Oral: The collective dynamics of urease as triangular oligomers composed of multistate-state dumbbells

Enzymes are nanoscale bioreactors that help regulate chemical reactions inside cells as well as help coordinate other cellular functions. While their underlying chemical basis has been well-studied, some enzymes also exhibit nontrivial dynamics, the effects of which have not been well-studied. For instance, the enzyme urease exhibits an enhancement of diffusion when catalyzing the breakdown of urea [1]. To search for biophysical mechanisms for this enhancement, we model urease as a triangular-like oligomer composed of three multi-state dumbbells, representing portions of the urease hexamer. Each dumbbell models the conformational changes of urease due to the binding with its substrate, urea, during catalysis. Specifically, different rest lengths of the dumbbell correspond to different conformational states. We simulate the motion of one oligomer utilizing a set of coupled overdamped Langevin equations for each dumbbell with harmonic interactions between the dumbbells. In addition to quantifying the motion of an individual model urease, we quantify the motion of two model ureases that are hydrodynamically coupled to begin to explore their potential for collective dynamics.