Modeling a simple enzyme reaction with delay and discretization

TL;DR

This paper compares traditional Michaelis-Menten kinetics with two delay-based models that incorporate conformational change durations and stochastic effects, revealing differences in dynamics such as oscillations and behavior under scarcity.

Contribution

It introduces two novel delay models for enzyme reactions that account for conformational change durations and stochastic effects, extending classical kinetics.

Findings

Delayed models exhibit oscillations not seen in Michaelis-Menten.

Out-of-equilibrium dynamics differ significantly between models.

Discrete and continuous delay models can behave differently under low reactant conditions.

Abstract

A comparison is made between conventional Michaelis-Menten kinetics and two models that take into account the duration of the conformational changes that take place at the molecular level during the catalytic cycle of a monomer. The models consider the time that elapses from the moment an enzyme-substrate complex forms until the moment a product molecule is released, as well as the recovery time needed to reset the conformational change that took place. In the first model the dynamics is described by a set of delayed differential equations, instead of the ordinary differential equations associated to Michaelis-Menten kinetics. In the second model the delay, the discretization inherent to enzyme reactions and the stochastic binding of substrates to enzimes at the molecular level is considered. All three models agree at equilibrium, as expected; however, out-of-equilibrium dynamics can differ substantially. In particular, both delayed models show oscillations at low values of the Michaelis constant which are not reproduced by the Michaelis-Menten model. Additionally, in certain cases, the dynamics shown by the continuous delayed model differs from the dynamics of the discrete delayed model when some reactant become scarce.