title: A complex-centric view of protein network evolution.
abstract: The recent availability of protein-protein interaction networks for several species makes it possible to study protein complexes in an evolutionary context. In this article, we present a novel network-based framework for reconstructing the evolutionary history of protein complexes. Our analysis is based on generalizing evolutionary measures for single proteins to the level of whole subnetworks, comprehensively considering a broad set of computationally derived complexes and accounting for both sequence and interaction changes. Specifically, we compute sets of orthologous complexes across species, and use these to derive evolutionary rate and age measures for protein complexes. We observe significant correlations between the evolutionary properties of a complex and those of its member proteins, suggesting that protein complexes form early in evolution and evolve as coherent units. Additionally, our approach enables us to directly quantify the extent to which gene duplication has played a role in the evolution of complexes. We find that about one quarter of the sets of orthologous complexes have originated from evolutionary cores of homodimers that underwent duplication and divergence, testifying to the important role of gene duplication in protein complex evolution.
authors.affiliation: The Blavatnik School of Computer Science, Department of Molecular Microbiology and Biotechnology and School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel.
authors.forename: Nir
authors.initials: N
authors.lastname: Yosef
authors.forename: Martin
authors.initials: M
authors.lastname: Kupiec
authors.forename: Eytan
authors.initials: E
authors.lastname: Ruppin
authors.forename: Roded
authors.initials: R
authors.lastname: Sharan
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology; D019143:Evolution, Molecular; D020440:Gene Duplication; D006801:Humans; D046912:Multiprotein Complexes / Q000235:genetics*; D025941:Protein Interaction Mapping
chemical_list: D046912:Multiprotein Complexes