title: Free-energy distribution of binary protein-protein binding suggests cross-species interactome differences.
abstract: Major advances in large-scale yeast two-hybrid screening have provided a global view of binary protein-protein interactions across species as dissimilar as human, yeast, and bacteria. Remarkably, these analyses have revealed that all species studied have a degree distribution of protein-protein binding that is approximately scale-free (varies as a power law) even though their evolutionary divergence times differ by billions of years. The universal power law shows only the surface of the rich information harbored by these high-throughput data. We develop a detailed mathematical model of the protein-protein interaction network based on association free energy, the biochemical quantity that determines protein-protein interaction strength. This model reproduces the degree distribution of all of the large-scale yeast two-hybrid data sets available and allows us to extract the distribution of free energy, the likelihood that a pair of proteins of a given species will bind. We find that across-species interactomes have significant differences that reflect the strengths of the protein-protein interaction. Our results identify a global evolutionary shift: more evolved organisms have weaker binary protein-protein binding. This result is consistent with the evolution of increased protein unfoldedness and challenges the dogma that only specific protein-protein interactions can be biologically functional.
authors.affiliation: Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA.
authors.forename: Yi Y
authors.initials: YY
authors.lastname: Shi
authors.forename: Gerald A
authors.initials: GA
authors.lastname: Miller
authors.forename: Hong
authors.initials: H
authors.lastname: Qian
authors.forename: Karol
authors.initials: K
authors.lastname: Bomsztyk
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D006801:Humans; D008433:Mathematics; D008962:Models, Theoretical; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D013816:Thermodynamics; D020798:Two-Hybrid System Techniques
chemical_list: D011506:Proteins