title: Relating three-dimensional structures to protein networks provides evolutionary insights.
abstract: Most studies of protein networks operate on a high level of abstraction, neglecting structural and chemical aspects of each interaction. Here, we characterize interactions by using atomic-resolution information from three-dimensional protein structures. We find that some previously recognized relationships between network topology and genomic features (e.g., hubs tending to be essential proteins) are actually more reflective of a structural quantity, the number of distinct binding interfaces. Subdividing hubs with respect to this quantity provides insight into their evolutionary rate and indicates that additional mechanisms of network growth are active in evolution (beyond effective preferential attachment through gene duplication).
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
authors.forename: Philip M
authors.initials: PM
authors.lastname: Kim
authors.forename: Long J
authors.initials: LJ
authors.lastname: Lu
authors.forename: Yu
authors.initials: Y
authors.lastname: Xia
authors.forename: Mark B
authors.initials: MB
authors.lastname: Gerstein
mesh_terms: D019943:Amino Acid Substitution; D001665:Binding Sites; D019295:Computational Biology; D019143:Evolution, Molecular; D020440:Gene Duplication; D053858:Metabolic Networks and Pathways; D009154:Mutation; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins