The intracellular equilibrium thermodynamic and steady-state concentrations of metabolites

Abstract

A new model for the organization and flow of metabolites through a metabolic pathway is presented. The model is based on four major findings. (1) The intracellular concentrations of enzyme sites exceed the concentrations of intermediary metabolites that bind specifically to these sites. (2) The concentration of the excessive enzyme sites in the cell is sufficiently high so that nearly all the cellular intermediary metabolites are enzyme-bound. (3) Enzyme conformations are perturbed by the interactions with substrates and products; the conformations of enzyme-substrate and enzyme-product complexes are different. (4) Two enzymes, catalyzing reactions that are sequential in a metabolic pathway, transfer the common metabolite back and forth via an enzyme-enzyme complex without the intervention of the solvent environment. The model proposes that the enzyme-enzyme recognition is ligand-induced. Conversion of E2S and E2P results in the loss of recognition of E2 by E1 and the concomitant recognition of E2 by E3. This model substantially alters existent views of the bioenergetics and the kinetics of intracellular metabolism. The rates of direct transfer of metabolite from enzyme to enzyme are comparable to the rates of interconversion between substrate and product within an individual enzyme. Consequently, intermediary metabolites are nearly equipartitioned among their high-affinity enzyme sites within a metabolic pathway. Metabolic flux involves the direct transfer of metabolite from enzyme to enzyme via a set of low and nearly equal energy barriers.