Fig. 1.
Overview of the model CofactorYeast. (A) Scope of the model. In addition to metabolism, the model accounts for synthesis of iron-sulfur (Fe-S) clusters, translation, and cofactor binding processes. In this study, the enzyme cofactors include eight metal ions, ISCs, and heme. Notably, the parameter θ can be used to decrease turnover rates for the enzymes losing cofactors. (B) Coupling constraint. The mathematical relationship between metabolic reaction rates and enzyme synthesis rates can be established based on reaction rate equation with the steady-state assumption. Vmet, metabolic reaction rate; kcat, turnover rate; [E], enzyme concentration; f(M), a function of metabolite concentrations; Vsyn, enzyme synthesis rate; Vdil, enzyme dilution rate; μ, growth rate; kmax, the maximal turnover rate.