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

Biological Physics;Molecular Networks