Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach

• Published in: Communications biology Vol. 5; no. 1; pp. 184 - 12
• Main Authors: Yunoki, Yasuhiro, Matsumoto, Atsushi, Morishima, Ken, Martel, Anne, Porcar, Lionel, Sato, Nobuhiro, Yogo, Rina, Tominaga, Taiki, Inoue, Rintaro, Yagi-Utsumi, Maho, Okuda, Aya, Shimizu, Masahiro, Urade, Reiko, Terauchi, Kazuki, Kono, Hidetoshi, Yagi, Hirokazu, Kato, Koichi, Sugiyama, Masaaki
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 10.03.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 101/58; 631/535/1261; 631/57/2266; Bacterial Proteins - chemistry; Biology; Biomedical and Life Sciences; Circadian Clocks; Circadian rhythm; Circadian Rhythm Signaling Peptides and Proteins - genetics; Circadian rhythms; Computer applications; Cyanobacteria; Hydrophobicity; Life Sciences; Scattering, Small Angle
• ISSN: 2399-3642; 2399-3642
• DOI: 10.1038/s42003-022-03143-z

In the cyanobacterial circadian clock system, KaiA, KaiB and KaiC periodically assemble into a large complex. Here we determined the overall structure of their fully assembled complex by integrating experimental and computational approaches. Small-angle X-ray and inverse contrast matching small-angle neutron scatterings coupled with size-exclusion chromatography provided constraints to highlight the spatial arrangements of the N-terminal domains of KaiA, which were not resolved in the previous structural analyses. Computationally built 20 million structural models of the complex were screened out utilizing the constrains and then subjected to molecular dynamics simulations to examine their stabilities. The final model suggests that, despite large fluctuation of the KaiA N-terminal domains, their preferential positionings mask the hydrophobic surface of the KaiA C-terminal domains, hindering additional KaiA-KaiC interactions. Thus, our integrative approach provides a useful tool to resolve large complex structures harboring dynamically fluctuating domains. The revealed full KaiA 12 B 6 C 6 complex is assembled including the dynamic and asynchronous KaiA N-terminal domains that have been missing in cryo-EM structures.