Stoichiometric analysis of self-maintaining metabolisms

Journal of Theoretical Biology

Volumn 252, Issue 3, 2008, Pages 427-432

  Montero, Francisco ^a   Nuño, Juan Carlos ^b   Meléndez Hevia, Enrique ^c   Olasagasti, Felix ^a   Vázquez, Sara ^a   Morán, Federico ^a  

^a UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

^b UNIVERSIDAD POLITÉCNICA DE MADRID   (Spain)

^c Instituto del Metabolismo Celular   (Spain)

Author keywords

Metabolic networks; Self maintaining systems; Stoichiometric analysis

Indexed keywords

ENZYME ACTIVITY; METABOLISM; NETWORK ANALYSIS; STEADY-STATE EQUILIBRIUM; STOICHIOMETRY;

ARTICLE; BIOLOGICAL MODEL; CATALYSIS; CATALYST; ENZYME ACTIVITY; ENZYME DEGRADATION; ENZYME METABOLISM; PRIORITY JOURNAL; STOICHIOMETRY;

ANIMALS; CATALYSIS; ENZYMES; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; SYSTEMS BIOLOGY;

EID: 43449130078     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2007.11.025     Document Type: Article

References (21)

1. Cornish-Bowden, A., Cárdenas, M.L., 2008. Self-organization in the origin of life. J. Theor. Biol., this issue, doi:10.1016/j.jtbi.2007.07.035.
2. Covert M.W., and Palsson B.O. Constrained-based models: regulation of gene expression reduces the steady-state solution space. J. Theor. Biol. 221 (2003) 309-325
3. Dittrich P., and di Fenizio P.S. Chemical organization theory. Bull. Math. Biol. 69 (2007) 1199-1231
4. Fontana W., and Buss L.W. The arrival of the fittest-toward a theory of biological organization. Bull. Math. Biol. 56 (1994) 1-64
5. Heinrich R., and Schuster S. The Regulation of Cellular Systems (1996), Chapman & Hall, New York
6. Kamp A., and Schuster S. METATOOL 5.0: fast and flexible elementary modes analysis. Bioinformatics 22 (2006) 1930-1931
7. Klamt S., and Stelling J. Stoichiometric and constraint-based modelling. In: Szallasi Z., Stelling S., and Periwal V. (Eds). System Modeling in Cellular Biology: From Concepts to Nuts and Bolts (2006), MIT Press, Cambridge 73-96
8. Letelier J.C., Soto-Andrade J., Guíñez Abarzúa F., Cornish-Bowden A., and Cárdenas M.L. Organizational invariance and metabolic closure: analysis in terms of (M,R) systems. J. Theor. Biol. 238 (2006) 949-961
9. Nuño J.C., Sánchez-Valdenebro I., Pérez-Iratxeta C., Meléndez-Hevia E., and Montero F. Network organization of monosaccharide interconversion. Biochem. J. 324 (1997) 103-111
10. Olasagasti F., Moreno A., Peretó J., and Morán F. Energetically plausible model of a self-maintaining protocellular system. Bull. Math. Biol. 69 4 (2007) 1423-1445
11. Pfeiffer T., Sánchez-Valdenebro I., Nuño J.C., Montero F., and Schuster S. METATOOL: for studying metabolic networks. Bioinformatics 15 (1999) 251-257
12. Rosen R. A relational theory of biological systems. Bull. Math. Biophys. 20 (1958) 245-316
13. Rosen R. The representation of biological systems from standpoint of the theory of categories. Bull. Math. Biophys. 20 (1958) 317-341
14. Rosen R. A relational theory of biological systems II. Bull. Math. Biophys. 21 (1959) 109-128
15. Schilling C., and Palsson B.O. The underlying pathway structure of biochemical reaction networks. Proc. Natl Acad. Sci. USA 95 (1998) 4193-4198
16. Schilling C.H., Schuster P., Palsson B.O., and Heinrich R. Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. Biotechnol. Prog. 15 (1999) 296-303
17. Schuster S., Dandekar T., and Fell D. Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trend. Biotechnol. 17 (1999) 53-60
18. Schuster S., Fell D.A., and Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol. 18 (2000) 326-332
19. Skulachev V.P. The laws of cell energetic. Eur. J. Biochem. 208 (1992) 203-209
20. Stephanopoulos G., Nielsen J.B., and Aristodou A. Metabolic Engineering: Principles and Methodologies (1998), Academic Press, San Diego
21. Varela F., Maturana H., and Uribe R. Autopoiesis: the organization of living systems, its characterization and a model. BioSystems 5 (1974) 187-196