title: Pathway thermodynamics highlights kinetic obstacles in central metabolism.
abstract: In metabolism research, thermodynamics is usually used to determine the directionality of a reaction or the feasibility of a pathway. However, the relationship between thermodynamic potentials and fluxes is not limited to questions of directionality: thermodynamics also affects the kinetics of reactions through the flux-force relationship, which states that the logarithm of the ratio between the forward and reverse fluxes is directly proportional to the change in Gibbs energy due to a reaction (ΔrG'). Accordingly, if an enzyme catalyzes a reaction with a ΔrG' of -5.7 kJ/mol then the forward flux will be roughly ten times the reverse flux. As ΔrG' approaches equilibrium (ΔrG' = 0 kJ/mol), exponentially more enzyme counterproductively catalyzes the reverse reaction, reducing the net rate at which the reaction proceeds. Thus, the enzyme level required to achieve a given flux increases dramatically near equilibrium. Here, we develop a framework for quantifying the degree to which pathways suffer these thermodynamic limitations on flux. For each pathway, we calculate a single thermodynamically-derived metric (the Max-min Driving Force, MDF), which enables objective ranking of pathways by the degree to which their flux is constrained by low thermodynamic driving force. Our framework accounts for the effect of pH, ionic strength and metabolite concentration ranges and allows us to quantify how alterations to the pathway structure affect the pathway's thermodynamics. Applying this methodology to pathways of central metabolism sheds light on some of their features, including metabolic bypasses (e.g., fermentation pathways bypassing substrate-level phosphorylation), substrate channeling (e.g., of oxaloacetate from malate dehydrogenase to citrate synthase), and use of alternative cofactors (e.g., quinone as an electron acceptor instead of NAD). The methods presented here place another arrow in metabolic engineers' quiver, providing a simple means of evaluating the thermodynamic and kinetic quality of different pathway chemistries that produce the same molecules.
authors.affiliation: Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Elad
authors.initials: E
authors.lastname: Noor
authors.affiliation: Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Arren
authors.initials: A
authors.lastname: Bar-Even
authors.affiliation: Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel ; Department of Molecular and Cellular Biology, University of California, Berkely, Berkely, California, United States of America.
authors.forename: Avi
authors.initials: A
authors.lastname: Flamholz
authors.affiliation: Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America.
authors.forename: Ed
authors.initials: E
authors.lastname: Reznik
authors.affiliation: Institut für Biochemie, Charité-Universitätsmedizin Berlin, Berlin, Germany.
authors.forename: Wolfram
authors.initials: W
authors.lastname: Liebermeister
authors.affiliation: Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Ron
authors.initials: R
authors.lastname: Milo
mesh_terms: D002952:Citric Acid Cycle; D019295:Computational Biology; D004798:Enzymes / Q000378:metabolism; D004926:Escherichia coli / Q000378:metabolism; D005285:Fermentation; D007700:Kinetics; D008291:Malate Dehydrogenase / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D009994:Osmolar Concentration; D010766:Phosphorylation; D013816:Thermodynamics
chemical_list: D004798:Enzymes; D008291:Malate Dehydrogenase