Free-Energy Transduction in Chemical Reaction Networks: from Enzymes to Metabolism

TL;DR

This paper rigorously defines free-energy transduction in chemical reaction networks, analyzing their thermodynamic efficiency and operation as machines, with applications to metabolic pathways.

Contribution

It introduces a general method to quantify free-energy transduction in open CRNs using stoichiometry and chemostats, applicable to linear and nonlinear systems.

Findings

CRNs operate as thermodynamic machines when driven against their spontaneous direction

The method links fundamental currents to metabolic pathways

Efficiency of energy transduction in metabolism is characterized

Abstract

We provide a rigorous definition of free-energy transduction and its efficiency in arbitrary -- linear or nonlinear -- open chemical reaction networks (CRNs) operating at steady state. Our method is based on the knowledge of the stoichiometric matrix and of the chemostatted species (i.e. the species maintained at constant concentration by the environment) to identify the fundamental currents and forces contributing to the entropy production. Transduction occurs when the current of a stoichiometrically balanced process is driven against its spontaneous direction (set by its force) thanks to other processes flowing along their spontaneous direction. In these regimes, open CRNs operate as thermodynamic machines. After exemplifying these general ideas using toy models, we analyze central energy metabolism. We relate the fundamental currents to metabolic pathways and discuss the efficiency with which they are able to transduce free energy.