Bringing metabolic networks to life: Convenience rate law and thermodynamic constraints

Theoretical Biology and Medical Modelling

Volumn 3, Issue , 2006, Pages

  Liebermeister, Wolfram ^a   Klipp, Edda ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING KINETICS; ENERGY; ENZYME ASSAY; ENZYME KINETICS; ENZYME MECHANISM; MATHEMATICAL MODEL; MATHEMATICAL PARAMETERS; METABOLISM; MICHAELIS CONSTANT; MOLECULAR DYNAMICS; RANDOMIZATION; THERMODYNAMICS; TURNOVER TIME; BIOLOGICAL MODEL; ENERGY METABOLISM; ENZYME ACTIVATION; KINETICS;

ENZYME;

ENERGY METABOLISM; ENZYME ACTIVATION; ENZYMES; KINETICS; MODELS, BIOLOGICAL; THERMODYNAMICS;

EID: 33846617808     PISSN: None     EISSN: 17424682     Source Type: Journal    
DOI: 10.1186/1742-4682-3-41     Document Type: Article

References (25)

1. The KEGG databases at GenomeNet. M Kanehisa S Goto SK S A Nakaya, Nucleic Acids Res 2002 30 42 46 11752249 10.1093/nar/30.1.42
2. Reactome: a knowledgebase of biological pathways. G Joshi-Tope M Gillespie I Vastrik P D'Eustachio E Schmidt B de Bono B Jassal G Gopinath G Wu L Matthews S Lewis E Birney L Stein, Nucleic Acids Res 2005 33 Issue D428 432 15608231
3. Biochemical systems analysis. III. Dynamic solutions using a power-law approximation. M Savageau, J Theor Biol 1970 26 2 215 226 10.1016/S0022-5193(70) 80013-3 5434343
4. Computation and analysis of time-dependent sensitivities in Generalized Mass Action systems. J Schwacke E Voit, J Theor Biol 2005 236 21 38 10.1016/j.jtbi.2005.02.013 15967181
5. Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics. D Visser J Heijnen, Metab Eng 2003 5 3 164 176 10.1016/S1096-7176(03)00025-9 12948750
6. Optimal re-design of primary metabolism in Escherichia coli using linlog kinetics. D Visser J Schmid K Mauch M Reuss J Heijnen, Metab Eng 2004 6 4 378 390 10.1016/j.ymben.2004.07.001 15491866
7. Die Kinetik der Invertinwirkung. L Michaelis ML Menten, Biochemische Zeitschrift 1913 49 333 369
8. A Cornish-Bowden, Fundamentals of Enzyme Kinetics London: Portland Press Ltd 3 2004
9. E Klipp R Herwig A Kowald C Wierling H Lehrach, Systems biology in practice. Concepts, implementation, and application Weinheim: Wiley-VCH 2005
10. BRENDA, the enzyme database: updates and major new developments. I Schomburg A Chang C Ebeling M Gremse C Heldt G Huhn D Schomburg, Nucleic Acids Res 2004 32 Database D431 433 14681450 10.1093/nar/gkh081
11. Thermodynamics of enzyme-catalyzed reactions - a database for quantitative biochemistry. RN Goldberg YB Tewari TN Bhat, Bioinformatics 2004 20 2874 7 10.1093/bioinformatics/bth314 15145806
12. [http://sabio.villa-bosch.de/SABIORK/].
13. An integrated study of threonine-pathway enzyme kinetics in Escherichia coli. C Chassagnole B Raïs E Quentin DA Fell J Mazat, Biochem J 2001 356 415 423 11368768 10.1042/0264-6021:3560415
14. Towards building the silicon cell: a modular approach. JL Snoep F Bruggeman BOH Westerhoff, Biosystems 2006 83 2-3 207 216 10.1016/j.biosystems. 2005.07.006 16242236
15. D Haynie, Biological Thermodynamics Cambridge: Cambridge University Press 2001
16. J Haldane, Enzymes London: Longmans, Grenn, and Co. (reprinted by M.I.T. press, Cambridge, MA 1965 1930
17. A generalization of Wegscheider's condition. Implications for properties of steady states and for quasi-steady-state approximation. S Schuster R Schuster, J Math Chem 1989 3 25 42 10.1007/BF01171883
18. Biochemical networks with uncertain parameters. W Liebermeister E Klipp, Syst Biol (Stevenage) 2005 152 3 97 107 10.1049/ip-syb:20045033 16986274
19. Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data. W Liebermeister E Klipp, Theor Biol Med Model 2006 3 1 42 Epub ahead of print 10.1186/1742-4682-3-42 17173670
20. A note on the kinetics of enzyme action. GE Briggs JBS Haldane, Biochem J 1925 19 338 339 16743508
21. Energy balance for analysis of complex metabolic networks. DA Beard S Liang H Qian, Biophys J 2002 83 79 86 12080101
22. Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. A Kümmel S Panke M Heinemann, Mol Syst Biol 2006 2 2006.0034 10.1038/msb4100074 16788595
23. Genome-scale thermodynamic analysis of E. coli metabolism. C Henry M Jankowski L Broadbelt V Hatzimanikatis, Biophys J 2006 90 1453 1461 10.1529/biophysj.105.071720 16299075
24. Transcriptional regulation by numbers: models. L Bintu N Buchler H Garcia U Gerland T Hwa J Kondev R Phillips, Curr Opin Genet Dev 2005 15 116 124 10.1016/j.gde.2005.02.007 15797194
25. Metabolic control theory: a structural approach. C Reder, J Theor Biol 1988 135 175 201 10.1016/S0022-5193(88)80073-0 3267767