Abstract
We predict that computational modeling platforms will soon become standard tools in experimental laboratories involved in the study of complex regulatory networks of various cellular processes—a field of research where an avalanche of genomic, proteomic and other biochemical data have recently been gleaned, and this trend is expected to continue in the foreseeable future. Quantitative kinetic modeling requires one to postulate detailed molecular pathways and to carry out analyses in the context of an integrated dynamic system so that predictions can be made and compared with experimental data as well as aid in the design of future experiments. The speed of modern computers is such that one can perform simulations of many possible models and discriminate against those that are less probable.
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References
Huang, C-Y. F. and Ferrell, J. E., Jr. (1996) Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc. Natl. Acad. Sci. USA 93, 10,078–10,083.
Gibson, M. A. and Mjolsness, E. (2001) Modeling the activity of single genes, in Computation Modeling of Genetic and Biochemical Networks (Bower, J. M. and Bolouri, H., eds.), MIT Press, Cambridge, MA, pp. 1–48.
Asthagiri, A. R. and Lauffenburger, D. A. (2001) A computational study of feedback effects on signal dynamics in a mitogen-activated protein kinase (MAPK) pathway model. Biotechnol. Prog. 17, 227–239.
Kholodenko, B. N. (2000) Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur. J. Biochem. 267, 1583–1588.
Cheng, J., Yang, J., Xia, Y., Karin, M., and Su, B. (2000) Synergistic interaction of MEK kinase 2, c-Jun N-terminal kinase (JNK) kinase 2, and JNK1 results in efficient and specific JNK1 activation. Mol. Cell. Biol. 20, 2334–2342.
Levchenko, A., Bruck, J., and Sternberg, P. W. (2000) Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. Proc. Natl. Acad. Sci. USA 97, 5818–5823.
Shapiro, B. E., Levchenko, A., and Mjolsness, E. (2002) Automatic model generation for signal transduction with applications to MAPK pathway, in Foundations of Systems Biology (Kitano, H., ed.), MIT Press, Cambridge, MA, pp. 145–162.
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© 2004 Humana Press Inc., Totowa, NJ
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Aguda, B.D., Sauro, H.M. (2004). Computer Simulation of MAPK Signal Transduction. In: Seger, R. (eds) MAP Kinase Signaling Protocols. Methods in Molecular Biology™, vol 250. Humana Press. https://doi.org/10.1385/1-59259-671-1:167
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DOI: https://doi.org/10.1385/1-59259-671-1:167
Publisher Name: Humana Press
Print ISBN: 978-0-89603-998-8
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