Centers and Institutes
Published December 13, 2024 | Version v1
Journal article Open

Temperature-dependent fold-switching mechanism of the circadian clock protein KaiB

Creators

  • 1. University of California, Merced
  • 2. University of Chicago
  • 3. University of California, Davis
  • 4. University of California, Santa Cruz

Description

The oscillator of the cyanobacterial circadian clock relies on the ability of the KaiB protein to switch reversibly between a stable ground-state fold (gsKaiB) and an unstable fold-switched fold (fsKaiB). Rare fold-switching events by KaiB provide a critical delay in the negative feedback loop of this posttranslational oscillator. In this study, we experimentally and computationally investigate the temperature dependence of fold switching and its mechanism. We demonstrate that the stability of gsKaiB increases with temperature compared to fsKaiB and that the Q10 value for the gsKaiB → fsKaiB transition is nearly three times smaller than that for the reverse transition in a construct optimized for NMR studies. Simulations and native-state hydrogen-deuterium exchange NMR experiments suggest that fold switching can involve both partially and completely unfolded intermediates. The simulations predict that the transition state for fold switching coincides with isomerization of conserved prolines in the most rapidly exchanging region, and we confirm experimentally that proline isomerization is a rate-limiting step for fold switching. We explore the implications of our results for temperature compensation, a hallmark of circadian clocks, through a kinetic model.

Data availability

The Upside model is available at https://github.com/sosnicklab/upside2-md (79). Analysis scripts for analyzing Upside trajectories are available at https://github.com/dinner-group/KaiB-fold-switching (83). Initial structures of unbiased trajectories, collective variables, and kinetic statistics have been deposited in Zenodo (84).

Files

zhang-et-al-2024-temperature-dependent-fold-switching-mechanism-of-the-circadian-clock-protein-kaib.pdf

Files (8.3 MB)

Additional details

Identifiers

DOI
10.1073/pnas.2412327121
Other
oai:uchicago.tind.io:14777

Funding

National Institutes of Health
R35GM144110
National Institutes of Health
R35GM136381
National Institutes of Health
R35GM148233
National Institutes of Health
R35GM141849
National Science Foundation
1953402
National Science Foundation
2023077
National Science Foundation
HRD-1547848
US Army
W911NF-23-1-0248
National Science Foundation
2140001
National Institutes of Health
1S10OD028655

UChicago Information

Division(s)
Biological Sciences Division, Physical Sciences Division
Department(s)
Biochemistry and Molecular Biology, Biophysical Sciences, Chemistry
Center(s) or Institute(s)
James Franck Institute