ArticlePLoS computational biology2017
A thermodynamically consistent model of the post-translational Kai circadian clock.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 50 citations in OpenAlex.
- An underlying bistability sets amplitude and explains temperature compensation in the cyanobacterial circadian clock.bioRxiv : the preprint server for biology · 2026Article
- Physical Frameworks and Theories on How Autonomous Biological Oscillators Synchronize.Advances in experimental medicine and biology · 2026Review
- Environmental and molecular noise buffering by the cyanobacterial clock in individual cells.Nature communications · 2025Article
- A topological mechanism for robust and efficient global oscillations in biological networks.Nature communications · 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
- Robust replication initiation from coupled homeostatic mechanisms.Nature communications · 2022Article
- KidA, a multi-PAS domain protein, tunes the period of the cyanobacterial circadian oscillator.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Role of the reaction-structure coupling in temperature compensation of the KaiABC circadian rhythm.PLoS computational biology · 2022Article
- Multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by ADP/ATP exchange inhibition.PLoS computational biology · 2022Article
- Mechanism for the Generation of Robust Circadian Oscillations through Ultransensitivity and Differential Binding Affinity.The journal of physical chemistry. B · 2021Article
- Mechanism of autonomous synchronization of the circadian KaiABC rhythm.Scientific reports · 2021Article
- Bayesian modeling reveals metabolite-dependent ultrasensitivity in the cyanobacterial circadian clock.Molecular systems biology · 2020Article
- The thermodynamic uncertainty relation in biochemical oscillations.Journal of the Royal Society, Interface · 2019Article
- Non-sinusoidal Waveform in Temperature-Compensated Circadian Oscillations.Biophysical journal · 2019Article
- Computational modelling unravels the precise clockwork of cyanobacteria.Interface focus · 2018Review
- Structure, function, and mechanism of the core circadian clock in cyanobacteria.The Journal of biological chemistry · 2018Review
- Single-molecular and ensemble-level oscillations of cyanobacterial circadian clock.Biophysics and physicobiology · 2018Article
- The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics.Natural computing · 2018Article
- Role of ATP Hydrolysis in Cyanobacterial Circadian Oscillator.Scientific reports · 2017Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The principal pacemaker of the circadian clock of the cyanobacterium S. elongatus is a protein phosphorylation cycle consisting of three proteins, KaiA, KaiB and KaiC. KaiC forms a homohexamer, with each monomer consisting of two domains, CI and CII. Both domains can bind and hydrolyze ATP, but only the CII domain can be phosphorylated, at two residues, in a well-defined sequence. While this system has been studied extensively, how the clock is driven thermodynamically has remained elusive. Inspired by recent experimental observations and building on ideas from previous mathematical models, we present a new, thermodynamically consistent, statistical-mechanical model of the clock. At its heart are two main ideas: i) ATP hydrolysis in the CI domain provides the thermodynamic driving force for the clock, switching KaiC between an active conformational state in which its phosphorylation level tends to rise and an inactive one in which it tends to fall; ii) phosphorylation of the CII domain provides the timer for the hydrolysis in the CI domain. The model also naturally explains how KaiA, by acting as a nucleotide exchange factor, can stimulate phosphorylation of KaiC, and how the differential affinity of KaiA for the different KaiC phosphoforms generates the characteristic temporal order of KaiC phosphorylation. As the phosphorylation level in the CII domain rises, the release of ADP from CI slows down, making the inactive conformational state of KaiC more stable. In the inactive state, KaiC binds KaiB, which not only stabilizes this state further, but also leads to the sequestration of KaiA, and hence to KaiC dephosphorylation. Using a dedicated kinetic Monte Carlo algorithm, which makes it possible to efficiently simulate this system consisting of more than a billion reactions, we show that the model can describe a wealth of experimental data.
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