Can inactive binding sites speed-up nonequilibrium kinetics?

Life is an out-of-equilibrium process. Therefore, it is not surprising that biological systems often inspire the study of nonequilibrium statistical mechanics. In a recent series of experiments, Zananiri et al. [Nat Commun 13, 1806 (2022)] studied a helicase called RecBCD. One of their main conclusions is the existence of several inactive ATP binding sites capable of accelerating the reaction rate of the enzyme. This result motivated us to ask how auxiliary inactive sites affect the kinetics of various out-of-equilibrium processes.

We investigate the turnover rate in an enzymatic process in which molecules flow from a molecular reservoir to a catalytic site, where they undergo a chemical reaction. We constructed a simple model consisting of an active site, an inactive auxiliary site, a connecting region, and a molecule reservoir. Our findings reveal that the auxiliary site can enhance the reaction rate in two distinct parameter regimes, each corresponds to a unique mechanism. In the first regime, the auxiliary site releases a molecule to block the molecule in the catalytic site from escaping without undergoing catalysis. In the second mechanism, the auxiliary site stores a molecule and releases it when the catalytic site is empty.