Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis

Journal of Cell Biology

Volumn 166, Issue 6, 2004, Pages 839-851

  Bentele, M ^a   Lavrik, I ^a   Ulrich, M ^a   Stosser S ^a   Heermann, D W ^b   Kalthoff, H ^c   Krammer, P H ^a   Eils, R ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^b INSTITUT FÜR THEORETISCHE PHYSIK   (Germany)

^c UNIVERSITY OF KIEL   (Germany)

Author keywords

CD95 induced apoptosis; Mathematical modeling; Parameter estimation; Sensitivity analysis; Threshold mechanism

Indexed keywords

FAS ANTIGEN;

APOPTOSIS; ARTICLE; AUTOIMMUNITY; CARCINOGENESIS; MATHEMATICAL MODEL; NERVE DEGENERATION; PRIORITY JOURNAL; SIGNAL TRANSDUCTION;

ANTIGENS, CD95; APOPTOSIS; CASPASES; CELL LINE, TUMOR; COMPUTER SIMULATION; DATABASES, FACTUAL; DOWN-REGULATION; ENZYME ACTIVATION; HUMANS; KINETICS; MATHEMATICS; MODELS, BIOLOGICAL; MODELS, THEORETICAL; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SIGNAL TRANSDUCTION; SYSTEMS ANALYSIS;

EID: 4544246088     PISSN: 00219525     EISSN: None     Source Type: Journal    
DOI: 10.1083/jcb.200404158     Document Type: Article

References (36)

1. Alon, U., M.G. Surette, N. Barkai, and S. Leibler. 1999. Robustness in bacterial chemotaxis. Nature. 397:168-171.
2. Ashkenazi, A., and V. Dixit. 1999. Apoptosis control by death and decoy receptors. Curr. Opin. Cell Biol. 11:255-260.
3. Bentele, M., and R. Eils. 2004. General stochastic hybrid method for the simulation of chemical reaction processes in cells, in CMSB '04. Lecture Notes in Computer Science. Springer, Heidelberg. In press.
4. Bhalla, U.S., and R. Iyengar. 1999. Emergent properties of networks of biological signaling pathways. Science. 283:381-387.
5. Carlson, J.M., and J.C. Doyle. 2002. Complexity and robustness. Proc. Natl. Acad. Sci. USA 99:2538-2545.
6. Csete, M.E., and J.C. Doyle. 2002. Reverse engineering of biological complexity. Science. 295:1664-1669.
7. Deuflhard, P. 1983. Numerical Treatment of Inverse Problems in Differential and Integral Equations. Birkhäuser, Boston. 354 pp.
8. French, L.E., and J. Tschopp. 1997. Thyroiditis and hepatitis: Fas on the road to disease. Nat. Med. 3:385-388.
9. Fussenegger, M., J. Bailey, and J. Varner. 2000. A mathematical model of caspase function in apoptosis. Nat. Biotechnol. 18:768-774.
10. Gear, C.W. 1971. Numerical Initial Value Problems in Ordinary Differential Equations. Englewood Cliffs, NJ. 253 pp.
11. Gilman, A.G., M.I. Simon, H.R. Bourne, B.A. Harris, R. Long, E.M. Ross, J.T. Stull, and R. Taussig. 2002. Overview of the alliance for cellular signaling. Nature. 420:703-706.
12. Goldstein, J.C., N. Waterhouse, P. Juin, G. Evan, and D. Green. 2000. The coordinate release of cytochrome c during apoptosis is rapid, complete and kinetically invariant. Nat. Cell Biol. 2:156-162.
13. Heinrich, R., and S. Schuster. 1996. The Regulation of Cellular Systems. Chapman & Hall, New York. 372 pp.
14. Kell, D.B., and H.V. Westerhoff. 1986. Metabolic control theory: its role in microbiology and biotechnology. FEMS Microbiol. Rev. 39:305-320.
15. Kholodenko, B.N., O.V. Demin, G. Moehren, and J.B. Hoek. 1999. Quantification of short term signaling by the epidermal growth factor receptor. J. Biol. Chem. 274:30169-30181.
16. Kitano, H. 2002. Systems biology: a brief overview. Science. 295:1662-1664.
17. Krammer, P. 2000. CD95's deadly mission in the immune system. Nature. 407: 789-795.
18. Krueger, A., I. Schmitz, S. Baumann, P.H. Krammer, and S. Kirchhoff. 2001. Cellular FLICE-inhibitory protein splice variants inhibit different steps of caspase-8 activation at the CD95 death-inducing signaling complex. J. Biol. Chem. 276:20633-20640.
19. Lauffenburger, D.A. 2000. Cell signaling pathways as control modules: complexity for simplicity? Proc. Natl. Acad. Sci. USA. 97:5031-5033.
20. Lavrik, I., A. Krueger, I. Schmitz, S. Baumann, H. Weyd, P. Krammer, and S. Kirchhoff. 2003. The active caspase-8 heterotetramer is formed at the CD95 DISC. Cell Death Differ. 10:144-145.
21. Mendes, P. 1997. Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci. 22:361-363.
22. Mendes, P., and D. Kell. 1998. Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics. 14:869-883.
23. Micheau, O. 2003. Cellular FLICE-inhibitory protein: an attractive therapeutic target? Expert Opin. Ther. Targets. 7:559-573.
24. Nagata, S. 1999. Fas ligand-induced apoptosis. Annu. Rev. Genet. 33:29-55.
25. Peter, M., and P. Krammer. 2003. The CD95(APO-1/Fas) DISC and beyond. Cell Death Differ. 10:26-35.
26. Regev, A., W. Silverman, and E.Y. Shapiro. 2001. Representation and simulation of biochemical processes using the pi-calculus process algebra. In Pacific Symposium on Biocomputing, vol. 6. World Scientific Publishers, Singapore. 459-470.
27. Salvesen, G.S. 2002. Caspases: opening the boxes and interpreting the arrows. Cell Death Differ. 9:3-5.
28. Salvesen, G.S., and C.S. Duckett. 2002. IAP Proteins: blocking the road to death's door. Nature Rev. Mol. Cell Biol. 3:401-410.
29. Sauro, H.M., and D.A. Fell. 1991. SCAMP: A metabolic simulator and control analysis program. Math. Comput. Model. 15:15-28.
30. Schacherer, F., C. Choi, U. Götze, M. Krull, S. Pistor, and E. Wingender. 2001. The TRANSPATH signal transduction database: a knowledge base on signal transduction networks. Bioinformatics. 17:1053-1057.
31. Schilling, C.H., S. Schuster, B.O. Palsson, and R. Heinrich. 1999. Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. Biotechnol. Prog. 15:296-303.
32. Schoeberl, B., C. Eichler-Jonsson, E.D. Gilles, and G. Müller. 2002. Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat. Biotechnol. 20:370-375.
33. Silke, J., P. Ekert, C. Day, C. Hawkins, M. Baka, and J. Chew. 2001. Direct inhibition of caspase 3 is dispensable for the anti-apoptotoc activity of XIAP. EMBO J. 20:3114-3123.
34. Swameye, I., T.G. Müller, J. Timmer, O. Sandra, and U. Klingmüller. 2003. Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by databased modeling. Proc. Natl. Acad. Sci. USA. 100:1028-1033.
35. Thornberry, N., and Y. Lazebnik. 1998. Caspases: enemies within. Science. 281: 1312-1316.
36. Trauzold, A., S. Schmiedel, C. Rôder, C. Tams, M. Christgen, S. Oestern, A. Arlt, S. Westphal, M. Kapischke, H. Ungefroren, and H. Kalthoff. 2003. Multiple and synergistic deregulations of apoptosis-controlling genes in pancreatic carcinoma cells. Br. J. Cancer. 89:1714-1721.