title: Propensity approach to nonequilibrium thermodynamics of a chemical reaction network: controlling single E-coli β-galactosidase enzyme catalysis through the elementary reaction steps.
abstract: In this work, we develop an approach to nonequilibrium thermodynamics of an open chemical reaction network in terms of the elementary reaction propensities. The method is akin to the microscopic formulation of the dissipation function in terms of the Kullback-Leibler distance of phase space trajectories in Hamiltonian system. The formalism is applied to a single oligomeric enzyme kinetics at chemiostatic condition that leads the reaction system to a nonequilibrium steady state, characterized by a positive total entropy production rate. Analytical expressions are derived, relating the individual reaction contributions towards the total entropy production rate with experimentally measurable reaction velocity. Taking a real case of Escherichia coli β-galactosidase enzyme obeying Michaelis-Menten kinetics, we thoroughly analyze the temporal as well as the steady state behavior of various thermodynamic quantities for each elementary reaction. This gives a useful insight in the relative magnitudes of various energy terms and the dissipated heat to sustain a steady state of the reaction system operating far-from-equilibrium. It is also observed that, the reaction is entropy-driven at low substrate concentration and becomes energy-driven as the substrate concentration rises.
authors.affiliation: S. N. Bose National Centre For Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700 098, India.
authors.forename: Biswajit
authors.initials: B
authors.lastname: Das
authors.affiliation: Department of Chemistry, University of Calcutta, 92 A.P.C. Road, Kolkata 700 009, India.
authors.forename: Kinshuk
authors.initials: K
authors.lastname: Banerjee
authors.affiliation: S. N. Bose National Centre For Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700 098, India.
authors.forename: Gautam
authors.initials: G
authors.lastname: Gangopadhyay
mesh_terms: D055162:Biocatalysis; D004926:Escherichia coli / Q000737:chemistry*; D007700:Kinetics; D008956:Models, Chemical; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D013816:Thermodynamics; D001616:beta-Galactosidase / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D001616:beta-Galactosidase