Systematic assignment of thermodynamic constraints in metabolic network models

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Kümmel, Anne ^a   Panke, Sven ^a   Heinemann, Matthias ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL FRAMEWORK; GENOME-SCALE METABOLIC MODELING; GENOME-SCALE METABOLIC MODELS; GENOME-SCALE METABOLIC NETWORK; GIBBS ENERGIES OF FORMATIONS; IRREVERSIBLE REACTIONS; METABOLIC NETWORK MODELS; THERMODYNAMIC CONSTRAINTS;

AUTOMATION; COMPUTATIONAL METHODS; ELECTRIC NETWORK TOPOLOGY; ESCHERICHIA COLI; GENES; METABOLISM; THERMODYNAMICS;

ALGORITHMS;

ALGORITHM; ARTICLE; AUTOMATION; BACTERIAL METABOLISM; BIOINFORMATICS; CONTROLLED STUDY; ENERGY CONSUMPTION; ENERGY YIELD; ESCHERICHIA COLI; MATHEMATICAL MODEL; NONHUMAN; THERMODYNAMICS; BIOLOGICAL MODEL; BIOLOGY; COMPARATIVE STUDY; COMPUTER SIMULATION; ENERGY METABOLISM; GENETICS; METABOLISM;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; ENERGY METABOLISM; ESCHERICHIA COLI; MODELS, BIOLOGICAL; THERMODYNAMICS;

EID: 33845238737     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-512     Document Type: Article

References (37)

1. Reed JL, Palsson BO: Thirteen years of building constraint-based in silico models of Escherichia coli. J Bacteriol 2003, 185(9):2692-2699.
2. Price ND, Reed JL, Palsson BO: Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2004, 2(11):886-897.
3. Förster J, Famili I, Fu P, Palsson BO, Nielsen J: Genome-Scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 2003, 13(2):244-253.
4. Reed JL, Vo TD, Schilling CH, Palsson BO: An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 2003, 4(9):R54.
5. Heinemann M, Kümmel A, Ruinatscha R, Panke S: In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network. Biotechnol Bioeng 2005, 92(7):850-864.
6. Patil KR, Nielsen J: Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc Natl Acad Sci USA 2005:2685-2689.
7. Kümmel A, Panke S, Heinemann M: Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol Syst Biol 2006, 2:2006.0034. doi:10.1038/msb4100074
8. Pharkya P, Burgard AP, Maranas CD: OptStrain: a computational framework for redesign of microbial production systems. Genome Res 2004, 14(11):2367-2376.
9. Patil KR, Rocha I, Förster J, Nielsen J: Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 2006, 6:308.
10. Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BO: Metabolic modeling of microbial strains in silico. Trends Biochem Sci 2001, 26(3):179-186.
11. Karp PD, Paley S, Romero P: The Pathway Tools software. Bioinformatics 2002, 18(Suppl 1):S225-32.
12. Green ML, Karp PD: A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics 2004, 5:76.
13. Kharchenko P, Chen L, Freund Y, Vitkup D, Church GM: Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics 2006, 7:177.
14. Kaneshisa M, Goto S, Kawashima S, Okuno Y, Hattori M: The KEGG resource for deciphering the genome. Nucleic Acids Res 2004, 32:D277-280.
15. Caspi R, Foerster H, Fulcher C, Hopkinson R, Ingraham JL, Kaipa P, Krummenacker M, Paley S, Pick J, Rhee S, Tissier C, Zhang P, Karp P: MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res 2006, 34:D511-516.
16. 13C metabolic flux analysis. Metab Eng 2001, 3(3):195-206.
17. Mavrovouniotis ML: Estimation of standard Gibbs energy changes of biotransformations. J Biol Chem 1991, 266(22):14440-14445.
18. Henry CS, Jankowski MD, Broadbelt LJ, Hatzimanikatis V: Genome-scale thermodynamic analysis of Escherichia coli metabolism. Biophys J 2006, 90(4):1453-1461.
19. Beard DA, Liang SC, Qian H: Energy balance for analysis of complex metabolic networks. Biophys J 2002, 83:79-86.
20. Yang F, Qian H, Beard DA: Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry. Metab Eng 2005, 7(4):251-259.
21. Maskow T, von Stockar U: How reliable are thermodynamic feasibility statements of biochemical pathways? Biotechnol Bioeng 2005, 92(2):223-30.
22. Alberty RA: Thermodynamics of biochemical reactions Hoboken, New Jersey: John Wiley & Sons Inc; 2003.
23. Fraenkel DG: Genetics and intermediary metabolism. Annu Rev Genetics 1992, 26:159-177.
24. Beard DA, Babson E, Curtis E, Qian H: Thermodynamic constraints for biochemical networks. J Theor Biol 2004, 228(3):327-333.
25. Palsson BO, Price ND, Papin JA: Development of network-based pathway definitions: the need to analyze real metabolic networks. Trends Biotechnol 2003, 21(5):195-198.
26. Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BO: Comparison of network-based pathway analysis methods. Trends Biotechnol 2004, 22(8):400-405.
27. EcoCyc: Encyclopedia of Escherichia coli K-12 Genes and Metabolism [http://ecocyc.org/]
28. Creaghan IT, Guest JR: Succinate dehydrogenase-dependent nutritional-requirement for succinate in mutants of Escherichia coli K12. Journal of General Microbiology 1978, 107:1-13.
29. Segre D, Zucker J, Katz J, Lin X, D'Haeseleer P, Rindone W, Kharchenko P, Nguyen D, Wright M, Church GM: From annotated genomes to metabolic flux models and kinetic parameter fitting. OMICS 2003, 7(3):301-316.
30. Notebaart RA, van Enckevort FHJ, Francke C, Siezen RJ, Teusink B: Accelerating the reconstruction of genome-scale metabolic networks. BMC Bioinformatics 2006, 7:296.
31. Wolfram Information Center [http://library.wolfram.com/infocenter/ MathSource/5704/]
32. NIST Database on Thermodynamics of Enzyme-Catalyzed Reactions [http://xpdb.nist.gov/enzyme_thermodynamics]
33. Tewari YB, Kishore N, Bauerle R, LaCourse WR, Goldberg RN: Thermochemistry of the reaction phosphoenolpyruvate(aq) + D-erythrose 4-phosphate(aq) + H2O(I) = 2-dehydro-3-deoxy-D-arabino-heptonate 7-phosphate(aq) + phosphate(aq). J Chem Thermodyn 2001, 33(12):1791-1805.
34. Tewari YB, Hawkins AP, Lamb HK, Goldberg RN: A thermodynamic study of the reactions: 2-dehydro-3-deoxy-D-arabino-heptanoate 7-phosphate(aq) = 3-dehydroquinate(aq) + phosphate(aq) and 3-dehydroquinate(aq) = 3-dehydroshikimate(aq) + H2O(I). J Chem Thermodyn 2002, 34(10):1671-1691.
35. + antiporter is essential for intracellular pH regulation under alkaline conditions in Escherichia coli. J Biochem 1994, 116(2):285-290.
36. Voets T, Droogmans G, Raskin G, Eggermont J, Nilius B: Reduced Intracellular ionic strength as the initial trigger for activation of endothelial volume-regulated anion channels. Proc Natl Acad Sci USA 1999, 96(9):5298-303.
37. Edwards JS, Covert M, Palsson B: Metabolic modelling of microbes: the flux-balance approach. Environ Microbiol 2002, 4:133-140.