Effects of nonproductive binding on the kinetics of enzymatic reactions with patterned substrates.

ABSTRACT

Existing models of ligand-receptor binding kinetics suggest that clustering surface-associated molecules tends to decrease the rates with which solution phase molecules associate and dissociate. Here, the authors use kinetic Monte Carlo simulations to study the case of an enzyme catalyzing the turnover of substrate molecules immobilized on a surface. The simulations reveal a crossover in the overall reaction rates for randomly distributed and clustered substrate molecules as the enzyme unbinding rate is varied. Approximate expressions for the effective kinetic parameters are introduced, and they show that the observed behavior derives from sequestration of the enzyme in the strong-sticking limit.