Fig. 3.
KaiA-dependent negative feedback loop is the noise bottleneck in a stochastic model of the Kai system. a Model of post-translational oscillator. KaiC hexamers undergo ordered phosphorylation (yellow box) and dephosphorylation (blue box). KaiA is required for KaiC phosphorylation, and dephosphorylating KaiC binds to KaiB to sequester and inhibit KaiA. (see Supplementary Fig. S5). b Simulated stochastic single cell trajectories (gray) at various Kai copy numbers with two example traces highlighted (blue and purple). “KaiC state” indicates the average position of KaiC molecules in the oscillator loop. c Distributions of peak-to-peak time intervals in the stochastic model. d Comparison of model and experimental data. Vertical error bars indicate 95% confidence interval from bootstrapping (5000 iterations). Horizontal error bars indicate standard error of the mean (n = 3). Gray interval indicates the 95% bootstrapping confidence interval for the model. e Mean phase shift caused by Poisson noise perturbations to molecular species in the model (n = 500 trials). Error bars indicate 95% confidence interval from bootstrapping. f Instantaneous KaiC phosphorylation rate vs. fraction of KaiC in KaiABC complexes in the stochastic model for NKaiC = 300 hexamers. Shaded area indicates the range over which KaiABC complexes oscillate