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

  • Thomas Hinze
  • Thorsten Lenser
  • Peter Dittrich
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4361)

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.

Keywords

Formal Language MAPK Cascade Protein Binding Domain Reaction Rule Membrane Computing 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Thomas Hinze
    • 1
  • Thorsten Lenser
    • 1
  • Peter Dittrich
    • 1
  1. 1.Bio Systems Analysis GroupFriedrich Schiller University JenaJenaGermany

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