Sensitivity analysis for the reduction of complex metabolism models

Journal of Process Control

Volumn 14, Issue 7, 2004, Pages 729-745

  Degenring, D ^a   Froemel, C ^b   Dikta, G ^c   Takors, R ^b  

^a UNIVERSITY OF ROSTOCK   (Germany)

^b FORSCHUNGSZENTRUM JÜLICH   (Germany)

^c AACHEN UNIVERSITY OF APPLIED SCIENCES   (Germany)

Author keywords

Metabolism; Model reduction; Model validation; Parameter sensitivity; Pca

Indexed keywords

CELLS; ENZYME KINETICS; GLUCOSE; THERMODYNAMICS; TRAJECTORIES;

METABOLISM MODELS; MODEL REDUCTION; MODEL VALIDATION; PARAMETER SENSITIVITY;

METABOLISM;

EID: 2342523297     PISSN: 09591524     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jprocont.2003.12.008     Document Type: Article

References (37)

1. Lengeler J.W. Metabolic networks: a signal oriented approach to cellular models. Biological Chemistry. 381:2000;911-920.
2. Ibarra R.U., Erwads J.S., Palsson B.O. Escherichia coli K12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature. 420:2002;186-189.
3. Wiechert W. 13C metabolic flux analysis. Metabolic Engineering. 3:2001;195-303.
4. Tomita M., Hashimoto K., Takahashi K., Shimizu T.S., Matsuzaki Y., Miyoshi F., Saito K., Tanida S., Yugi K., Venter J.C., Hutchinson C.A. III E-cell: a software environment for whole cell simulation. Bioinformatics. 15:1999;72-84.
5. Westerhoff H.V. The silicon cell, not dead but live. Metabolic Engineering. 3:2001;207-210.
6. Rizzi M., Baltes M., Theobald U., Reuss M. In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: II Mathematical model. Biotechnological Bioengeering. 55(4):1997;592-608.
7. Schäfer U., Boos W., Takors R., Weuster-Botz D. Automated sampling device for monitoring intracellular metabolite dynamics. Analytical Biochemistry. 270:1999;88-96.
8. Weuster-Botz D. Sampling tube device for monitoring intracellular metabolite dynamics. Analytical Biochemistry. 246:1997;225-233.
9. Buchholz A., Takors R., Wandrey C. Quantification of intracellular metabolites in Escherichia coli K12 using liquid chromatographic-electrospray ionization tandem mass spectrometric techniques. Analytical Biochemistry. 295:2001;129-137.
10. Schomburg I., Chang A., Schomburg D. BRENDA, enzyme data and metabolic information. Nucleic Acids Research. 30:2002;47-49.
11. Appel R.D., Bairoch A., Hochstrasser D.F. A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. Trends in Biochemical Sciences. 19:1994;258-260.
12. W. Wiechert, R. Takors, Validation of metabolic models: concepts, tools and problems, in: H.V. Westerhoff, B.N. Kholodenko (Eds.), Metabolic Engineering in a Post Genomic Era (in press).
13. D. Degenring, R. Takors, In vivo investigation of metabolic dynamics in Escherichia coli K12 by evaluation of rapid sampling experiments, in: J. Kim (Ed.), Proceedings of the 5th German Workshop on Artificial Life, 2002.
14. A. Buchholz, Quantitative Untersuchungen intrazellulärer Metabolitdynamiken zur Identifizierung mikrobieller Stoffwechselnetzwerke, Ph.D. Thesis, Friedrich-Wilhelms-Universität Bonn, Germany, 2002.
15. Notley-McRobb L., Death A., Ferenci T. The relationship between external glucose concentration and cAMP levels inside Escherichia coli: implications for models of phosphotransferase-mediated regulation of adenylate cyclase. Microbiology. 143:1997;1909-1918.
16. Kaback H.R. Tergulation of sugar transport in isolated bacterial membrane preparations from Escherichia coli. Proceedings of the National Academical Science, USA. 63:1969;724-731.
17. Schmidt P.P., Travers F., Barman T. Transient and equilibrium kinetic studies on yeast 3-phosphoglycerate kinase. Evidence that an intermediate containing 1,3-bisphophoglycerate accumulates in the steady-state. Biochemistry. 34:1995;824-832.
18. 2+ affects the binding of ADP but not ATP to 3-phosphoglycerate kinase. Correlation between equilibrium dialysis binding and enzyme kinetic data. Biochemical Journal. 293:1993;595-599.
19. Spring T.G., Wold F. The purification and characterization of Escherichia coli enolase. Journal of the Biological Chemistry. 52:1971;6797-6802.
20. Cornish-Bowden A. Fundamentals of Enzyme Kinetics. 1995;Portland Press, London.
21. Segel I. Enzyme Kinetics Behavior and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems. 1975;John Wiley and Sons, New York.
22. Hayes J.G. Numerical methods for curve and surface fitting. Bulletin of the Institute of Mathematics and its Applications. 10:1974;144-152.
23. Hurlebaus J., Buchholz A., Alt W., Wiechert W., Takors R. MMT - a pathway modeling tool for data from rapid sampling experiments. In Silico Biology. 2:2002;0042.
24. Saltelli A., Chan K., Scott E.M. Sensitivity Analysis. 2000;John Wiley and Sons, New York.
25. Turányi T. Sensitivity analysis of complex kinetic systems. Tools and applications. Journal of Mathematical Chemistry. 5:1990;203-248.
26. Mauch K., Arnold S., Reuss M. Dynamic sensitivity analysis for metabolic systems. Chemical Engineering Science. 52(15):1997;2589-2598.
27. M.D. Haunschild, B. Freisleben, R. Takors, W. Wiechert, Distributed simulation of metabolic networks with model variants, in: Proceedings of the 16th European Simulation Multiconference, 2002, pp. 436-440.
28. Dougherty E.P., Hwang J.T., Rabitz H. Journal of Chemical Physics. 71:1979;1794.
29. Seigneur C., Stephanopoulos G., Carr R.W. Chemical Engineering Science. 37:1982;845.
30. Jolliffe I.T. Discarding variables in a principal component analysis. I: artificial data. Journal of the Royal Statistical Society. 21:1972;160-172.
31. Turányi T., Bérces T., Vajda S. Reaction rate analysis of complex kinetic systems. International Journal of Chemical Kinetics. 21:1989;83-99.
32. Vajda S., Valkó P., Turányi T. Principal component analysis of kinetic models. International Journal of Chemical Kinetics. 17:1985;55-81.
33. Chassagnole C., Noisommit-Rizzi N., Schmid J.W., Mauch K., Reuss M. Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnology and Bioengineering. 79:2002;53-73.
34. Nelder J.A., Mead R. The downhill simplex method. Computer Journal. 7:1965;308.
35. T. Rowan, Functional stability analysis of numerical algorithms, Ph.D. Thesis, University of Texas at Austin, Austin, TX, USA, 1990.
36. Available from 〈 http://www.nag.com/numeric/cl/CLdescription. asp〉.
37. M.G. Cox, J.G. Hayes, Curve fitting: a guide and suite of algorithms for the non-specialist user. NPL Report NAC 26, National Physical Laboratory, 1973.