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The revolution evolution

Nature Plants volume 8, pages 14–17 (2022)Cite this article

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Machine-learning algorithms for protein structure prediction can now generate models directly from sequences. However, photosynthetic assemblies represent a challenge due to additional levels of complexity arising from their multi-protein nature and presence of cofactors.

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Fig. 1: Evolutionary progress in structural biology of photosynthetic proteins.
Fig. 2: The structure of the PSI dimer features 614 non-protein cofactors.
Fig. 3: Structural details of cofactors in photosynthetic complexes.

References

  1. Jumper, J. et al. Nature 596, 583–589 (2021).

    Article  CAS  Google Scholar 

  2. Baek, M. et al. Science 373, 871–876 (2021).

    Article  CAS  Google Scholar 

  3. Kühlbrandt, W. Science 343, 1443–1444 (2014).

    Article  Google Scholar 

  4. McMullan, G., Faruqi, A. R. & Henderson, R. Methods Enzymol. 579, 1–17 (2016).

    Article  CAS  Google Scholar 

  5. Pan, X. et al. Science 360, 1109–1113 (2018).

    Article  CAS  Google Scholar 

  6. Iwai, M., Grob, P., Iavarone, A. T., Nogales, E. & Niyogi, K. K. Nat. Plants 4, 904–909 (2018).

    Article  CAS  Google Scholar 

  7. Caspy, I., Borovikova-Sheinker, A., Klaiman, D., Shkolnisky, Y. & Nelson, N. Nat. Plants 6, 1300–1305 (2020).

    Article  CAS  Google Scholar 

  8. Perez-Boerema, A. et al. Nat. Plants 6, 321–327 (2020).

    Article  CAS  Google Scholar 

  9. Naschberger, A. et al. Preprint at bioRxiv https://doi.org/10.1101/2021.08.30.458224 (2021).

  10. Qin, X. et al. Nat. Plants 5, 263–272 (2019).

    Article  Google Scholar 

  11. Suga, M. et al. Nat. Plants 5, 626–636 (2019).

    Article  Google Scholar 

  12. Su, X. et al. Nat. Plants 5, 273–281 (2019).

    Article  CAS  Google Scholar 

  13. Yan, Q. et al. Cell Discov. 7, 10 (2021).

    Article  CAS  Google Scholar 

  14. Gorski et al. Preprint at bioRxiv https://doi.org/10.1101/2021.11.26.470156 (2021).

  15. Chen, M. et al. Nat. Plants 6, 314–320 (2020).

    Article  CAS  Google Scholar 

  16. Zheng, L. et al. Nat. Plants 5, 1087–1097 (2019).

    Article  CAS  Google Scholar 

  17. Kato, K. et al. Nat. Commun. 10, 4929 (2019).

    Article  Google Scholar 

  18. Huang, Z. et al. Nat. Commun. 12, 1100 (2021).

    Article  CAS  Google Scholar 

  19. Pan, X. et al. Nat. Plants 7, 1119–1131 (2021).

    Article  CAS  Google Scholar 

  20. Xu, C. et al. Nat. Commun. 11, 5081 (2020).

    Article  CAS  Google Scholar 

  21. Amunts, A. et al. Science 343, 1485–1489 (2014).

    Article  CAS  Google Scholar 

  22. Lawson, C. L., Berman, H. M. & Chiu, W. Struct. Dyn. 7, 014701 (2020).

    Article  CAS  Google Scholar 

  23. Graça, A. T., Hall, M., Persson, K. & Schröder, W. P. Sci. Rep. 11, 15534 (2021).

    Article  Google Scholar 

  24. Waltz, F., Soufari, H., Bochler, A., Giegé, P. & Hashem, Y. Nat. Plants 6, 377–383 (2020).

    Article  Google Scholar 

  25. Yuzuru, I. J. et al. Science 371, 846–849 (2021).

    Article  Google Scholar 

  26. Grade Web Server (Global Phasing Ltd, 2021); http://grade.globalphasing.org

  27. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).

    Article  CAS  Google Scholar 

  28. Caspy, I. et al. Nat. Plants 7, 1314–1322 (2021).

    Article  CAS  Google Scholar 

  29. Yong, T., Báti, G., García, F. & Stuparu, M. C. Nat. Commun. 12, 5187 (2021).

    Article  CAS  Google Scholar 

  30. Pagliano, C., Barera, S., Chimirri, F., Saracco, G. & Barber, J. Bioenergetics 1817, 1506–1515 (2012).

    Article  CAS  Google Scholar 

  31. Minoda, A. et al. Eur. J. Biochem. 269, 2353–2358 (2002).

    Article  CAS  Google Scholar 

  32. Aoki, M., Sato, N., Meguro, A. & Tsuzuki, M. Eur. J. Biochem. 271, 685–693 (2004).

    Article  CAS  Google Scholar 

  33. Qian, P. et al. Biochem. J. 478, 3923–3937 (2021).

    Article  CAS  Google Scholar 

  34. Croll, T. Twitter (5 September 2021); https://twitter.com/sjwill99/status/1434662442118778883

  35. Hooke, R. Micrographia or Some Physiological Descriptions made by Magnifying Glasses with Observations and Inquiries Thereupon (Royal Society, 1665).

  36. Schleiden, M. J. Arch. Anat. Physiol. Wiss. Med. 1838, 137–176 (1839).

    Google Scholar 

  37. Schwann, T. Mikroskopische Untersuchungen über die Uebereinstimmung: Struktur und dem Wachsthum der Thiere und Pflanzen (Sander, 1839).

  38. Feynman, R. Lecture on Quantum Electrodynamics at the University of Auckland, New Zealand. http://www.vega.org.uk/video/programme/45 (1979).

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Acknowledgements

The author thanks A. Naschberger and N. Nelson for help with figures and comments, EMBO Young Investigator Program and Swedish Foundation for Strategic Research grant ARC19:0051 for support.

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  1. Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden

    Alexey Amunts

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Amunts, A. The revolution evolution. Nat. Plants 8, 14–17 (2022). https://doi.org/10.1038/s41477-021-01050-5

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