Combining flux and energy balance analysis to model large-scale biochemical networks

Journal of Bioinformatics and Computational Biology

Volumn 4, Issue 6, 2006, Pages 1227-1243

  Heuett, William J ^a   Qian, Hong ^b  

^a UNIVERSITY OF COLORADO   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Constraints based optimization; Reaction networks; Sequential quadratic programming; Stoichiometric Network Theory; Systems biology; Yeast glycolysis

Indexed keywords

ALGORITHM; ARTICLE; BIOINFORMATICS; ENERGY BALANCE; FERMENTATION; GLYCOLYSIS; NONHUMAN; NONLINEAR SYSTEM; PROCESS OPTIMIZATION; SACCHAROMYCES CEREVISIAE; STOICHIOMETRY; SYSTEM ANALYSIS; SYSTEMS BIOLOGY; THERMODYNAMICS;

ALGORITHMS; COMPUTER SIMULATION; ENERGY METABOLISM; GLUCOSE; GLYCOLYSIS; MODELS, BIOLOGICAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SIGNAL TRANSDUCTION;

SACCHAROMYCES CEREVISIAE;

EID: 33846571064     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720006002430     Document Type: Article

References (26)

1. Reed JL, Famili I, Thiele I, Palsson BØ, Towards multidimensional genome annotation, Nature Rev Gen 7:130-141, 2006.
2. Edwards JS, Palsson BØ, The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities, Proc Natl Acad Sci USA 97:5528-5533, 2000.
3. Westerhoff HV, Palsson BØ, The evolution of molecular biology into systems biology, Nature Biotech 22:1249-1252, 2004.
4. Érdi, P, Tóth J, Mathematical Methods of Chemical Reactions: Theory and Applications of Deterministic and Stochastic Models, Manchester Univ. Press, Manchester, 1989.
5. Beard DA, Liang SD, Qian H, Energy balance for analysis of complex metabolic networks, Biophys J 83:79-86, 2002.
6. Qian H, Beard DA, Liang SD, Stoichiometric network theory for nonequilibrium biochemical systems, Eur J Biochem 270:415-421, 2003.
7. Edwards JS, Palsson BØ, Systems properties of the Haemophilus influenzae Rd metabolic genotype, J Biol Chem 274:17410-17416, 1999.
8. Ramakrishna R, Edwards JS, McCulloch A, Palsson BØ, Flux-balance analysis of mitochondrial energy metabolism: Consequences of systemic stoichiometric constraints, Am J Physiol Reg Int Comp Physiol 280:R695-R704, 2001.
9. Nigam R, Liang S, A pivoting algorithm for metabolic networks in the presence of thermodynamic constraints, in Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05), IEEE, Stanford, pp. 259-267, 2005.
10. Yang F, Qian H, Beard DA, Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry, Metabol Eng 7:251-259, 2005.
11. Beard DA, Babson E, Curtis E, Qian H, Thermodynamic constraints for biochemical networks, J Theor Biol 228:327-333, 2004.
12. Oliveira JS, Bailey CG, Jones-Oliveira JB, Dixon DA, Gull DW, Hyperdigraph-theoretic analysis of the EGFR signaling network: Initial steps leading to GTP:RAS complex formation, J Comp Biol 11:812-842, 2005.
13. Hill TL, Free Energy Transduction in Biology: The Steady-State Kinetic and Thermodynamic Formalism, Academic Press, New York, 1974.
14. Qian H, Beard DA, Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium, Biophys Chem 114:213-220, 2005.
15. Qian H, Open-system nonequilibrium steady state: Statistical thermodynamics, fluctuations, and chemical oscillations, J Phys Chem B 110:15063-15074, 2006.
16. Nocedal J, Wright SJ, Numerical Optimization, Springer, New York, 1999.
17. Kuhn HW, Tucker AW, Non-lineax programming, in Neyman J (ed.), Proceedings of the Second Berkeley Symposium on Mathematical Statistics and Probability, University of California Press, Berkeley, pp. 481-492, 1951.
18. Fletcher R, Practical Methods of Optimization, 2nd ed., John Wiley, New York, 1987.
19. Teusink B, Passarge J, Reijenga CA, Esgalhado E, van der Weijden CC, Schepper M, Walsh MC, Bakker BM, van Dam K, Westerhoff HV, Snoep JL, Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry, Eur J Biochem 267:5313-5329, 2000.
20. Ruoff P, Christensen MK, Wolf J, Heinrich R, Temperature dependency and temperature compensation in a model of yeast glycolytic oscillations, Biophys Chem 106:179-192, 2003.
21. Atkins PW, de Paula J, Physical Chemistry, 7th ed., WH Freeman, New York, 2002.
22. Heinrich R, Schuster S, The Regulation of Cellular Systems, Chapman & Hall, New York, 1996.
23. McKinney RE, Environmental Pollution Control Microbiology, Marcel Dekker Inc, New York, 2004.
24. Bonini BM, Van Vaeck C, Larsson C, Gustafsson L, Ma P, Winderickx J, Van Dijck P, Thevelein JM, Expression of Escherichia coli otsA in a Saccharomyces cerevisiae tps1 mutant restores trehalose 6-phosphate levels and partly restores growth and fermentation with glucose and control of glucose influx into glycolysis, Biochem J 350:261-268, 2000.
25. Amerine MA, Singleton VL (eds.), Wine: An Introduction, 2nd ed., University of California Press, Berkeley, 1977.
26. Cortassa S, Aon MA, Iglesias AA, Lloyd D (eds.), An Introduction to Metabolic and Cellular Engineering, World Scientific, River Edge, 2002.