ArticleProceedings of the National Academy of Sciences of the United States of America2018
Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- An underlying bistability sets amplitude and explains temperature compensation in the cyanobacterial circadian clock.bioRxiv : the preprint server for biology · 2026Article
- The Phenotypic Landscape of a Circadian Clock.bioRxiv : the preprint server for biology · 2026Article
- The free-running property of circadian clocks is needed to tolerate changing photoperiods.Current biology : CB · 2026Article
- The cyanobacterial circadian clock.Npj biological timing and sleep · 2025Review
- A topological mechanism for robust and efficient global oscillations in biological networks.Nature communications · 2024Article
- Exploring Kinase Asp-Phe-Gly (DFG) Loop Conformational Stability with AlphaFold2-RAVE.Journal of chemical information and modeling · 2024Article
- The inner workings of an ancient biological clock.Trends in biochemical sciences · 2024Review
- Determining subunit-subunit interaction from statistics of cryo-EM images: observation of nearest-neighbor coupling in a circadian clock protein complex.Nature communications · 2023Article
- Article
- Coupling of distant ATPase domains in the circadian clock protein KaiC.Nature structural & molecular biology · 2022Article
- Spectres of Clock Evolution: Past, Present, and Yet to Come.Frontiers in physiology · 2021Review
- Molecular dynamics free energy simulations of ATP:MgMolecular simulation · 2021Article
- Monitoring Protein-Protein Interactions in the Cyanobacterial Circadian Clock in Real Time via Electron Paramagnetic Resonance Spectroscopy.Biochemistry · 2020Article
- Bayesian modeling reveals metabolite-dependent ultrasensitivity in the cyanobacterial circadian clock.Molecular systems biology · 2020Article
- Orchestration of Circadian Timing by Macromolecular Protein Assemblies.Journal of molecular biology · 2020Review
- Myosin and Other Energy-Transducing ATPases: Structural Dynamics Studied by Electron Paramagnetic Resonance.International journal of molecular sciences · 2020Review
- ATP hydrolysis by KaiC promotes its KaiA binding in the cyanobacterial circadian clock system.Life science alliance · 2019Article
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5 authors.
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Abstract
The cyanobacterial clock proteins KaiA, KaiB, and KaiC form a powerful system to study the biophysical basis of circadian rhythms, because an in vitro mixture of the three proteins is sufficient to generate a robust ∼24-h rhythm in the phosphorylation of KaiC. The nucleotide-bound states of KaiC critically affect both KaiB binding to the N-terminal domain (CI) and the phosphotransfer reactions that (de)phosphorylate the KaiC C-terminal domain (CII). However, the nucleotide exchange pathways associated with transitions among these states are poorly understood. In this study, we integrate recent advances in molecular dynamics methods to elucidate the structure and energetics of the pathway for Mg·ADP release from the CII domain. We find that nucleotide release is coupled to large-scale conformational changes in the KaiC hexamer. Solvating the nucleotide requires widening the subunit interface leading to the active site, which is linked to extension of the A-loop, a structure implicated in KaiA binding. These results provide a molecular hypothesis for how KaiA acts as a nucleotide exchange factor. In turn, structural parallels between the CI and CII domains suggest a mechanism for allosteric coupling between the domains. We relate our results to structures observed for other hexameric ATPases, which perform diverse functions.
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