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Visualisation and graph-theoretic analysis of a large-scale protein structural interactome.

Dan Bolser1, Panos Dafas, Richard Harrington

  • 1Department of Computing, City University, London EC1V 0HB, UK. dmb@mrc-dunn.cam.ac.uk

BMC Bioinformatics
|October 9, 2003
PubMed
Summary

The Protein Structural Interactome Map (PSIMAP) reveals the P-loop superfamily as central to protein interactions and evolution. This highly interactive and diverse group is key to understanding protein function and life's molecular history.

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Evolutionary biology

Background:

  • Protein interaction maps offer a global view of protein function.
  • The Protein Structural Interactome Map (PSIMAP) database compiles structurally observed protein domain superfamily interactions.
  • PSIMAP integrates functional and evolutionary data into a unified network.

Purpose of the Study:

  • To perform a comprehensive network analysis of PSIMAP.
  • To apply network measures including centrality, interactivity, fault-tolerance, and taxonomic diversity.
  • To understand the global properties of protein structural interactome.

Main Methods:

  • Network analysis using graph-theoretic measures.
  • Assessment of centrality (center vs. barycenter).

Related Experiment Videos

  • Evaluation of interactivity, taxonomic diversity, and network robustness (fault-tolerance).

    • Main Results:

    • The center and barycenter of PSIMAP differ; barycenter superfamilies have general functions, while center superfamilies are enzymatic.
    • P-loop and immunoglobulin superfamilies are the most interactive.
    • Highly interactive superfamilies exhibit significant taxonomic diversity, suggesting ancient origins.
    • The PSIMAP network demonstrates high robustness and fault-tolerance.

    Conclusions:

    • The P-loop containing nucleotide triphosphate hydrolases superfamily is identified as the most connected and taxonomically diverse.
    • This superfamily acts as the network's barycenter and an articulation vertex, highlighting its critical role.
    • Graph-theoretic and taxonomic analysis of PSIMAP advances understanding of protein function and molecular evolution.