland
    Benz Corinna, 
    Benz Corinna
    • Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
    Cristina Pecorilla, 
    Cristina Pecorilla
    • Department of Physics, University of Helsinki, Helsinki, Finland
    Kun Huang, 
    Kun Huang
    • University of Münster, Schlossplatz 8, Münster, Germany
    • Institute of Bio-Architecture and Bio-Interactions, Shenzhen Medical Academy of Research and Translation, Shenzhen, Guangdong, China
    Tomáš Bílý, 
    Tomáš Bílý
    • Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
    • Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
    Hongtao Tian, 
    Hongtao Tian
    • Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
    Menglu Teng, 
    Menglu Teng
    • MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, P. R. China
    Fangzhu Han, 
    Fangzhu Han
    • Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
    Mengchen Wu, 
    Mengchen Wu
    • Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
    Naiwen Zhang, 
    Naiwen Zhang
    • Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
    • The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
    Qijun Chen, 
    Qijun Chen
    • Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
    • The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
    Jiancang Zhou, 
    Jiancang Zhou
    • Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
    Dehua Lai, 
    Dehua Lai
    • MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, P. R. China
    Alena Zíková, 
    Alena Zíková
    • Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
    • Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
    Martijn Huynen, 
    Martijn Huynen
    • Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
    Hassan Hashimi, 
    Hassan Hashimi
    • Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
    • Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
    Vivek Sharma, 
    Vivek Sharma
    • Department of Physics, University of Helsinki, Helsinki, Finland
    • HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    Ondřej Gahura, 
    Ondřej Gahura
    • Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
    Alexey Amunts, 
    Alexey Amunts
    • University of Münster, Schlossplatz 8, Münster, Germany
    • Institute of Bio-Architecture and Bio-Interactions, Shenzhen Medical Academy of Research and Translation, Shenzhen, Guangdong, China
    Long Zhou
    Long Zhou
    • Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
分类
关键词
cristae; mitochondrial supercomplex; respiratory chain; cryo-EM; kinetoplastid; ATP synthase

摘要

The mitochondrial oxidative phosphorylation system powering most aerobic organisms is typically depicted as two spatially segregated machineries(1): electron transport chain complexes I-IV (ETC CI-CIV) that generates proton motive force and adenosine triphosphate (ATP) synthase (complex V, CV) that consumes it(2,3). Using the kinetoplastid parasite Trypanosoma brucei in its procyclic form, we characterize a bona fide ETC-ATP synthase supercomplex that directly incorporates CII, CIV dimer and ATP synthase (CIICIV2CV) alongside conventional assemblies. Cryo-EM structure shows a clear organizing principle in which ATP synthase engages CIV2 via a non-canonical hetero-dimerization module of two subunit g paralogs, g’ and g’’, replacing the canonical g/g dimerization interface required for ATP synthase dimerization(4). The resulting ~2 MDa assembly forms an arc-shaped membrane region, which stabilizes shallow positive membrane curvature as indicated by atomistic simulations. Genetic disruption of g’/g’’ selectively destabilizes the supercomplex and triggers pronounced cristae remodeling from discoidal to elongated tubular form, accompanied by a reduced maximal polarization capacity and comparatively modest effects on steady-state ATP output. These findings establish a structurally defined ETC-ATP synthase supercomplex and suggest its primary role in architectural quality control, constraining ATP synthase supramolecular organization to safeguard mitochondrial integrity rather than simply enhancing chemiosmotic coupling.

参考文献

1. Davies, K. M. et al. Macromolecular organization of ATP synthase and complex I in whole mitochondria. Proceedings of the National Academy of Sciences of the United States of America 108, 14121–6 (2011).

2. MITCHELL, P. Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism. Nature 191, 144–8 (1961).

3. Mitchell, P. Chemiosmotic coupling in oxidative and photosynthetic phosphorylation. Biological reviews of the Cambridge Philosophical Society 41, 445–502 (1966).

4. Gahura, O. et al. An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases. Nature communications 13, 5989 (2022).

5. Wikström, M., Sharma, V., Kaila, V. R. I., Hosler, J. P. & Hummer, G. New perspectives on proton pumping in cellular respiration. Chemical reviews 115, 2196–221 (2015).

6. Walker, J. E. The ATP synthase: the understood, the uncertain and the unknown. Biochemical Society transactions 41, 1–16 (2013).

7. Vercellino, I. & Sazanov, L. A. The assembly, regulation and function of the mitochondrial respiratory chain. Nature reviews. Molecular cell biology 23, 141–161 (2022).

8. Fernández-Vizarra, E. & Ugalde, C. Cooperative assembly of the mitochondrial respiratory chain. Trends in biochemical sciences 47, 999–1008 (2022).

9. Zhang, L. et al. Structural basis for the regulatory mechanism of mammalian mitochondrial respiratory chain megacomplex-I2III2IV2. hLife 2, 189–200 (2024).

10. Vercellino, I. & Sazanov, L. A. Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature 598, 364–367 (2021).

11. Rathore, S. et al. Cryo-EM structure of the yeast respiratory supercomplex. Nature structural & molecular biology 26, 50–57 (2019).

12. Moe, A., Dimogkioka, A.-R., Rapaport, D., Öjemyr, L. N. & Brzezinski, P. Structure and function of the S. pombe III-IV-cyt c supercomplex. Proceedings of the National Academy of Sciences of the United States of America 120, e2307697120 (2023).

13. Letts, J. A., Fiedorczuk, K. & Sazanov, L. A. The architecture of respiratory supercomplexes. Nature 537, 644–648 (2016).

14. Wu, M., Gu, J., Guo, R., Huang, Y. & Yang, M. Structure of Mammalian Respiratory Supercomplex I1III2IV1. Cell 167, 1598-1609.e10 (2016).

15. Letts, J. A., Fiedorczuk, K., Degliesposti, G., Skehel, M. & Sazanov, L. A. Structures of Respiratory Supercomplex I+III2 Reveal Functional and Conformational Crosstalk. Molecular cell 75, 1131-1146.e6 (2019).

16. Davies, K. M., Blum, T. B. & Kühlbrandt, W. Conserved in situ arrangement of complex I and III2 in mitochondrial respiratory chain supercomplexes of mammals, yeast, and plants. Proceedings of the National Academy of Sciences of the United States of America 115, 3024–3029 (2018).

17. Vercellino, I. & Sazanov, L. A. SCAF1 drives the compositional diversity of mammalian respirasomes. Nature structural & molecular biology 1, (2024).

18. Liang, C. et al. Formation of I2+III2 supercomplex rescues respiratory chain defects. Cell metabolism 37, 441-459.e11 (2025).

19. Shin, Y.-C. et al. Structural basis of respiratory complex adaptation to cold temperatures. Cell 187, 6584-6598.e17 (2024).

20. Guo, R., Zong, S., Wu, M., Gu, J. & Yang, M. Architecture of Human Mitochondrial Respiratory Megacomplex I2III2IV2. Cell 170, 1247-1257.e12 (2017).

21. Mühleip, A. et al. Structural basis of mitochondrial membrane bending by the I-II-III2-IV2 supercomplex. Nature 615, 934–938 (2023).

22. Han, F. et al. Structures of Tetrahymena thermophila respiratory megacomplexes on the tubular mitochondrial cristae. Nature communications 14, 2542 (2023).

23. Wú, F. et al. Structure of the II2-III2-IV2 mitochondrial supercomplex from the parasite Perkinsus marinus. (2024). doi:10.1101/2024.05.25.595893

24. Zheng, W., Chai, P., Zhu, J. & Zhang, K. High-resolution in situ structures of mammalian respiratory supercomplexes. Nature 631, 232–239 (2024).

25. Waltz, F. et al. In-cell architecture of the mitochondrial respiratory chain. Science (New York, N.Y.) 387, 1296–1301 (2025).

26. Kohler, A., Barrientos, A., Fontanesi, F. & Ott, M. The functional significance of mitochondrial respiratory chain supercomplexes. EMBO reports 24, e57092 (2023).

27. Pánek, T., Eliáš, M., Vancová, M., Lukeš, J. & Hashimi, H. Returning to the Fold for Lessons in Mitochondrial Crista Diversity and Evolution. Current biology : CB 30, R575–R588 (2020).

28. Kühlbrandt, W. Structure and Mechanisms of F-Type ATP Synthases. Annual review of biochemistry 88, 515–549 (2019).

29. Mühleip, A. W. et al. Helical arrays of U-shaped ATP synthase dimers form tubular cristae in ciliate mitochondria. Proceedings of the National Academy of Sciences of the United States of America 113, 8442–7 (2016).

30. Flygaard, R. K., Mühleip, A., Tobiasson, V. & Amunts, A. Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization. Nature communications 11, 5342 (2020).

31. Mühleip, A. W., Dewar, C. E., Schnaufer, A., Kühlbrandt, W. & Davies, K. M. In situ structure of trypanosomal ATP synthase dimer reveals a unique arrangement of catalytic subunits. Proceedings of the National Academy of Sciences of the United States of America 114, 992–997 (2017).

32. Mühleip, A., McComas, S. E. & Amunts, A. Structure of a mitochondrial ATP synthase with bound native cardiolipin. eLife 8, 1–23 (2019).

33. Davies, K. M., Anselmi, C., Wittig, I., Faraldo-Gómez, J. D. & Kühlbrandt, W. Structure of the yeast F1Fo-ATP synthase dimer and its role in shaping the mitochondrial cristae. Proceedings of the National Academy of Sciences of the United States of America 109, 13602–7 (2012).

34. Guo, H., Bueler, S. A. & Rubinstein, J. L. Atomic model for the dimeric FO region of mitochondrial ATP synthase. Science 358, 936–940 (2017).

35. Gu, J. et al. Cryo-EM structure of the mammalian ATP synthase tetramer bound with inhibitory protein IF1. Science (New York, N.Y.) 364, 1068–1075 (2019).

36. Spikes, T. E., Montgomery, M. G. & Walker, J. E. Structure of the dimeric ATP synthase from bovine mitochondria. Proceedings of the National Academy of Sciences of the United States of America 117, 23519–23526 (2020).

37. Spikes, T. E., Montgomery, M. G. & Walker, J. E. Interface mobility between monomers in dimeric bovine ATP synthase participates in the ultrastructure of inner mitochondrial membranes. Proceedings of the National Academy of Sciences of the United States of America 118, 1–9 (2021).

38. Blum, T. B., Hahn, A., Meier, T., Davies, K. M. & Kühlbrandt, W. Dimers of mitochondrial ATP synthase induce membrane curvature and self-assemble into rows. Proceedings of the National Academy of Sciences of the United States of America 116, 4250–4255 (2019).

39. Murphy, B. J. et al. Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F1-Fo coupling. Science (New York, N.Y.) 364, 543108 (2019).

40. Dietrich, L., Agip, A.-N. A., Kunz, C., Schwarz, A. & Kühlbrandt, W. In situ structure and rotary states of mitochondrial ATP synthase in whole Polytomella cells. Science (New York, N.Y.) 385, 1086–1090 (2024).

41. Nesterov, S. et al. Ordered Clusters of the Complete Oxidative Phosphorylation System in Cardiac Mitochondria. International journal of molecular sciences 22, 1–10 (2021).

42. Nakano, A. et al. Structures of respiratory supercomplexes and ATP synthase oligomers in mammalian mitochondrial inner membrane. Nature communications (2026). doi:10.1038/s41467-026-70578-x

43. Acín-Pérez, R., Fernández-Silva, P., Peleato, M. L., Pérez-Martos, A. & Enriquez, J. A. Respiratory active mitochondrial supercomplexes. Molecular cell 32, 529–39 (2008).

44. Ukolova, I. V. et al. New insights into the organisation of the oxidative phosphorylation system in the example of pea shoot mitochondria. Biochimica et biophysica acta. Bioenergetics 1861, 148264 (2020).

45. Miranda-Astudillo, H. V., Yadav, K. N. S., Boekema, E. J. & Cardol, P. Supramolecular associations between atypical oxidative phosphorylation complexes of Euglena gracilis. Journal of bioenergetics and biomembranes (2021). doi:10.1007/s10863-021-09882-8

46. Burki, F., Roger, A. J., Brown, M. W. & Simpson, A. G. B. The New Tree of Eukaryotes. Trends in ecology & evolution 35, 43–55 (2020).

47. Zíková, A. Mitochondrial adaptations throughout the Trypanosoma brucei life cycle. The Journal of eukaryotic microbiology 69, e12911 (2022).

48. Bílý, T. et al. Ultrastructural Changes of the Mitochondrion During the Life Cycle of Trypanosoma brucei. The Journal of eukaryotic microbiology 68, e12846 (2021).

49. Morales, J. et al. Novel mitochondrial complex II isolated from Trypanosoma cruzi is composed of 12 peptides including a heterodimeric Ip subunit. The Journal of biological chemistry 284, 7255–63 (2009).

50. Zhou, L., Maldonado, M., Padavannil, A., Guo, F. & Letts, J. A. Structures of Tetrahymena’s respiratory chain reveal the diversity of eukaryotic core metabolism. Science (New York, N.Y.) 376, 831–839 (2022).

51. Senoo, N. & Claypool, S. M. Emerging Roles of Phospholipids in the Structure and Function of the Oxidative Phosphorylation Complexes. in The Dynamic Nature of Mitochondria 63–86 (CRC Press, 2024). doi:10.1201/9781003221180-6

52. Williamson, K. et al. A robustly rooted tree of eukaryotes reveals their excavate ancestry. Nature 640, 974–981 (2025).

53. He, Z. et al. Euglena’s atypical respiratory chain adapts to the discoidal cristae and flexible metabolism. Nature communications 15, 1628 (2024).

54. Valach, M., Léveillé-Kunst, A., Gray, M. W. & Burger, G. Respiratory chain Complex I of unparalleled divergence in diplonemids. The Journal of biological chemistry 293, 16043–16056 (2018).

55. Kaur, B. et al. Gene fragmentation and RNA editing without borders: eccentric mitochondrial genomes of diplonemids. Nucleic acids research 48, 2694–2708 (2020).

56. Surve, S., Heestand, M., Panicucci, B., Schnaufer, A. & Parsons, M. Enigmatic presence of mitochondrial complex I in Trypanosoma brucei bloodstream forms. Eukaryotic cell 11, 183–93 (2012).

57. David, V. et al. Gene Loss and Error-Prone RNA Editing in the Mitochondrion of Perkinsela, an Endosymbiotic Kinetoplastid. mBio 6, e01498-15 (2015).

58. Gastineau, R. et al. Mitogenome sequence of a Black Sea isolate of the kinetoplastid Bodo saltans. Mitochondrial DNA. Part B, Resources 3, 968–969 (2018).

59. Duarte, M. & Tomás, A. M. The mitochondrial complex I of trypanosomatids--an overview of current knowledge. Journal of bioenergetics and biomembranes 46, 299–311 (2014).

60. Cermáková, P., Verner, Z., Man, P., Lukes, J. & Horváth, A. Characterization of the NADH:ubiquinone oxidoreductase (complex I) in the trypanosomatid Phytomonas serpens (Kinetoplastida). The FEBS journal 274, 3150–8 (2007).

61. Verner, Z. et al. Comparative analysis of respiratory chain and oxidative phosphorylation in Leishmania tarentolae, Crithidia fasciculata, Phytomonas serpens and procyclic stage of Trypanosoma brucei. Molecular and biochemical parasitology 193, 55–65 (2014).

62. Gerasimov, E. S. et al. Evolutionary divergent kinetoplast genome structure and RNA editing patterns in the trypanosomatid Vickermania. Proceedings of the National Academy of Sciences of the United States of America 122, e2426887122 (2025).

63. Čermáková, P. et al. Differences in mitochondrial NADH dehydrogenase activities in trypanosomatids. Parasitology 148, 1161–1170 (2021).

64. Kampjut, D. & Sazanov, L. A. The coupling mechanism of mammalian respiratory complex I. Science (New York, N.Y.) 370, e0227226 (2020).

65. Nawathean, P. & Maslov, D. A. The absence of genes for cytochrome c oxidase and reductase subunits in maxicircle kinetoplast DNA of the respiration-deficient plant trypanosomatid Phytomonas serpens. Current genetics 38, 95–103 (2000).

66. Hierro-Yap, C. et al. Bioenergetic consequences of FoF1-ATP synthase/ATPase deficiency in two life cycle stages of Trypanosoma brucei. The Journal of biological chemistry 296, 100357 (2021).

67. Cabrera-Alarcón, J. L. et al. Structural diversity and evolutionary constraints of oxidative phosphorylation. Cell genomics 100945 (2025). doi:10.1016/j.xgen.2025.100945

68. Kravchuk, V. et al. A universal coupling mechanism of respiratory complex I. Nature 609, 808–814 (2022).

69. Parey, K. et al. High-resolution structure and dynamics of mitochondrial complex I-Insights into the proton pumping mechanism. Science advances 7, eabj3221 (2021).

70. Hernansanz-Agustín, P. et al. A transmitochondrial sodium gradient controls membrane potential in mammalian mitochondria. Cell 1–15 (2024). doi:10.1016/j.cell.2024.08.045

71. Kaila, V. R. I. Resolving Chemical Dynamics in Biological Energy Conversion: Long-Range Proton-Coupled Electron Transfer in Respiratory Complex I. Accounts of chemical research 54, 4462–4473 (2021).

72. Heberle, J., Riesle, J., Thiedemann, G., Oesterhelt, D. & Dencher, N. A. Proton migration along the membrane surface and retarded surface to bulk transfer. Nature 370, 379–82 (1994).

73. Nilsson, T. et al. Lipid-mediated Protein-protein Interactions Modulate Respiration-driven ATP Synthesis. Scientific reports 6, 24113 (2016).

74. Sjöholm, J. et al. The lateral distance between a proton pump and ATP synthase determines the ATP-synthesis rate. Scientific reports 7, 2926 (2017).

75. Kaila, V. R. I., Sharma, V. & Wikström, M. The identity of the transient proton loading site of the proton-pumping mechanism of cytochrome c oxidase. Biochimica et biophysica acta 1807, 80–4 (2011).

76. Yano, N. et al. The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle. The Journal of biological chemistry 291, 23882–23894 (2016).

77. Maldonado, M., Guo, F. & Letts, J. A. Atomic structures of respiratory complex III2, complex IV, and supercomplex III2-IV from vascular plants. eLife 10, 1–34 (2021).

78. MacLean, A. E. et al. Structure, assembly and inhibition of the Toxoplasma gondii respiratory chain supercomplex. Nature structural & molecular biology 32, 1424–1433 (2025).

79. Calvo, E. et al. Functional role of respiratory supercomplexes in mice: SCAF1 relevance and segmentation of the Qpool. Science advances 6, eaba7509 (2020).

80. Allen, R. D., Schroeder, C. C. & Fok, A. K. An investigation of mitochondrial inner membranes by rapid-freeze deep-etch techniques. The Journal of cell biology 108, 2233–40 (1989).

81. Niemann, M. & Schneider, A. A Scalable Purification Method for Mitochondria from Trypanosoma brucei. Methods in molecular biology (Clifton, N.J.) 2116, 611–626 (2020).

82. Schneider, A., Charrière, F., Pusnik, M. & Horn, E. K. Isolation of mitochondria from procyclic Trypanosoma brucei. Methods in molecular biology (Clifton, N.J.) 372, 67–80 (2007).

83. Gahura, O. et al. The F1 -ATPase from Trypanosoma brucei is elaborated by three copies of an additional p18-subunit. The FEBS journal 285, 614–628 (2018).

84. Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nature methods 14, 290–296 (2017).

85. Punjani, A., Zhang, H. & Fleet, D. J. Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Nature methods 17, 1214–1221 (2020).

86. Zivanov, J., Nakane, T. & Scheres, S. H. W. Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1. IUCrJ 7, 253–267 (2020).

87. Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta crystallographica. Section D, Structural biology 75, 861–877 (2019).

88. Kimanius, D., Dong, L., Sharov, G., Nakane, T. & Scheres, S. H. W. New tools for automated cryo-EM single-particle analysis in RELION-4.0. The Biochemical journal 478, 4169–4185 (2021).

89. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta crystallographica. Section D, Biological crystallography 66, 486–501 (2010).

90. Pettersen, E. F. et al. UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein science : a publication of the Protein Society 30, 70–82 (2021).

91. Goddard, T. D. et al. UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein science : a publication of the Protein Society 27, 14–25 (2018).

92. Meng, E. C. et al. UCSF ChimeraX: Tools for structure building and analysis. Protein science : a publication of the Protein Society 32, e4792 (2023).

93. Sun, F. et al. Crystal structure of mitochondrial respiratory membrane protein complex II. Cell 121, 1043–57 (2005).

94. Ho, C.-M. et al. Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu. Nature methods 17, 79–85 (2020).

95. Hall, N. et al. The DNA sequence of chromosome I of an African trypanosome: gene content, chromosome organisation, recombination and polymorphism. Nucleic acids research 31, 4864–73 (2003).

96. Berriman, M. et al. The genome of the African trypanosome Trypanosoma brucei. Science (New York, N.Y.) 309, 416–22 (2005).

97. Shanmugasundram, A. et al. TriTrypDB: An integrated functional genomics resource for kinetoplastida. PLoS neglected tropical diseases 17, e0011058 (2023).

98. Aslett, M. et al. TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic acids research 38, D457-62 (2010).

99. Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta crystallographica. Section D, Biological crystallography 68, 352–67 (2012).

100. Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta crystallographica. Section D, Structural biology 74, 531–544 (2018).

101. Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024).

102. Williams, C. J. et al. MolProbity: More and better reference data for improved all-atom structure validation. Protein science : a publication of the Protein Society 27, 293–315 (2018).

103. Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research 25, 3389–402 (1997).

104. Zimmermann, L. et al. A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. Journal of molecular biology 430, 2237–2243 (2018).

105. Sinha, S. D. & Wideman, J. G. The persistent homology of mitochondrial ATP synthases. iScience 26, 106700 (2023).

106. Ronquist, F. et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic biology 61, 539–42 (2012).

107. Larkin, M. A. et al. Clustal W and Clustal X version 2.0. Bioinformatics (Oxford, England) 23, 2947–8 (2007).

108. Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics (Oxford, England) 23, 127–8 (2007).

109. Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic acids research 49, W293–W296 (2021).

110. Letunic, I. & Bork, P. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic acids research 52, W78–W82 (2024).

111. Sali, A. & Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints. Journal of molecular biology 234, 779–815 (1993).

112. Søndergaard, C. R., Olsson, M. H. M., Rostkowski, M. & Jensen, J. H. Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values. Journal of chemical theory and computation 7, 2284–95 (2011).

113. Chang, C. H. & Kim, K. Density Functional Theory Calculation of Bonding and Charge Parameters for Molecular Dynamics Studies on [FeFe] Hydrogenases. Journal of chemical theory and computation 5, 1137–45 (2009).

114. Johansson, M. P., Kaila, V. R. I. & Laakkonen, L. Charge parameterization of the metal centers in cytochrome c oxidase. Journal of computational chemistry 29, 753–67 (2008).

115. Jo, S., Kim, T., Iyer, V. G. & Im, W. CHARMM-GUI: a web-based graphical user interface for CHARMM. Journal of computational chemistry 29, 1859–65 (2008).

116. Smith, D. M. A., Xiong, Y., Straatsma, T. P., Rosso, K. M. & Squier, T. C. Force-Field Development and Molecular Dynamics of [NiFe] Hydrogenase. Journal of chemical theory and computation 8, 2103–14 (2012).

117. Teixeira, V. H., Baptista, A. M. & Soares, C. M. Pathways of H2 toward the active site of [NiFe]-hydrogenase. Biophysical journal 91, 2035–45 (2006).

118. Huang, J. & MacKerell, A. D. CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. Journal of computational chemistry 34, 2135–45 (2013).

119. Lomize, M. A., Pogozheva, I. D., Joo, H., Mosberg, H. I. & Lomize, A. L. OPM database and PPM web server: Resources for positioning of proteins in membranes. Nucleic Acids Research 40, 370–376 (2012).

120. Tsukihara, T. et al. The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process. Proceedings of the National Academy of Sciences of the United States of America 100, 15304–9 (2003).

121. Bussi, G., Donadio, D. & Parrinello, M. Canonical sampling through velocity rescaling. The Journal of chemical physics 126, 014101 (2007).

122. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A. & Haak, J. R. Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics 81, 3684–3690 (1984).

123. Evans, D. J. & Holian, B. L. The Nose–Hoover thermostat. The Journal of Chemical Physics 83, 4069–4074 (1985).

124. Parrinello, M. & Rahman, A. Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics 52, 7182–7190 (1981).

125. Darden, T., York, D. & Pedersen, L. Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems. The Journal of Chemical Physics 98, 10089–10092 (1993).

126. Hess, B., Bekker, H., Berendsen, H. J. C. & Fraaije, J. G. E. M. LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry 18, 1463–1472 (1997).

127. Abraham, M. J. et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25 (2015).

128. Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. Journal of molecular graphics 14, 33–8, 27–8 (1996).

129. Michaud-Agrawal, N., Denning, E. J., Woolf, T. B. & Beckstein, O. MDAnalysis: a toolkit for the analysis of molecular dynamics simulations. Journal of computational chemistry 32, 2319–27 (2011).

130. Gowers, R. et al. MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. in Proceedings of the 15th Python in Science Conference 98–105 (2016). doi:10.25080/Majora-629e541a-00e

131. Dahl, A. C. E., Chavent, M. & Sansom, M. S. P. Bendix: intuitive helix geometry analysis and abstraction. Bioinformatics (Oxford, England) 28, 2193–4 (2012).

132. Eisenhaber, F., Lijnzaad, P., Argos, P., Sander, C. & Scharf, M. The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. Journal of Computational Chemistry 16, 273–284 (1995).

133. Tomar, S. Converting video formats with FFmpeg. Linux Journal 2006, (2006).

134. Alves, A. A. et al. Control of assembly of extra-axonemal structures: the paraflagellar rod of trypanosomes. Journal of cell science 133, (2020).

135. Beneke, T. & Gluenz, E. LeishGEdit: A Method for Rapid Gene Knockout and Tagging Using CRISPR-Cas9. Methods in molecular biology (Clifton, N.J.) 1971, 189–210 (2019).

136. Schneider, A., Bouzaidi-Tiali, N., Chanez, A.-L. & Bulliard, L. ATP production in isolated mitochondria of procyclic Trypanosoma brucei. Methods in molecular biology (Clifton, N.J.) 372, 379–87 (2007).

137. Doleželová, E. et al. Cell-based and multi-omics profiling reveals dynamic metabolic repurposing of mitochondria to drive developmental progression of Trypanosoma brucei. PLoS biology 18, e3000741 (2020).

138. Knott, G., Rosset, S. & Cantoni, M. Focussed ion beam milling and scanning electron microscopy of brain tissue. Journal of visualized experiments : JoVE e2588 (2011). doi:10.3791/2588

139. Kaurov, I. et al. The Diverged Trypanosome MICOS Complex as a Hub for Mitochondrial Cristae Shaping and Protein Import. Current biology : CB 28, 3393-3407.e5 (2018).

140. Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. Journal of structural biology 152, 36–51 (2005).

141. Mastronarde, D. N. & Held, S. R. Automated tilt series alignment and tomographic reconstruction in IMOD. Journal of structural biology 197, 102–113 (2017).

142. Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nature methods 9, 676–82 (2012).

指标

查看次数: 35
下载次数: 18

下载次数

已发布

2026-04-04

如何引用

Hu, Y., Wong, J., Endres, E., Corinna, B., Pecorilla, C., Huang, K., Bílý, T., Tian, H., Teng, M., Han, F., Wu, M., Zhang, N., Chen, Q., Zhou, J., Lai, D., Zíková, A., Huynen, M., Hashimi, H., Sharma, V., … Zhou, L. (2026). A Supercomplex Incorporating Both Electron Transport Chain and ATP Synthase. 浪淘沙预印本平台. https://doi.org/10.65215/LTSpreprints.2026.04.03.000171

利益冲突声明

作者声明无任何需要披露的利益冲突。