Bioinformatics analysis of PTM-modified protein interaction networks and complexes

Abstract

Normal cellular functioning is maintained by macromolecular machines that control both core and specialized molecular tasks. These machines are in large part multi-subunit protein complexes that undergo regulation at multiple levels, from expression of requisite components to a vast array of post-translational modifications (PTMs). PTMs such as phosphorylation, ubiquitination, and acetylation currently number more than 200,000 in the human proteome and function within all molecular pathways. Here we provide a framework for systematically studying these PTMs in the context of global protein–protein interaction networks. This analytical framework allows insight into which functions specific PTMs tend to cluster in, and furthermore which complexes either single or multiple PTM signaling pathways converge on.