Dynamic analysis of feedback loops in extra-cellular signal regulated kinase signal network

Journal of Next Generation Information Technology

Volumn 2, Issue 1, 2011, Pages 88-96

  Han, Yong ^a   Li, Yan ^a   Liu, Jing ^a   Wang, Yonghua ^b   Zhang, Shuwei ^a  

^a DALIAN UNIVERSITY OF TECHNOLOGY   (China)

^b NORTHWEST A F UNIVERSITY   (China)

Author keywords

ERK; Feedback loops; MAPK

Indexed keywords

EID: 84863276838     PISSN: 20928637     EISSN: 22339388     Source Type: Journal    
DOI: 10.4156/jnit.vol2.issue1.10     Document Type: Article

References (32)

1. English, J., Pearson G, Wilsbacher J., Swantek J., Karandikar M., Xu S., Cobb M.H., "New insightsinto the control of MAP kinase pathways", Experimental Cell Research, vol. 253, no. 1, pp. 255-270, 1999.
2. Lewis, T. S., Shapiro, P. S., and Ahn, N. G., "Signal transduction through MAP kinase cascades",Advances in Cancer Research, vol. 74, pp. 49-139, 1998.
3. Chong, H., Vikis, H.G. and Guan, K.L., "Mechanisms of regulating the Raf kinase family", CellularSignalling, vol.15, no. 5, pp. 463-469, 2003.
4. Kolch, W., "Coordinating ERK/MAPK signalling through scaffolds and inhibitors", Nature Reviews Molecular Cell Biology, vol. 6, no. 11, pp. 827-837, 2005.
5. O'Neill, E., Kolch, W., "Conferring specificity on the ubiquitous Raf/MEK signalling pathway". British Journal of Cancer, vol. 90, no. 2, pp. 283-288, 2004.
6. Chang, L., Karin, M., "Mammalian MAP kinase signalling cascades", Nature vol. 410, pp. 37-40, 2001.
7. Orton, R.J., Sturm, O.E., Vyshemersky, V., Calder M, Gilbert D.R., Kolch W., "Computational modelling of the receptor- tyrosine- kinase-activated MAPK pathway", Biochemical Journal, vol. 392, no. 2, pp. 249-261, 2005.
8. Farooq, A., Zhou, M. M., "Structure and regulation of MAPK phosphatases", Cellular Signalling, vol. 16, pp. 769-779, 2004.
9. Dougherty, M.K., Muller, J., Ritt, D.A., Zhou, M., Zhou, X.Z., Copeland, T.D., Conrads, T.P., Veenstra, T.D., Lu, K.P., Morrison, D.K., "Regulation of raf-1 by direct feedback phosphorylation", Molecular Cell, vol. 17, no. 2, pp. 215-224, 2005.
10. Kholodenko, B.N., "Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades", European Journal of Biochemistry, Vol. 267, no. 6, pp. 1583-1588, 2000.
11. Kholodeno, B.N., Kiyatkin, A., Bruggeman, F.J., Sontag, E., Westerhoff, H.V., Hoek, J.B., "Untangling the wires: A strategy to trace functional interactions in signaling and gene networks", Proceedings of the National Academy of Sciences, vol. 99, no. 20, pp. 12841-12846, 2002.
12. Keilhack, H., Tenev, T., Nyakatura, E., Godovac-Zimmermann J., Nielsen L., Seedorf K., Böhmer F.D., "Phosphotyrosine 1173 mediates binding of the protein-tyrosine phosphatase Shp-1 to the epidermal growth factor receptor and attenuation of receptor signaling", Journal of Biological Chemistry, vol. 273, no. 38, pp. 24839-24846, 1998.
13. Hubbard, S.R., Mohammadi, M., Schlessinger, J., "Autoregulatory mechanisms in protein-tyrosine kinases", Journal of Biological Chemistry, vol. 273, no. 20, pp. 11987-11990, 1998.
14. Marshall, C.J., "Specificity of receptor tyrosine kinase signaling: transient versus sustained extracellular signal-regulated kinase activation", Cell, vol. 80, no. 1, pp. 179-185, 1995.
15. Kolch, W., Calder, M., Gilbert, D. "When kinases meet mathematics: the systems biology of MAPK signalling", FEBS Letters, vol. 579, no. 8, pp. 1891-1895, 2005.
16. Eungdamrong, N.J., Iyengar, R., "Computational approaches for modeling regulatory cellular networks", Trends in Cell Biology, vol. 14, no. 12, pp. 661-669, 2005.
17. Kholodenko, B.N., Demin, O.V., Moehren, G., Hoek J.B., "Quantification of short term signaling by the epidermal growth factor receptor", Journal of Biological Chemistry, vol. 274, no. 42, pp. 30169-30181, 1999.
18. Brightman, F.A. and Fell, D.A., "Differential feedback regulation of the MAPK cascade underlies the quantitative differences in EGF and NGF signalling in PC12 cells", FEBS Letters, vol. 482, no. 3, pp. 169-174, 2000.
19. Asthargiri, A. and Lauffenburger, D., "A Computational Study of Feedback Effects on Signal Dynamics in a Mitogen-Activated Protein Kinase (mapk) Pathway Model", Biotechnology Progress, vol. 17, no. 2, pp. 227-239, 2001.
20. Schoeberl, B., Eichler-Jonsson, C., Gilles, E.D., Muller, G. "Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors", Nature Biotechnology, vol. 20, no. 4, pp. 370-375, 2002.
21. Moehren, G., Markevich, N., Demin, O., Kiyatkin, A., Goryanin, I., Hoek, J.B., Kholodenko,B.N., "Temperature dependence of the epidermal growth factor receptor signaling network can be accounted for by a kinetic model", Biochemistry, vol. 41, no. 1, pp. 306-320, 2002.
22. Shvartsman, S.Y. Hagan M.P., Yacoub A., Dent P., Wiley H.S., Lauffenburger D.A., "Autocrine loops with positive feedback enable context-dependent cell signaling", American Journal of Physiology-cell Physiology, vol. 282, no. 3, pp. 545-559, 2002.
23. Wiley, H.S., Shvartsman, S.Y., Lauffenburger, D.A., "Computational modeling of the EGFreceptor system: a paradigm for systems biology", Trends in Cell Biology, vol. 13, no. 1, pp. 43-50, 2003.
24. Aksan, I. and Kurnaz, M.L., "A computer-based model for the regulation of mitogen activated protein kinase (MAPK) activation", Journal of Receptor and Signal Transduction Research, vol. 23, no. 2-3, pp. 197-209, 2003.
25. Kolch, W. "Meaningful relationships: the regulation of the Ras/Raf/MEK/ERK pathway by protein interactions", Biochemical Journal, vol. 351, no. 2, pp. 289-305, 2000.
26. Kholodenko, B.N., "Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades", European Journal of Biochemistry. vol. 267, no. 6, pp. 1583-1588, 2000.
27. Kholodeno, B.N., Kiyatkin, A., Bruggeman, F.J., Sontag, E., Westerhoff, H.V., Hoek, J.B., "Untangling the wires: A strategy to trace functional interactions in signaling and gene networks", Proceedings of the National Academy of Sciences, vol. 99, no. 20, pp. 12841-12846, 2002.
28. Sauro, H.M., Kholodenko, B.N., "Quantitative analysis of signalling networks", Progress in Biophysics & Molecular Biology, vol. 86, no. 1, pp. 5-43, 2004.
29. Hess, B., Boiteux, A., "Oscillatory phenomena in biochemistry", Annual Review of Biochemistry, vol. 40, pp. 237-258, 1971.
30. Richard, P., Diderich, J.A., Bakker, B.M., Teusink, B., van Dam, K., Westerhoff, H.V. "Yeast cells with a specific cellular make-up and an environment that removes acetaldehyde are prone to sustained glycolytic oscillations", FEBS Letters, vol. 341, no. 2-3, pp. 223-226,1994.
31. Brown, G.C., Kholodenko, B.N., "Spatial gradients of cellular phospho-proteins", FEBS Letters, vol. 457, no. 3, pp. 452-454, 1999.
32. Marshall, C.J., "Specificity of receptor tyrosine kinase signaling: transient versus sustained extracellular signal-regulated kinase activation", Cell, vol. 80, no. 2, pp. 179-185, 1995.