Modeling Biological Networks

• IV.6.ii Subproject 2 Topology of Signaling Protein Networks and the Cytoskeleton
  • IV.6.ii.a Datasources
  • IV.6.ii.b Overview
  • IV.6.ii.c Hypotheses
  • IV.6.ii.d Specific Aims
  • IV.6.ii.e Preliminary Results and Research Plan
    • IV.6.ii.e.1 Aim 1
    • IV.6.ii.e.2 Aim 2
    • IV.6.ii.e.3 Aim 3
    • IV.6.ii.e.4 Aim 4
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The distance measure and the number of nearest neighbors are abstract quantities, which in principle reveal no information on the spatial distribution of proteins inside the cell. However, if the distance between two proteins in the topological map of protein-protein interactions is small, these proteins tend to interact strongly with each other, requiring their close proximity inside the cell. The larger the distance on the topological map between two proteins, the smaller the probability that they will chemically interact and thus the less their need to be close to each other. Thus distance on the topological map may correlate with physical distance between proteins. We will use our topological map's distance distribution to establish spatial correlations between signaling and cytoskeletal proteins and compare them with data on the intracellular localization of proteins. To analyze the correlation between the topological and spatial distance distribution in more detail we will also consider further neighbor distributions from the protein-protein interaction maps.

If we can prove a correlation between cytoskeletal and signaling proteins in yeast, we will extend our research to other organisms. Interacting-protein maps are under way for Drosophila m., which, like yeast, does not have intermediate filaments. Applying our methods to Drosophila will test the generality of our approach. Another organism which we will analyze as soon as appropriate information becomes available is C. elegans, which does have intermediate filaments and thus a more complex cytoskeleton.