Thermodynamics and Kinetics of Glycolytic Reactions. Part I: Kinetic Modeling Based on Irreversible Thermodynamics and Validation by Calorimetry.

Kristina Vogel,Thomas Maskow,Thorsten Greinert,Hauke Harms,Christoph Held,Monique Reichard

doi:10.3390/ijms21218341

Abstract

In systems biology, material balances, kinetic models, and thermodynamic boundary conditions are increasingly used for metabolic network analysis. It is remarkable that the reversibility of enzyme-catalyzed reactions and the influence of cytosolic conditions are often neglected in kinetic models. In fact, enzyme-catalyzed reactions in numerous metabolic pathways such as in glycolysis are often reversible, i.e., they only proceed until an equilibrium state is reached and not until the substrate is completely consumed. Here, we propose the use of irreversible thermodynamics to describe the kinetic approximation to the equilibrium state in a consistent way with very few adjustable parameters. Using a flux-force approach allowed describing the influence of cytosolic conditions on the kinetics by only one single parameter. The approach was applied to reaction steps 2 and 9 of glycolysis (i.e., the phosphoglucose isomerase reaction from glucose 6-phosphate to fructose 6-phosphate and the enolase-catalyzed reaction from 2-phosphoglycerate to phosphoenolpyruvate and water). The temperature dependence of the kinetic parameter fulfills the Arrhenius relation and the derived activation energies are plausible. All the data obtained in this work were measured efficiently and accurately by means of isothermal titration calorimetry (ITC). The combination of calorimetric monitoring with simple flux-force relations has the potential for adequate consideration of cytosolic conditions in a simple manner.

Highlights

In systems biology, models are expected to describe enzyme kinetics with high precision at relatively low metabolite concentrations
The latter is more common in biochemistry and bioengineering but the use of molality is important for the link to thermodynamics
In order to exclude that the ionization of the buffer plays a role for the obtained reaction enthalpy, the measurements were performed in other buffers [39]

Summary

Introduction

Models are expected to describe enzyme kinetics with high precision at relatively low metabolite concentrations (in the lower micro- to millimolar range). Since all metabolic fluxes decay when reaching a thermodynamic equilibrium, the approximation to the state of equilibrium must be well described. Only the kinetic data of enzyme-catalyzed reactions are published. Based on such data, various kinetic models for data analysis of enzyme-catalyzed reactions have been developed in the literature. The most common approach is Michaelis-Menten kinetics, which is based on the publications of Brown [1] and Henri [2,3].

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Methods

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Discussion

Conclusion