Abstract
Cellular signalling pathways are fundamental to the control and regulation of cell behavior. Understanding of biosignalling network functions is crucial to the study of different diseases and to the design of effective therapies. In this paper we present P systems as a feasible computational modeling tool for cellular signalling pathways that takes into consideration the discrete character of the components of the system and the key role played by membranes in their functioning. We illustrate these cellular models simulating the epidermal growth factor receptor (EGFR) signalling cascade and the FAS–induced apoptosis using a deterministic strategy for the evolution of P systems.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Alimonti, J.B., Ball, T.B., Fowke, K.R.: Mechanisms of CD4+ T lymphocyte cell death in human immunodeficiency virus infection and AIDS. Journal of General Virology 84, 1649–1661 (2003)
Bhalla, U.S., Iyengar, R.: Emergent properties of networks of biological signaling pathways. Science 283, 381–387 (1999)
Blossey, R., Cardelli, L., Phillips, A.: A compositional approach to the stochastic dynamics of gene networks. In: Priami, C., Cardelli, L., Emmott, S. (eds.) Transactions on Computational Systems Biology IV. LNCS (LNBI), vol. 3939, pp. 99–122. Springer, Heidelberg (2006)
Cheng, E.H., Wei, M.C., Weiler, S., Flavell, R.A., Mak, T.W., Lindsten, T., Korsmeyer, S.J.: BCL-2, BCL-XL sequester BH3 domain-only molecules preventing BAX- and BAK-mediated mitochondrial apoptosis. Molecular Cell 8, 705–711 (2001)
Cheruku, S., Păun, A., Romero, F.J., Pérez–Jiménez, M.J., Ibarra, O.H.: Simulating FAS–induced apoptosis by using P systems. In: Proceedings of the First International Conference on Bio–Inspired Computing: Theory and Applications, Wuhan, China, September 18-22 (2006)
Hua, F., Cornejo, M., Cardone, M., Stokes, C., Lauffenburger, D.: Effects of Bcl-2 levels on FAS signaling-induced caspase-3 activation: Molecular genetic tests of computational model predictions. The Journal of Immunology 175(2), 985–995 (2005); correction 175(9), 6235–6237 (2005)
Ibarra, O.H., Păun, A.: Counting time in computing with cells. In: Proceedings of DNA Based Computing, DNA11, London, Ontario, pp. 25–36 (2005)
Kerr, J.F., Wyllie, A.H., Currie, A.R.: Apoptosis: a basic biological phenomenon with wide-ranging implications in tissue kinetics. British Journal Cancer 26, 239 (1972)
Pogson, M., Smallwood, R., Qwarnstrom, E.: Holcombe, Formal agent–based of intracellular chemical interactions. BioSystems 85(1), 37–45 (2006)
Holcombe, M., Gheorghe, M., Talbot, N.: A hybrid machine model of rice blast fungus, Magnaphorte Grisea. BioSystems 68(2-3), 223–228 (2003)
Jaatela, M.: Multiple cell death pathways as regulators of tumour initiation and progression. Oncogene 23, 2746–2756 (2004)
Jackson, D., Holcombe, M., Ratnieks, F.: Trail geometry gives polarity to ant foraging networks. Nature 432, 907–909 (2004)
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 41, 306–320 (2002)
Moghal, N., Sternberg, P.W.: Multiple positive and negative regulators of signaling by the EGFR receptor. Curr. Opin. Cell Biology 11, 190–196 (1999)
Nijhawan, D., Honarpour, N., Wang, X.: Apotosis in neural development and disease. Annual Reviews Neuroscience 23, 73–87 (2000)
Oltavi, Z.N., Milliman, C.L., Korsmeyer, S.J.: Bcl-2 heterodimerizes in vivo with a conserved homolog, Bax, that accelerates programmed cell death. Cell 74(4), 609–619 (1993)
Păun, G.: Computing with membranes. Journal of Computer and System Sciences 61(1), 108–143 (2000); Turku Center for Computer Science-TUCS Report Nr. 208 (1998)
Păun, G.: Membrane Computing. An Introduction. Springer, Berlin (2002)
Păun, G., Rozenberg, G.: A guide to membrane computing. Theoretical Computer Science 287, 73–100 (2002)
Jesús Pérez-Jímenez, M., Romero-Campero, F.J.: P systems, a new computational modelling tool for systems biology. In: Priami, C., Plotkin, G. (eds.) Transactions on Computational Systems Biology VI. LNCS (LNBI), vol. 4220, pp. 176–197. Springer, Heidelberg (2006)
Jesús Pérez-Jímenez, M., Romero-Campero, F.J.: A study of the robustness of the EGFR signalling cascade using continuous membrane systems. In: Mira, J., Álvarez, J.R. (eds.) IWINAC 2005. LNCS, vol. 3561, pp. 268–278. Springer, Heidelberg (2005)
Regev, A., Shapiro, E.: The π-calculus as an abstraction for biomolecular systems. In: Ciobanu, G., Rozenberg, G. (eds.) Modelling in Molecular Biology. Springer, Berlin (2004)
Scaffidi, C., Fulda, S., Srinivasan, A., Friesen, C., Li, F., Tomaselli, K.J., Debatin, K.M., Krammer, P.H., Peter, M.E.: Two CD95 (APO-1/Fas) signaling pathways. The Embo Journal 17, 1675–1687 (1998)
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 20(4), 370–375 (2002)
Van Kampen, N.G.: Stochastics Processes in Physics and Chemistry. Elsevier Science B.V., Amsterdam (1992)
Walker, D.C., Southgate, J., Hill, G., Holcombe, M., Hose, D.R., Wood, S.M., MacNeil, S., Smallwood, R.H.: The epitheliome: modelling the social behaviour of cells. BioSystems 76(1-3), 89–100 (2004)
Wang, K., Yin, X.M., Chao, D.T., Milliman, C.L., Korsmeyer, S.J.: BID: a novel BH3 domain-only death agonist. Genes & Development 10, 2859–2869 (1996)
Wells, A.: EGFR–receptor. Int. Journal Biochem. Cell Biology 31, 637–643 (1999)
Wiley, H.S., Shvartsman, S.Y., Lauffenburger, D.A.: Computational modeling of the EGFR–receptor system: A paradigm for systems biology. Trends in Cell Biology 13(1), 43–50 (2003)
ISI web page: http://esi-topics.com/erf/october2003.html
SciLab Web Site: http://scilabsoft.inria.fr/
P Systems Modelling Framework Web Site: http://www.dcs.shef.ac.uk/~marian/PSimulatorWeb/P_Systems_applications.htm
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Păun, A., Pérez-Jiménez, M.J., Romero-Campero, F.J. (2006). Modeling Signal Transduction Using P Systems. In: Hoogeboom, H.J., Păun, G., Rozenberg, G., Salomaa, A. (eds) Membrane Computing. WMC 2006. Lecture Notes in Computer Science, vol 4361. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11963516_7
Download citation
DOI: https://doi.org/10.1007/11963516_7
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-69088-7
Online ISBN: 978-3-540-69090-0
eBook Packages: Computer ScienceComputer Science (R0)