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A Protein Substructure Based P System for Description and Analysis of Cell Signalling Networks

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Membrane Computing (WMC 2006)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 4361))

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Abstract

The way how cell signals are generated, encoded, transferred, modified, and utilized is essential for understanding information processing inside living organisms. The tremendously growing biological knowledge about proteins and their interactions draws a more and more detailed image of a complex functional network. Considering signalling networks as computing devices, the detection of structural principles, especially modularization into subunits and interfaces between them, can help to seize ideas for their description and analysis. Algebraic models like P systems prove to be appropriate to this. We utilize string-objects to carry information about protein binding domains and their ligands. Embedding these string-objects into a deterministic graph structured P system with dynamical behavior, we introduce a model that can describe cell signalling pathways on a submolecular level. Beyond questions of formal languages, the model facilitates tracing the evolutionary development from single protein components towards functional interacting networks. We exemplify the model by means of the yeast pheromone pathway.

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Authors and Affiliations

  1. Bio Systems Analysis Group, Friedrich Schiller University Jena, Ernst-Abbe-Platz 1–4, D-07743, Jena, Germany

    Thomas Hinze, Thorsten Lenser & Peter Dittrich

Authors
  1. Thomas Hinze
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  2. Thorsten Lenser
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  3. Peter Dittrich
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Editor information

Editors and Affiliations

  1. Leiden Institute of Advanced Computer Science, Universiteit Leiden, Niels Bohrweg 1, 2333, Leiden, CA, The Netherlands

    Hendrik Jan Hoogeboom

  2. Institute of Mathematics of the Romanian Academy, PO Box 1-764, 014700, Bucureşti, Romania

    Gheorghe Păun

  3. Leiden Center of Advanced Computer Science (LIACS), Leiden University, Niels Bohrweg 1, 2333, Leiden, CA, The Netherlands

    Grzegorz Rozenberg

  4. Turku Centre for Computer Science (TUCS), Leminkäisenkatu 14, 20520, Turku, Finland

    Arto Salomaa

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© 2006 Springer-Verlag Berlin Heidelberg

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Hinze, T., Lenser, T., Dittrich, P. (2006). A Protein Substructure Based P System for Description and Analysis of Cell Signalling Networks. 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_26

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  • DOI: https://doi.org/10.1007/11963516_26

  • 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)

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