Enzyme kinetics simulation at the scale of individual particles

Enzyme-catalysed reactions involve two distinct timescales. There is a short timescale on which enzymes bind to substrate molecules to produce bound complexes, and a comparatively long timescale on which the complex is transformed into a product. The rate at which the substrate is converted into product is characteristically non-linear and is traditionally derived by applying singular perturbation theory to the system's governing equations. Central to this analysis is the assumption that complex formation is effectively instantaneous on the timescale over which significant substrate degradation occurs. This prevents accurate modelling of enzyme kinetics by many particle-based simulations of reaction-diffusion systems as they rely on proximity-based reaction conditions that do not correctly model the fast reactions associated with the complex on the long timescale. In this paper we derive a new proximity-based reaction condition that correctly incorporates the reactions that occur on the short timescale for a specific enzymatic system. We present proof of concept particle-based simulations and demonstrate that non-linear reaction rates typical of enzyme kinetics can be reproduced without needing to explicitly simulate reactions on the short timescale.

Taylor Kearney, Mark B. Flegg · 2023