Optimization of regulatory architectures in metabolic reaction networks

Biotechnology and Bioengineering

Volumn 52, Issue 4, 1996, Pages 485-500

  Hatzimanikatis, Vassily ^a,b   Floudas, Christodoulos A ^c   Bailey, James E ^a  

^a ETH ZURICH   (Switzerland)

^b California Institute of Technology   (United States)

^c Princeton University   (United States)

Author keywords

guanosine monophosphate synthesis; mathematical modeling; metabolic reaction network; xanthine monophosphate synthesis

Indexed keywords

BIOSYNTHESIS; ENZYME KINETICS; LINEAR PROGRAMMING; MATHEMATICAL MODELS; METABOLISM; OPTIMIZATION;

GUANOSINE MONOPHOSPHATE SYNTHESIS; METABOLIC PATHWAYS; METABOLIC REACTION NETWORKS; XANTHINE MONOPHOSPHATE SYNTHESIS;

BIOTECHNOLOGY;

GUANOSINE PHOSPHATE; UNCLASSIFIED DRUG; XANTHINE DERIVATIVE; XANTHINE PHOSPHATE;

ARTICLE; LINEAR SYSTEM; MATHEMATICAL MODEL; METABOLIC REGULATION;

EID: 10244255126     PISSN: 00063592     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0290(19961120)52:4<485::AID-BIT4>3.0.CO;2-L     Document Type: Article

References (40)

1. Bailey, J. E. 1990. Toward a science of metabolic engineering. Science 252: 1668-1675.
2. Cornish-Bowden, A., Cárdenas M. L. 1990. Control of metabolic processes. NATO ASl Series A: Lifesciences, Vol. 190. Plenum Press, New York.
3. Fell, D. A. Metabolic control analysis - a survey of its theoretical and experimental development. Biochem. J. 152: 313-330.
4. Floudas, C. A. 1995. Nonlinear and mixed integer optimization: Fundamentals and applications. Oxford University Press, New York.
5. Fredrickson, A. G. 1976. Formulation of structured growth models. Biotechnol. Bioeng. 28: 1481-1486.
6. Gallazo, J. L., Bailey, J. E. 1990. Fermentation pathway kinetics and metabolic flux control in suspended and immobilized Saccharomyces cerevisiae. Enzyme Microb. Technol. 12: 162-172.
7. Hatzimanikatis, V., Floudas, C. A., Bailey, J. E. 1996. Analysis and design of metabolic reaction networks via mixed-integer linear optimization. AIChE J., 42: 1277-1292.
8. Hatzimanikatis, V., Lee, K. H., Renner, W. A., Bailey, J. E. 1995. A mathematical model for the G1/S transition of the mammalian cell cycle. Biotech. Lett. 17: 669-674.
9. Heinrich, R., Holzhütter, H.-G., Schuster, S. 1987. A theoretical approach to the evolution and structural design of enzymatic networks. Bull. Math. Biol. 49: 539-595.
10. Heinrich, R., Rapoport, T. A. 1974. A Linear steady-state treatment of enzymatic chains. Eur. J. Biochem. 42: 89-95.
11. Joshi, A., Palsson, B. O. 1989. Metabolic dynamics in the human red cell. Part I - a comprehensive kientic model. J. Theor. Biol. 141: 515-528.
12. Kacser, H., Burns, J. A. 1973. The control of flux. Symp. Soc. Exp. Biol. 27: 65-104.
13. Katsumata, R., Ikeda, M. 1993. Hyperproduction of tryptophan in Corynebacterium glutamicum by pathway engineering. Bio/Technol. 11: 921-925.
14. Lee, S. L., Bailey, J. E. 1984. A mathematical model for lambda-dv plasmid replication - analysis of wild-type plasmid. Plasmid 11: 151-165.
15. Luenberger, D. 1984. Linear and nonlinear programming. Addison-Wesley, Reading, MA.
16. Majewski, R. A., Domach, M. M. 1990. Simple constrained-optimization view of acetate overflow in E. coli. Biotechnol. Bioeng. 35: 732-738.
17. Marr, A. G. 1991. Growth rate of Escherichia coli. Microbiol. Rev. 55: 316-333.
18. Nemhauser, R., Wolsey, L. 1988. Integer and combinatorial optimization. John Wiley & Sons, San Diego.
19. Reder, C. 1988. Metabolic control theory: A structural approach. J. Theor. Biol. 135: 175-201.
20. Regan, L., Bogle, D. L., Dunnill, P. 1993. Simulation and optimization of metabolic pathways. Comp. Chem. Eng. 17: 627-637.
21. Sanwal, B. D., Kapoor, M., Duckworth, H. W. 1971. The regulation of branched and converging pathways. Curr. Top. Cell. Regul. 3: 1-115.
22. Savageau, M. A. 1969a. Biochemical systems analysis, I. Some mathematical properties of the rate law for the component enzymatic reactions. J. Theor. Biol. 25: 365-369.
23. Savageau, M. A. 1969b. Biochemical systems analysis, II. The steady-state solutions for an n-pool system using a power-law approximation. J. Theor. Biol. 25: 370-379.
24. Savageau, M. A. 1970. Biochemical systems analysis, III. Dynamic solutions using a power-law approximation. J. Theor. Biol. 26: 215-226.
25. Savageau, M. A. 1972. The behavior of intact biochemical control systems. Curr. Top. Cell Reg. 6: 63-130.
26. Savageau, M. A. 1976. Biochemical systems analysis: A study of function and design in molecular biology. Addison-Wesley, Reading, MA.
27. Savageau, M. A. 1992. Critique of the enzymologist's test tube, pp. 45-108. In: E. E. Bittar (ed.), Fundamentals of medical cell biology, Vol. 3A, Chemistry of the Living Cell. JAI Press, Greenwich, CT.
28. Savageau, M. A., Voit, E. O., Irvine, D. H. 1987. Biochemical systems theory and metabolic control theory: 2. The role of summation and connectivity relationships. Math. Biosci. 86: 147-169.
29. Schlosser, P. M., Bailey, J. E. 1990. An integrated modelling-experimental strategy for the analysis of metabolic pathways. Math. Biosci. 100: 87-114.
30. Schlosser, P. M., Holcomb, T., Bailey, J. E. 1993. Determining metabolic sensensitivity coefficients directly from experimental data. Biotechnol. Bioeng. 41: 1027-1038.
31. Schuster, S., Heinrich, R. 1991. Minimization of intermediate concentrations as a suggested optimality principle for biochemical networks I. Theoretical analysis. J. Math. Biol. 29: 425-442.
32. Shiraishi, F., Savageau, M. A. 1992. The tricarboxylic-acid cycle in Dictyostelium-discoideum. 1. Formulation of alternative kinetic representations. J. Biol. Chem. 267: 22912-222918.
33. Shuler, M. L., Domach, M. M. 1983. Mathematical models of the growth of individual cells - tools for testing biochemical mechanisms. ACS Symposium Series 207: 93-133.
34. Starbuck, C., Lauffenburger, D. A. 1992. Mathematical model for the effects of epidermal growth-factor receptor trafficking dynamics on fibroblast proliferation responses. Biotech. Prog. 8: 132-143.
35. Stephanopoulos, G., Vallino, J. J. 1991. Network rigidity and metabolic engineering in metabolite overproduction. Science 252: 1675-1681.
36. Torres, N. V. 1994. Application of transition time of metabolic systems as a criterion for optimization of metabolic processes. Biotechnol. Bioeng. 44: 291-296.
37. Voit, E. O. 1992. Optimization in integrated biochemical systems. Biotechnol. Bioeng. 40: 572-582.
38. Voit, E. O., Savageau, M. A. 1987. Accuracy of alternative representations for integrated biochemical systems. Biochem. 26: 6869-6880.
39. Winston, W. L. 1995. Introduction to mathematical programming: Applications and algorithms. Duxbury Press, Belmont, CA.
40. Zhang, M., Eddy, C., Deanda, K., Finkenstein, M., Picataggio, S. 1995. Metabolic engineering of a pentose metabolism pathway in ethanologenic Zymomonas mobilis. Science 267: 240-243.