What makes biochemical networks tick? A graphical tool for the identification of oscillophores

European Journal of Biochemistry

Volumn 271, Issue 19, 2004, Pages 3877-3887

  Goldstein, Boris N ^a   Ermakov, Gennady ^a   Centelles, Josep J ^c   Westerhoff, Hans V ^b,d   Cascante, Marta ^c  

^a INSTITUTE OF THEORETICAL AND EXPERIMENTAL BIOPHYSICS   (Russian Federation)

^b BioCentrum Amsterdam   (Netherlands)

^c UNIVERSITY OF BARCELONA   (Spain)

^d VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

Graph theoretic approach; Kinetic modelling; Oscillations; System identification; Systems biology

Indexed keywords

ARTICLE; CHEMICAL REACTION KINETICS; CONCENTRATION (PARAMETERS); MATHEMATICAL MODEL; MOLECULAR DYNAMICS; OSCILLATION; PRIORITY JOURNAL; REACTION TIME; SIGNAL TRANSDUCTION;

ALGORITHMS; ANIMALS; CELL PHYSIOLOGY; COMPUTER SIMULATION; FEEDBACK, BIOCHEMICAL; GENE EXPRESSION REGULATION; HOMEOSTASIS; HUMANS; MODELS, BIOLOGICAL; NUMERICAL ANALYSIS, COMPUTER-ASSISTED; SIGNAL TRANSDUCTION;

ACARI;

EID: 4944229009     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1432-1033.2004.04324.x     Document Type: Article

References (42)

1. Betz, A. & Sel'kov, E. (1969) Control of phosphofructokinase (PFK) activity in conditions simulating those of glycolysing yeast extract. FEBS Lett. 3, 5-9.
2. Richard, P., Bakker, B.M., Teusink, B., Van Dam, K. & Westerhoff, H.V. (1996) Acetaldehyde mediates the synchronization of sustained glycolytic oscillations in populations of yeast cells. Eur. J. Biochem. 235, 238-241.
3. Berridge, M.J., Bootman, M.D. & Lipp, P. (1998) Calcium - a life and death signal. Nature 395, 645-648.
4. Schuster, S., Marhl, M. & Höfer, T. (2002) Modeling of simple and complex calcium oscillations. Eur. J. Biochem. 269, 1333-1355.
5. Nurse, P. (2001) The cell cycle and development. Introduction. Novartis Found Symp 237, 1-2.
6. Heinrich, R., Rapoport, S.M. & Rapoport, T.A. (1977) Metabolic regulation and mathematical models. Progr. Biophys. Mol. Biol. 32, 1-82.
7. Nicolis, G. & Prigogine, I. (1977) Self-Organization in Non-equilibrium Systems. John Wiley & Sons, New York.
8. Wolf, J., Passarge, J., Somsen, O.J., Snoep, J.L., Heinrich, R. & Westerhoff, H.V. (2000) Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations. Biophys. J. 78, 1145-1153.
9. Tyson, J.J. & Novak, B. (2001) Regulation of the eucaryotic cell cycle: molecular antagonism, hysteresis, and irreversible transitions. J. Theor. Biol. 210, 249-263.
10. Goldbeter, A. (1990) Rythms et Chaos Dans les Systèmes Biochimiques et Cellulaires. Hasson, Paris.
11. Westerhoff, H.V. (2001) The silicon cell, not dead but live! Metab. Eng. 3, 207-210.
12. Kholodenko, B.N. (2000) Negative feed-back and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur. J. Biochem. 267, 1583-1588.
13. Demin, O.V., Westerhoff, H.V. & Kholodenko, B.N. (1999) Control analysis of stationary forced oscillations. J. Phys. Chem. B 103, 10695-10710.
14. Markus, M. & Hess, B. (1990) Control of metabolic oscillations: unpredictability, critical slowing down, optimal stability, and hysteresis. In Control of Metabolic Processes (Cornish-Bowden, A. & Cardenas, M.L., eds.), pp. 303-313.
15. King, E.L. & Altman, C. (1956) A schematic method of deriving the rate laws for enzyme-catalyzed reactions. J. Phys. Chem. 60, 1375-1378.
16. Hill, T.L. (1977) Free Energy Transduction in Biology. Academic Press, New York.
17. Volkenstein, M.V. & Goldstein, B.N. (1966) A new method for solving the problems of stationary kinetics of enzymological reactions. Biochim. Biophys. Acta 115, 471-477.
18. Volkenstein, M.V. & Goldstein, B.N. (1966) Allosteric enzyme models and their analysis by the theory of graphs. Biochim. Biophys. Acta. 115, 478-485.
19. Goldstein, B.N. (1983) Analysis of cyclic enzyme reaction schemes by graph - theoretic method. J. Theor. Biol. 103, 247-264.
20. Goldstein, B.N. & Shevelev, E. (1985) Stability of multienzyme systems with feedback regulation: a graph theoretical approach. J. Theor. Biol. 112, 493-503.
21. Goldstein, B.N. & Ivanova, A. (1987) Hormonal regulation of 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase: kinetic model. FEBS Lett. 217, 212-215.
22. Clarke, B.L. (1980) Stability of complex reaction networks. Adv. Chem. Phys. 43, 1-115.
23. Ivanova, A.N. (1979) Conditions for the unique steady state of kinetic systems as connected with structure of the reaction schemes. Kinetika i Kataliz (in Russian) 20, 1019-1028.
24. Goldstein, B.N., Holmuhamedov, E.L., Ivanova, A.N. & Furman, G.A. (1987) Ionophore-induced oscillations in erythrocytes. Mol. Biol. 21, 110-117.
25. Eiswirth, M., Freund, A. & Ross, J. (1991) Operational procedure toward the classification of chemical oscillators. J. Phys. Chem. 95, 1294-1299.
26. Eiswirth, M., Freund, A. & Ross, J. (1991) Operational procedure toward the classification of chemical oscillators. Adv. Chem. Phys. 190, 127-150.
27. Goldstein, B.N. & Maevsky, A.A. (2002) Critical switch of the metabolic fluxes by phospho-fructo-2-kinase: fructose-2,6-bisphosphatase. A kinetic model. FEBS Lett. 532, 295-299.
28. Selivanov, V.A., Zakrzhevskaya, D.T. & Goldstein, B.N. (1994) Activity oscillations predicted for pyruvate dehydrogenase complexes. FEBS Lett. 345, 151-153.
29. Savageau, M.A. (1969) Biochemical Systems Theory. J. Theor. Biol. 25, 365-379.
30. Savageau, M.A., Voit, E.O. & Irvine, D.H. (1987) Biochemical systems theory and metabolic control theory. Math. Biosci. 86, 147-169.
31. Kacser, H. & Burns, J.A. (1973) The control of flux. Symp Soc. Exp. Biol. 27, 65-104.
32. Reder, Ch (1988) Metabolic control theory: a structural approach. J. Theor. Biol. 135, 175-201.
33. McDonald, A.G. (2003) Implications of enzyme kinetics. Biochem. Soc. Trans. 31, 719-722.
34. McDonald, M.J., Fahien, L.A., Buss, J.D., Hasan, N.M., Fallon, M.J. & Kendrick, M.A. (2003) Citrate oscillates in liver and pancreatic beta cell mitochondria and in INS-1 insuloma cells. J. Biol. Chem. 278, 51894-51900.
35. Aon, M.A., Cortassa, S., Marban, E. & O'Rourke, B. (2003) Synchronized whole cell oscillations in mitochondrial metabolism triggered by a local release of reactive oxygen species in cardial myocytes. J. Biol. Chem. 278, 44735-44744.
36. Olsen, L.F., Hauser, M.J.B. & Kummer, U. (2003) Mechanism of protection of peroxidase activity by oscillatory dynamics. Eur. J. Biochem. 270, 2796-2804.
37. Lloyd, D., Eshantha, L., Salgado, J., Turner, M.P. & Murray, D.B. (2002) Respiratory oscillations in yeast: clock-driven mitochondrial cycles of energization. FEBS Lett. 519, 41-44.
38. Wolf, J., Sohn, H.Y., Heinrich, R. & Kuriyama, H. (2001) Mathematical analysis of a mechanism for autonomous metabolic oscillations in continuous of Saccharomyces cerevisiae. FEBS Lett. 499, 230-234.
39. Westermark, P.O. & Lansner, A. (2003) A model of phosphofructokinase and glycolytic oscillations in the pancreatic cell. Biophys. J. 85, 126-139.
40. Lahav, G., Rosenfeld, N., Sigal, A., Geva-Zatorsky, N., Levine, A.J., Elowitz, M.B. & Alon, U. (2004) Dynamics of the p53-Mdm2 feedback loop in individual cells. Nat. Genet. 36, 113-114.
41. Brady, N.R., Elmore, S.O., Van Beek, J.H.G.M., Krab, K., Courtoy, P.J., Hue, L. & Westerhoff, H.V. (2004) Coordinated behavior of mitochondria in both space and time: a reactive oxygen species-activated wave of mitochondrial depolarization. Biophys. J. in press.
42. Westerhoff, H.V. & Van Dam, K. (1987) Thermodynamics and Control of Biological Free Energy Transduction. Elsevier, Amsterdam.