Modeling the Mechanism of Circadian KaiC Phosphorylation in Cyanobacterium Synechococcus elongatus

Until recently, it was believed that the mechanisms for circadian rhythm in all organisms were very complex, requiring many cofactors which were difficult to identify. However, Nakajima et al. showed that one organism, the cyanobacterium Synechococcus elongatus, contains three clock proteins, KaiA, KaiB, and KaiC, that, when purified and mixed with ATP, produce circadian oscillations in vitro1. In this project, an attempt to determine the mechanism for these circadian oscillations is made; building on previously published work2 of Dr. David Lubensky, professor at the University of Michigan. The approach relies on relatively simple mass-action kinetics to model the system. Two adaptions of the van Zon model2 were attempted: slowing the binding rate of KaiB and introducing a dimer/tetramer interaction to the model. Unfortunately, both of these mechanisms failed to model the experimental oscillating system. Proving that this simple model is most likely not the mechanism controlling this phenomenon