Rate calculation for metabolic reactions in a~living and growing cell by the method of steady-state stoichiometric flux balance

N. N. Nazipova ; Yu. E. El'kin ; V. V. Panyukov ; L. N. Drozdov-Tikhomirov

Matematičeskaâ biologiâ i bioinformatika, Tome 2 (2007) no. 1, pp. 98-119.

Résumé

Software for a mathematical modeling of stationary metabolism in a growing cell has been developed. The software allows making calculation for optimal economic coefficients of growth of biomass and excretion of products of biosynthesis, which are achievable at the ideal regulation of the processes. It also allows calculating of distribution of rates of reactions inside a cell and in its compartments (including rates of exchange of metabolites between compartments), which corresponds to these optimal regimes. The program FLUX II can operate in the Windows environment. The program has a convenient interface; it is provided with means, which prevent infinite looping of the algorithm and allow performing contensive analysis of the model having been developed. The program also enables presentation of the results of calculation and analysis of the model in a digital or graphical form. By means of the program a mathematical model of the steady-state metabolism of a cell of E.coli has been developed, and the best possible economic coefficients of growth of biomass of these cells under aerobic conditions on glucose, and the distribution of rates of reactions, which corresponds to this regime of metabolism, have been calculated. Satisfactory agreement of the results of calculations and analysis with experimental data has been demonstrated. Possible ways of use of the program for solving practical problems in modern biotechnology have been discussed.

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