Using chemical reaction network theory to discard a kinetic mechanism hypothesis

IEE Proceedings Systems Biology

Volumn 152, Issue 4, 2005, Pages 243-248

  Conradi, C ^a   Saez Rodriguez, J ^b   Gilles, E D ^b   Raisch, J ^a,b  

^a OTTO VON GUERICKE UNIVERSITY   (Germany)

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

Author keywords

[No Author keywords available]

Indexed keywords

BIFURCATION (MATHEMATICS); BIOCHEMISTRY; MATHEMATICAL MODELS; ORDINARY DIFFERENTIAL EQUATIONS; PROTEINS; REACTION KINETICS;

CHEMICAL REACTION NETWORK THEORY (CRNT); DEPHOSPHORYLATION; MITOGEN-ACTIVATED PROTEIN KINASE (MAPK); PHOSPHORYLATION; SYSTEMS BIOLOGY;

BIOLOGY;

MITOGEN ACTIVATED PROTEIN KINASE;

ARTICLE; CHEMICAL REACTION KINETICS; ENZYME PHOSPHORYLATION; HYPOTHESIS; MOLECULAR MODEL; PROTEIN DEPHOSPHORYLATION; THEORY;

ALGORITHMS; ANIMALS; CELL PHYSIOLOGY; COMPUTER SIMULATION; HUMANS; KINETICS; MAP KINASE SIGNALING SYSTEM; METABOLIC CLEARANCE RATE; MITOGEN-ACTIVATED PROTEIN KINASES; MODELS, BIOLOGICAL; MODELS, CHEMICAL; PHOSPHORYLATION;

EID: 31144454273     PISSN: 17412471     EISSN: None     Source Type: Journal    
DOI: 10.1049/ip-syb:20050045     Document Type: Article

References (12)

1. Bailey, J.E.: 'Complex biology with no parameters', Nature Biotech. 2001, 19, p. 503
2. Sontag, E.: 'Structure and stability of certain chemical networks and applications to the kinetic proofreading model of T-cell receptor signal transduction', IEEE Trans. Autom. Control, 2001, 46, (7), p. 1028-1047 10.1109/9.935056 0018-9286
3. Feinberg, M.: 'Chemical reaction network structure and the stability of complex isothermal reactors: I. The deficiency zero and deficiency one theorems', Chem. Eng. Sci., 1987, 42, (10), p. 2229-2268 0009-2509
4. Markevich, N., Hoek, J., and Kholodenko, B.: 'Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades', J. Cell Biol., 2004, 164, (3), p. 353-359
5. Feinberg, M., and Ellison, P.: 'The chemical reaction network toolbox', http//www.chbmeng.ohio-state.edu/~feinberg/crnt
6. Chang, L., and Karin, M.: 'Mammalian MAP kinase signaling cascades', Nature, 2001, 410, (6824), p. 37-40 0028-0836
7. Krauss, G.: 'Biochemistry of signal transduction and regulation', (Wiley VCH, Weinheim, Germany 2003)
8. Feinberg, M.: 'Lectures on chemical reaction networks', (Mathematics Research Center, University of Wisconsin 1979), written versions of Lectures 1-5 (out of nine) delivered at the 1979; http//www.chbmeng.ohio-state.edu/~feinberg/LecturesOnReactionNetworks
9. Feinberg, M.: 'Chemical reaction network structure and the stability of complex isothermal reactors: II. Multiple steady states for networks of deficiency one', Chem. Eng. Sci., 1988, 43, p. 1-25 0009-2509
10. Ellison, P., and Feinberg, M.: 'How catalytic mechanisms reveal themselves in multiple steady-state data: I. Basic principles', J. Molecular Catalysis A, 2000, 154, p. 155-167
11. Gatermann, K., and Huber, B.: 'A family of sparse polynomial systems arising in chemical reaction systems', J. Symbolic Comput., 2002, 33, p. 275-305 10.1006/jsco.2001.0512
12. Ginkel, M., Kremling, A., Nutsch, T., Rehner, R., and Gilles, E.D.: 'Modular modeling of cellular systems with ProMoT/Diva', Bioinformatics, 2003, 19, (9), p. 1169-1176