dorsal/arxiv
View SchemaBinding properties and evolution of homodimers in protein-protein interaction networks
| Authors | Iaroslav Ispolatov, Anton Yuryev, Ilya Mazo, Sergei Maslov |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0501004 |
| URL | https://arxiv.org/abs/q-bio/0501004 |
| Journal | Nucleic Acids Research 2005 33(11):3629-3635 |
Abstract
We demonstrate that Protein-Protein Interaction (PPI) networks in several eucaryotic organisms contain significantly more self-interacting proteins than expected if such homodimers randomly appeared in the course of the evolution. We also show that on average homodimers have twice as many interaction partners than non-self-interacting proteins. More specifically the likelihood of a protein to physically interact with itself was found to be proportional to the total number of its binding partners. These properties of dimers are are in agreement with a phenomenological model in which individual proteins differ from each other by the degree of their ``stickiness'' or general propensity towards interaction with other proteins including oneself. A duplication of self-interacting proteins creates a pair of paralogous proteins interacting with each other. We show that such pairs occur more frequently than could be explained by pure chance alone. Similar to homodimers, proteins involved in heterodimers with their paralogs on average have twice as many interacting partners than the rest of the network. The likelihood of a pair of paralogous proteins to interact with each other was also shown to decrease with their sequence similarity. This all points to the conclusion that most of interactions between paralogs are inherited from ancestral homodimeric proteins, rather than established de novo after the duplication. We finally discuss possible implications of our empirical observations from functional and evolutionary standpoints.
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"abstract": "We demonstrate that Protein-Protein Interaction (PPI) networks in several\neucaryotic organisms contain significantly more self-interacting proteins than\nexpected if such homodimers randomly appeared in the course of the evolution.\nWe also show that on average homodimers have twice as many interaction partners\nthan non-self-interacting proteins. More specifically the likelihood of a\nprotein to physically interact with itself was found to be proportional to the\ntotal number of its binding partners. These properties of dimers are are in\nagreement with a phenomenological model in which individual proteins differ\nfrom each other by the degree of their ``stickiness\u0027\u0027 or general propensity\ntowards interaction with other proteins including oneself. A duplication of\nself-interacting proteins creates a pair of paralogous proteins interacting\nwith each other. We show that such pairs occur more frequently than could be\nexplained by pure chance alone. Similar to homodimers, proteins involved in\nheterodimers with their paralogs on average have twice as many interacting\npartners than the rest of the network. The likelihood of a pair of paralogous\nproteins to interact with each other was also shown to decrease with their\nsequence similarity. This all points to the conclusion that most of\ninteractions between paralogs are inherited from ancestral homodimeric\nproteins, rather than established de novo after the duplication. We finally\ndiscuss possible implications of our empirical observations from functional and\nevolutionary standpoints.",
"arxiv_id": "q-bio/0501004",
"authors": [
"Iaroslav Ispolatov",
"Anton Yuryev",
"Ilya Mazo",
"Sergei Maslov"
],
"categories": [
"q-bio.GN",
"cond-mat.dis-nn",
"q-bio.MN"
],
"journal_ref": "Nucleic Acids Research 2005 33(11):3629-3635",
"title": "Binding properties and evolution of homodimers in protein-protein interaction networks",
"url": "https://arxiv.org/abs/q-bio/0501004"
},
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