dorsal/arxiv
View SchemaA simple physical model for scaling in protein-protein interaction networks
| Authors | Eric J. Deeds, Orr Ashenberg, Eugene I. Shakhnovich |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0509001 |
| URL | https://arxiv.org/abs/q-bio/0509001 |
| DOI | 10.1073/pnas.0509715102 |
Abstract
It has recently been demonstrated that many biological networks exhibit a scale-free topology where the probability of observing a node with a certain number of edges (k) follows a power law: i.e. p(k) ~ k^-g. This observation has been reproduced by evolutionary models. Here we consider the network of protein-protein interactions and demonstrate that two published independent measurements of these interactions produce graphs that are only weakly correlated with one another despite their strikingly similar topology. We then propose a physical model based on the fundamental principle that (de)solvation is a major physical factor in protein-protein interactions. This model reproduces not only the scale-free nature of such graphs but also a number of higher-order correlations in these networks. A key support of the model is provided by the discovery of a significant correlation between number of interactions made by a protein and the fraction of hydrophobic residues on its surface. The model presented in this paper represents the first physical model for experimentally determined protein-protein interactions that comprehensively reproduces the topological features of interaction networks. These results have profound implications for understanding not only protein-protein interactions but also other types of scale-free networks.
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"abstract": "It has recently been demonstrated that many biological networks exhibit a\nscale-free topology where the probability of observing a node with a certain\nnumber of edges (k) follows a power law: i.e. p(k) ~ k^-g. This observation has\nbeen reproduced by evolutionary models. Here we consider the network of\nprotein-protein interactions and demonstrate that two published independent\nmeasurements of these interactions produce graphs that are only weakly\ncorrelated with one another despite their strikingly similar topology. We then\npropose a physical model based on the fundamental principle that (de)solvation\nis a major physical factor in protein-protein interactions. This model\nreproduces not only the scale-free nature of such graphs but also a number of\nhigher-order correlations in these networks. A key support of the model is\nprovided by the discovery of a significant correlation between number of\ninteractions made by a protein and the fraction of hydrophobic residues on its\nsurface. The model presented in this paper represents the first physical model\nfor experimentally determined protein-protein interactions that comprehensively\nreproduces the topological features of interaction networks. These results have\nprofound implications for understanding not only protein-protein interactions\nbut also other types of scale-free networks.",
"arxiv_id": "q-bio/0509001",
"authors": [
"Eric J. Deeds",
"Orr Ashenberg",
"Eugene I. Shakhnovich"
],
"categories": [
"q-bio.MN",
"q-bio.BM"
],
"doi": "10.1073/pnas.0509715102",
"title": "A simple physical model for scaling in protein-protein interaction networks",
"url": "https://arxiv.org/abs/q-bio/0509001"
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