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The role of spatial confinement and heterogeneity in interfacial enzyme reactions

The Michaelis-Menten (MM) equation has dominated biochemistry for more than a century by providing the mathematical framework for the kinetic characterization of enzymes. This classical description of enzyme reactions relies on the assumption that all species are homogenous and freely diffusible in a uniform and well-mixed three-dimensional space. However, the premise of a homogenous environment is not justified for a large group of enzyme reactions both in vivo (1) and in industrial applications (2-4) which takes place at the solid-liquid interface. The gap between the industrial application of enzymes and the theoretical framework to capture their kinetic is growing as authoritative textbooks in biochemistry generally do not cover heterogeneous enzyme reactions. This project aims to close this gap by addressing the influence of spatial confinement (2D diffusion) and surface heterogeneity on enzyme kinetics. Concepts that are almost unexplored in conventional (bulk phase) enzyme kinetics but may be of general importance for enzyme reactions in heterogenous environments and in particular for interfacial enzymes. We will in the project explore the validity and applicability of the Michaelis-Menten model for interfacial enzyme reactions by including both substrate heterogeneity and spatial constraints in the classical model for enzyme reactions.















The interdisciplinary project will be organized into 3 work packages (WP):

  1. Experimental WP – Associate Professor Jeppe Kari (PI, chemistry, RUC).  Assay development and experimental characterization of interfacial enzymes. We will use specially designed kinetic assays and in-house techniques such as atomic force microscopy and calorimetry to characterize the morphology and crystallinity of the insoluble substrate. State-of-the-art single-enzyme imaging at the solid-liquid interface will be conducted at Professor William Hancock's laboratory at Pennsylvania State University as a part of the project.

  2. Computational WP - Associate Professor Ulf Rørbæk Pedersen (Physics, RUC). Stochastic simulations of interfacial enzyme reactions will be done using a two-dimensional heterogeneous square lattice. Substrate heterogeneity and spatial confinement will be explored using different distribution functions and constraints in the Monte Carlo simulations.C

  3. Modeling WP - Assistant Professor Johanne Gudmand-Høyer (Mathematics, RUC). Spatial constraints and heterogeneity will be modeled using ordinary differential equations. Population kinetic analysis will be explored as a tool to gain insight into surface heterogeneity by extraction of potential probability distributions of the kinetic parameters in the kinetic models. Fractal kinetics will be explored as an alternative to mass-action kinetics for spatial confined reactions.

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