Collective Properties of Hydrodynamically-interacting Active Oligomeric Assemblies

Enzymes are nanoscale bioreactors that help regulate chemical reactions inside cells and coordinate other cellular functions. While their underlying chemical basis has been well-studied, some enzymes also exhibit non-trivial 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. To search for biophysical mechanisms for this enhancement, we first simulate the motion of individual multi-state dumbbells (representing the enzyme's basic active unit)

to establish its fundamental active properties. We then model urease as a triangular-like oligomer composed of three of these 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, where different rest lengths correspond to different conformational states. We simulate the motion of these oligomers utilizing a set of coupled overdamped Langevin equations for each dumbbell incorporating harmonic interactions

between them. We then quantify the motion of an individual model urease oligomer as well as explore the collective dynamics mediated by hydrodynamic interactions between oligomers to potentially enhance their effect as nanoscale remodelers of their environment.