Steady state and (bi-) stability evaluation of simple protease signalling networks

BioSystems

Volumn 90, Issue 3, 2007, Pages 591-601

  Eißing, Thomas ^a   Waldherr, Steffen ^a   Allgöwer, Frank ^a   Scheurich, Peter ^a   Bullinger, Eric ^a,b  

^a UNIVERSITY OF STUTTGART   (Germany)

^b NATIONAL UNIVERSITY OF IRELAND   (Ireland)

Author keywords

Apoptosis; Bistability; Caspases; Proteases; Signalling; Switch; Threshold

Indexed keywords

PROTEINASE; PROTEINASE INHIBITOR;

APOPTOSIS; BLOOD; ENZYME ACTIVITY; EXPERIMENTAL STUDY; INHIBITOR; NUMERICAL MODEL; THRESHOLD;

ANALYTIC METHOD; APOPTOSIS; ARTICLE; BLOOD CLOTTING; COMPARATIVE STUDY; MATHEMATICAL MODEL; PROTEIN DEGRADATION; SIGNAL TRANSDUCTION; STEADY STATE;

EID: 34547836607     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2007.01.003     Document Type: Article

References (54)

1. Angeli D. New analysis technique for multistability detection. Syst. Biol. 153 2 (2006) 61-69
2. Angeli D., Ferrell J.E., and Sontag Jr. E.D. Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. Proc. Natl. Acad. Sci. U.S.A. 101 7 (2004) 1822-1827
3. Bagci E.Z., Vodovotz Y., Billiar T.R., Ermentrout G.B., and Bahar I. Bistability in apoptosis: roles of Bax, Bcl-2 and mitochondrial permeability transition pores. Biophys. J. 90 (2006) 1546-1559
4. Beltrami E., and Jesty J. Mathematical analysis of activation thresholds in enzyme-catalyzed positive feedbacks: application to the feedbacks of blood coagulation. Proc. Natl. Acad. Sci. U.S.A. 92 19 (1995) 8744-8748
5. Bhalla U.S., Ram P.T., and Iyengar R. MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science 297 5583 (2002) 1018-1023
6. Blüthgen N., Bruggeman F.J., Legewie S., Herzel H., Westerhoff H.V., and Kholodenko B.N. Effects of sequestration on signal transduction cascades. FEBS J. 273 5 (2006) 895-906
7. Cherry J.L., and Adler F.R. How to make a biological switch. J. Theor. Biol. 203 2 (2000) 117-133
8. Dahlbäck B. Blood coagulation. Lancet 355 9215 (2000) 1627-1632
9. Danial N.N., and Korsmeyer S.J. Cell death: critical control points. Cell 116 2 (2004) 205-219
10. Dash C., Kulkarni A., Dunn B., and Rao M. Aspartic peptidase inhibitors: implications in drug development. Crit. Rev. Biochem. Mol. Biol. 38 2 (2003) 89-119
11. Eißing T., Allgöwer F., and Bullinger E. Robustness properties of apoptosis models with respect to parameter variations and stochastic influences. Syst. Biol. 152 4 (2005) 221-228
12. Eißing T., Conzelmann H., Gilles E.D., Allgöwer F., Bullinger E., and Scheurich P. Bistability analyses of a caspase activation model for receptor-induced apoptosis. J. Biol. Chem. 279 35 (2004) 36892-36897
13. Ferrell Jr. J.E. Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs. Trends Biochem. Sci. 21 12 (1996) 460-466
14. Ferrell Jr. J.E. How responses get more switch-like as you move down a protein kinase cascade. Trends Biochem. Sci. 22 8 (1997) 288-289
15. Ferrell J.E., and Machleder Jr. E.M. The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science 280 5365 (1998) 895-898
16. Ferrell J.E., and Xiong Jr. W. Bistability in cell signaling: how to make continuous processes discontinuous, and reversible processes irreversible. Chaos 11 1 (2001) 227-236
17. Goldbeter A., and Koshland D.E. An amplified sensitivity arising from covalent modification in biological systems. Proc. Natl. Acad. Sci. U.S.A. 78 11 (1981) 6840-6844
18. Goldbeter A., and Koshland D.E. Ultrasensitivity in biochemical systems controlled by covalent modification. Interplay between zero-order and multistep effects. J. Biol. Chem. 259 23 (1984) 14441-14447
19. Grabowskal U., Chambers T.J., and Shiroo M. Recent developments in cathepsin K inhibitor design. Curr. Opin. Drug Discov. Dev. 8 5 (2005) 619-630
20. Hengartner M.O. The biochemistry of apoptosis. Nature 407 6805 (2000) 770-776
21. Hodgkin A.L., and Huxley A.F. A quantitative description of membrane current and its application to conduction and excitation in nerve. J. Physiol. 117 4 (1952) 500-544
22. Huang C.Y., and Ferrell Jr. J.E. Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc. Natl. Acad. Sci. U.S.A. 93 19 (1996) 10078-10083
23. Koshland D.E. The era of pathway quantification. Science 280 5365 (1998) 852-853
24. Legewie S., Blüthgen N., and Herzel H. Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability. PLoS Comput. Biol. 2 9 (2006) e120
25. Leist M., and Jaattela M. Four deaths and a funeral: from caspases to alternative mechanisms. Nat. Rev. Mol. Cell Biol. 2 8 (2001) 589-598
26. Lisman J.E. A mechanism for memory storage insensitive to molecular turnover: a bistable autophosphorylating kinase. Proc. Natl. Acad. Sci. U.S.A. 82 9 (1985) 3055-3057
27. Ma L., and Iglesias P.A. Quantifying robustness of biochemical network models. BMC Bioinformat. 3 (2002) 38
28. Mangan S., and Alon U. Structure and function of the feed-forward loop network motif. Proc. Natl. Acad. Sci. U.S.A. 100 21 (2003) 11980-11985
29. Markevich N.I., Hoek J.B., and Kholodenko B.N. Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. J. Cell Biol. 164 3 (2004) 353-359
30. Ortega F., Acerenza L., Westerhoff H.V., Mas F., and Cascante M. Product dependence and bifunctionality compromise the ultrasensitivity of signal transduction cascades. Proc. Natl. Acad. Sci. U.S.A. 99 3 (2002) 1170-1175
31. Overall C.M., and López-Otín C. Strategies for MMP inhibition in cancer: innovations for the post-trial era. Nat. Rev. Cancer 2 9 (2002) 657-672
32. Piccardi C., and Rinaldi S. Remarks on excitability, stability and sign of equilibria in cooperative systems. Syst. Cont. Lett. 46 (2002) 153-163
33. Qu Z., MacLellan W.R., and Weiss J.N. Dynamics of the cell cycle: checkpoints, sizers, and timers. Biophys. J. 85 6 (2003) 3600-3611
34. Rehm M., Huber H.J., Dussmann H., and Prehn J.H.M. Systems analysis of effector caspase activation and its control by X-linked inhibitor of apoptosis protein. EMBO J. 25 18 (2006) 4338-4349
35. Shmulevich I., Kauffman S.A., and Aldana M. Eukaryotic cells are dynamically ordered or critical but not chaotic. Proc. Natl. Acad. Sci. U.S.A. 102 38 (2005) 13439-13444
36. Slee E.A., Harte M.T., Kluck R.M., Wolf B.B., Casiano C.A., Newmeyer D.D., Wang H.G., Reed J.C., Nicholson D.W., Alnemri E.S., Green D.R., and Martin S.J. Ordering the cytochrome c-initiated caspase cascade: hierarchical activation of caspases-2, -3, -6, -7, -8, and -10 in a caspase-9-dependent manner. J. Cell Biol. 144 2 (1999) 281-292
37. Sloane B.F., Yan S., Podgorski I., Linebaugh B.E., Cher M.L., Mai J., Cavallo-Medved D., Sameni M., Dosescu J., and Moin K. Cathepsin B and tumor proteolysis: contribution of the tumor microenvironment. Semin. Cancer Biol. 15 2 (2005) 149-157
38. Sohn D., Schulze-Osthoff K., and Jänicke R.U. Caspase-8 can be activated by interchain proteolysis without receptor-triggered dimerization during drug-induced apoptosis. J. Biol. Chem. 280 7 (2005) 5267-5273
39. Stelling J., Sauer U., Szallasi Z., Dolye F.J., and Doyle III J. Robustness of cellular functions. Cell 118 6 (2004) 675-685
40. Stennicke H.R., and Salvesen G.S. Catalytic properties of the caspases. Cell Death Differ. 6 11 (1999) 1054-1059
41. Strogatz S.H. Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering (2001), Perseus Books, Cambridge, MA
42. Thron C.D. Theoretical dynamics of the cyclin B-MPF system: a possible role for p13suc1. BioSystems 32 2 (1994) 97-109
43. Thron C.D. Bistable biochemical switching and the control of the events of the cell cycle. Oncogene 15 3 (1997) 317-325
44. Thurmond R.L., Sun S., Karlsson L., and Edwards J.P. Cathepsin S inhibitors as novel immunomodulators. Curr. Opin. Invest. Drugs 6 5 (2005) 473-482
45. Tyson J.J., Chen K.C., and Novak B. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr. Opin. Cell Biol. 15 2 (2003) 221-231
46. Tyson J.J., and Othmer H.G. The dynamics of feedback control circuits in biochemical pathways. Progress in Theoretical Biology, vol. 5 (1978), Academic Press, New York 1-62
47. Van de Craen M., Declercq W., Van den brande I., Fiers W., and Vandenabeele P. The proteolytic procaspase activation network: an in vitro analysis. Cell Death Differ. 6 11 (1999) 1117-1124
48. Ventura B.D., Lemerle C., Michalodimitrakis K., and Serrano L. From in vivo to in silico biology and back. Nature 443 7111 (2006) 527-533
49. Weiss J.N. The Hill equation revisited: uses and misuses. FASEB J. 11 11 (1997) 835-841
50. Wolf D.M., and Arkin A.P. Motifs, modules and games in bacteria. Curr. Opin. Microbiol. 6 2 (2003) 125-134
51. Xiong W., and Ferrell Jr. J.E. A positive-feedback-based bistable 'memory module' that governs a cell fate decision. Nature 426 6965 (2003) 460-465
52. 2+-dependent proteases in ischemic neuronal death: a conserved 'calpain-cathepsin cascade' from nematodes to primates. Cell Calcium 36 3/4 (2004) 285-293
53. Yeger-Lotem E., Sattath S., Kashtan N., Itzkovitz S., Milo R., Pinter R.Y., Alon U., and Margalit H. Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc. Natl. Acad. Sci. U.S.A. 101 16 (2004) 5934-5939
54. Zarnitsina V.I., Ataullakhanov F.I., Lobanov A.I., and Morozova O.L. Dynamics of spatially nonuniform patterning in the model of blood coagulation. Chaos 11 1 (2001) 57-70