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Significance Organisms use the central carbon metabolism for both breakdown of substrate into biomass precursors and extraction of energy, making the pathways overlapping. We present a modeling concept that can decompose the overlapping pathways and hence account for protein cost for each of them. This enables comparisons between pathways within an organism or between organisms. Using this concept, we model energy metabolism for Escherichia coli and Saccharomyces cerevisiae , and accurately predict metabolic switches. Besides, we find that the total mass of the proteins involved in energy metabolism is conserved across conditions, which is simulated to correlate with ATP production rate in cells growing at unlimited conditions.
Chen et al. (Mon,) studied this question.