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The KaiABC circadian clock from cyanobacteria is the only known three-proteinoscillatory system which can be reconstituted outside the cell and whichdisplays sustained periodic dynamics in various molecular state variables.Despite many recent experimental and theoretical studies there are several openquestions regarding the central mechanism(s) responsible for creating this ~24hour clock in terms of molecular assembly/disassembly of the proteins andsite-dependent phosphorylation and dephosphorylation of KaiC monomers.Simulations of protein-protein interactions and phosphorylation reactionsconstrained by analytical fits to partial reaction experimental data supportthe central mechanism of oscillation as KaiB-induced KaiA sequestration inKaiABC complexes associated with the extent of Ser431 phosphorylation in KaiChexamers. A simple two-state deterministic model in terms of the degree ofphosphorylation of Ser431 and Thr432 sites alone can reproduce the previouslyobserved circadian oscillation in the four population monomer phosphoforms interms of waveform, amplitude and phase. This suggests that a cyclicphosphorylation scheme (involving cooperativity between adjacent Ser431 andThr432 sites) is not necessary for creating oscillations. Direct simulations ofthe clock predict the minimum number of serine-only monomer subunits associatedwith KaiA sequestration and release, highlight the role of monomer exchange inrapid synchronization, and predict the average number of KaiA dimerssequestered per KaiC hexamer.

Computational modeling of protein interactions and phosphoform kinetics in the KaiABC cyanobacterial circadian clock