Thermodynamic constraints in kinetic modeling: Thermodynamic-kinetic modeling in comparison to other approaches

Engineering in Life Sciences

Volumn 8, Issue 5, 2008, Pages 467-476

  Ederer, M ^a   Gilles, E D ^a  

^a MAX PLANCK INSTITUTE FOR DYNAMICS OF COMPLEX TECHNICAL SYSTEMS   (Germany)

Author keywords

Irreversible thermodynamics; Thermodynamic kinetic modeling (TKM); Wegscheider conditions

Indexed keywords

BIOCHEMICAL REACTION NETWORKS; DETAILED BALANCES; DRIVING FORCES; ELECTRICAL NETWORKS; GRAPHICAL REPRESENTATIONS; IRREVERSIBLE THERMODYNAMICS; KINETIC MODELS; LARGE NETWORKS; LAWS OF THERMODYNAMICS; MODEL EQUATIONS; MODELING FORMALISMS; RATE LAWS; REACTION NETWORKS; REACTION SYSTEMS; STATE VARIABLES; THERMODYNAMIC CONSTRAINTS; WEGSCHEIDER CONDITIONS;

BIOCHEMICAL ENGINEERING; GRAPHIC METHODS; IGNEOUS ROCKS;

THERMODYNAMICS;

KINETICS; PARAMETERIZATION; STOICHIOMETRY; THERMODYNAMICS;

EID: 62349110806     PISSN: 16180240     EISSN: 16182863     Source Type: Journal    
DOI: 10.1002/elsc.200800040     Document Type: Review

References (32)

1. R. Wegscheider, Über simultane Gleichgewichte und die Beziehungen zwischen Thermodynamik und Reaktionskinetik homogener Systeme, Z. Phys. Chem. 1902, 39, 257-203.
2. L. Onsager, Reciprocal relations in irreversible processes I, Phys. Rev. 1931, 37, 405-426.
3. L. Onsager, Reciprocal relations in irreversible processes II, Phys. Rev. 1931, 38, 2265-2279.
4. H. Kitano, Systems biology: a brief overview, Science 2002, 295 (5560), 1662-1664.
5. H. Kitano, Computational systems biology, Nature 2002, 420 (6912), 206-210.
6. R. A. Alberty, Thermodynamics of Biochemical Reactions, Wiley-Interscience, Hoboken, New Jersey (USA) 2003.
7. A. M. Feist, C. S. Henry, J. L. Reed, M. Krummenacker, A. R. Joyce, P.D. Karp et al., A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 orfs and thermodynamic information, Mol. Syst. Biol. 2007, 3, 121.
8. D. A. Beard, S. Liang, H. Qian, Energy balance for analysis of complex metabolic networks, Biophys. J. 2002, 83 (1), 79-86.
9. D. A. Beard, E. Babson, E. Curtis, H. Qian, Thermodynamic constraints for biochemical networks, J. Theor. Biol. 2004, 228 (3), 327-333.
10. H. Qian, D. A. Beard, S. Liang, Stoichiometric network theory for nonequilibrium biochemical systems, Eur. J. Biochem. 2003, 270 (3), 415-421.
11. F. Yang, H. Qian, D. A. Beard, Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry, Metabol. Eng. 2005, 7 (4), 251-259.
12. A. Kümmel, S. Panke, M. Heinemann, Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data, Mol. Syst. Biol. 2006, 2, 2006.0034.
13. C. S. Henry, M.D. Jankowski, L. J. Broadbelt, V. Hatzimanikatis, Genome-scale thermodynamic analysis of Escherichia coli metabolism, Biophys. J. 2006, 90 (4), 1453-1461.
14. C. S. Henry, L. J. Broadbelt, V. Hatzimanikatis, Thermodynamics- based metabolic flux analysis, Biophys. J. 2007, 92 (5), 1792-1805.
15. H. B. Callen, Thermodynamics and an Introduction to Thermostatistics, John Wiley & Sons, Inc., New York (USA) 1985.
16. L. H. Hartwell, J. J. Hopfield, S. Leibler, A.W. Murray, From molecular to modular cell biology, Nature 1999, 402, C47-C52.
17. M. Ederer, E.D. Gilles, Thermodynamically feasible kinetic models of reaction networks, Biophys. J. 2007, 92 (6), 1846-1857.
18. R. Heinrich, S. Schuster, The Regulation of Cellular Systems, Chapman & Hall, New York (USA) 1996.
19. J. Stelling, U. Sauer, Z. Szallasi, F. J. Doyle, J. Doyle, Robustness of cellular functions, Cell 2004, 118 (6), 675-685.
20. J. L. Reed, B. Ø. Palsson, Thirteen years of building constraint- based in silico models of Escherichia coli, J. Bacteriol. 2003, 185 (9), 2692-2699.
21. J. L. Snoep, F. Bruggeman, B. G. Olivier, H. V. Westerhoff, Towards building the silicon cell: a modular approach, Biosystems 2006, 83 (2-3), 207-216.
22. J. L. Reed, T.D. Vo, C.H. Schilling, B.Ø. Palsson, An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR), Genome Biol. 2003, 4 (9), R54.
23. M. Ederer, E.D. Gilles, Thermodynamic-kinetic modeling and electrical engineering, in Proc. of the FOSBE 2007 (Ed: F. Allgöwer, M. Reuss), Fraunhofer IRB Verlag, Stuttgart (Germany) 2007, 135-140.
24. D. Colquhoun, K. A. Dowsland, M. Beato, A. J. R. Plested, How to impose microscopic reversibility in complex reaction mechanisms, Biophys. J. 2004, 86 (6), 3510-3518.
25. J. Yang, W. J. Bruno, W. S. Hlavacek, J. Pearson, On imposing detailed balance in complex reaction mechanisms, Biophys. J. 2006, 91, 1136-1141.
26. W. Liebermeister, E. Klipp, Bringing metabolic networks to life: convenience rate law and thermodynamic constraints, Theor. Biol. Med. Model. 2006, 3, 41.
27. F. Horn, R. Jackson, General mass action kinetics, Archive for Rational Mechanics and Analysis 1972, 47 (2), 81-116.
28. D. A. Beard, A biophysical model of the mitochondrial respiratory system and oxidative phosphorylation, PLoS Comput. Biol. 2005, 1 (4), e36.
29. S. Klamt, H. Grammel, R. Straube, R. Ghosh, E.D. Gilles, Modeling the electron transport chain of purple non-sulfur bacteria, Mol. Syst. Biol. 2008, 4, 156.
30. B. Korzeniewski, Simulation of oxidative phosphorylation in hepatocytes, Biophys. Chem. 1996, 58 (3), 215-224.
31. B. Korzeniewski, J. A. Zoladz, A model of oxidative phosphorylation in mammalian skeletal muscle, Biophys. Chem. 2001, 92 (1-2), 17-34.
32. B. Korzeniewski, Thermodynamic regulation of cytochrome oxidase, Mol. Cell. Biochem. 1997, 174 (1-2), 137-141.