Molecular Dynamics Simulation of the KaiC Protein
- Author(s): Crouch, Theo
- Advisor(s): Colvin, Michael
- et al.
Circadian clocks are an integral part of cellular and molecular regulation. The protein KaiC is the central player in the well-characterized circadian clock system of cyanobacteria. The simplicity of the cyanobacterial cellular structures makes this protein system highly favorable for the study of the circadian rhythm. KaiC forms an overall structure that looks like two stacked homohexamer rings. The two hexameric domains are called the C1 and C2 ring. The clock’s 24-hour period is driven by sequential phosphorylation of residues in the C2 ring and the choreographed binding of KaiA and KaiB to the C2 and C1 rings, respectively. Although the specific steps have been mapped, the structural changes causing, and caused by, the phosphorylation and protein binding are not fully understood. This project will aim to
perform 500ns time-scale all-atom and coarse-grained MD of multiple experimental structures of the KaiC.