Emergence of Dynamic Cooperativity in the Stochastic Kinetics of Fluctuating Enzymes

TL;DR

This paper investigates how enzyme conformational fluctuations and molecular discreteness influence enzyme kinetics, revealing the emergence of dynamic cooperativity and the transition from stochastic to deterministic Michaelis-Menten behavior.

Contribution

It introduces a stochastic, bottom-up approach to understand enzyme turnover kinetics at mesoscopic concentrations, linking single-molecule insights to collective enzyme behavior.

Findings

Dynamic cooperativity manifests as slowed MM kinetics and negative cooperativity.

Enzymatic fluctuations dominate at low enzyme numbers, causing cooperativity.

Increasing enzyme numbers suppress fluctuations, leading to classical MM kinetics.

Abstract

Dynamic cooperativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic cooperativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative cooperativity. For fewer enzymes, dynamic cooperativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic cooperativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.