dorsal/arxiv
View SchemaFree-energy distribution of binary protein-protein binding suggests cross-species interactome differences
| Authors | Yi Y. Shi, Gerald A. Miller, Hong Qian, Karol Bomsztyk |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0607046 |
| URL | https://arxiv.org/abs/q-bio/0607046 |
| DOI | 10.1073/pnas.0604316103 |
| Journal | PNAS 103, 11527- 11532 (2006); Aug 1, 2006 no 31 |
Abstract
Major advances in large-scale yeast two hybrid (Y2H) 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 Y2H 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..
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"abstract": "Major advances in large-scale yeast two hybrid (Y2H) screening have provided\na global view of binary protein-protein interactions across species as\ndissimilar as human, yeast, and bacteria. Remarkably, these analyses have\nrevealed that all species studied have a degree distribution of protein-protein\nbinding that is approximately scale-free (varies as a power law) even though\ntheir evolutionary divergence times differ by billions of years. The universal\npower-law shows only the surface of the rich information harbored by these\nhigh-throughput data. We develop a detailed mathematical model of the\nprotein-protein interaction network based on association free energy, the\nbiochemical quantity that determines protein-protein interaction strength. This\nmodel reproduces the degree distribution of all of the large-scale Y2H data\nsets available and allows us to extract the distribution of free energy, the\nlikelihood that a pair of proteins of a given species will bind. We find that\nacross-species interactomes have significant differences that reflect the\nstrengths of the protein-protein interaction. Our results identify a global\nevolutionary shift: more evolved organisms have weaker binary protein-protein\nbinding. This result is consistent with the evolution of increased protein\nunfoldedness and challenges the dogma that only specific protein-protein\ninteractions can be biologically functional..",
"arxiv_id": "q-bio/0607046",
"authors": [
"Yi Y. Shi",
"Gerald A. Miller",
"Hong Qian",
"Karol Bomsztyk"
],
"categories": [
"q-bio.QM",
"cond-mat.stat-mech",
"physics.bio-ph",
"q-bio.MN"
],
"doi": "10.1073/pnas.0604316103",
"journal_ref": "PNAS 103, 11527- 11532 (2006); Aug 1, 2006 no 31",
"title": "Free-energy distribution of binary protein-protein binding suggests cross-species interactome differences",
"url": "https://arxiv.org/abs/q-bio/0607046"
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