Calculation of theoretical yields in metabolic networks*

Nature has created elaborate networks of reactions to convert substrates into the building blocks of living cells as well as a myriad of natural products. The biosynthetic pathways responsible for each metabolite produced have a certain material and energetic "cost" associated with them. The theoretical calculation of these costs aid in analyzing metabolic pathways and engineering metabolic changes in cells. Depending on the complexity and structure of the metabolic system under consideration, different approaches need to be taken for the calculations. In this article, a systematic method to calculate theoretical yields is described for simple linear and cyclic pathways. A published error in the theoretical cost calculations for photorespiration is corrected (J. N. Siedow and D.A. Day (2000) Biochemistry and Molecular Biology of Plants, American Society of Plant Physiologists, Rockville, MD, pp. 676-726). A matrix-vector formulation of the stoichiometric pathways is presented for more complex systems.