Complexity of Protein-Protein Interaction Networks, Complexes, and Pathways

Abstract

The focus of proteomic research in developing experimental techniques for protein identification and interaction studies is shifting from individual proteins to their organization in reaction pathways, complexes, and networks, i.e., to the proteome-the large-scale network comprising all protein-protein interactions in a cell, tissue, or organism. The number of complete proteomes in accessible databases exceeds 100 (1) thus making possible proteome-wide and across-proteomes analyses. Such a systemic approach offers a view of the biological machine as a whole, revealing important new details of its work. Thus, one could regard aging and diseases as specific patterns of protein network degradation and, vice versa, evolutionary beneficial factors as creating patterns of larger proteome complexity. Medicines’ side effects could be analyzed in terms of the extremely high network connectivity, thus orienting the search for new medicines toward protein complexes, rather than individual compounds (2). Potential drug and marker candidates could be identified proceeding from protein connectivity and centrality patterns.