dorsal/arxiv
View SchemaStructural similarity enhances interaction propensity of proteins
| Authors | D. B. Lukatsky, B. E. Shakhnovich, J. Mintseris, E. I. Shakhnovich |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0609048 |
| URL | https://arxiv.org/abs/q-bio/0609048 |
Abstract
We study statistical properties of interacting protein-like surfaces and predict two strong, related effects: (i) statistically enhanced self-attraction of proteins; (ii) statistically enhanced attraction of proteins with similar structures. The effects originate in the fact that the probability to find a pattern self-match between two identical, even randomly organized interacting protein surfaces is always higher compared with the probability for a pattern match between two different, promiscuous protein surfaces. This theoretical finding explains statistical prevalence of homodimers in protein-protein interaction networks reported earlier. Further, our findings are confirmed by the analysis of curated database of protein complexes that showed highly statistically significant overrepresentation of dimers formed by structurally similar proteins with highly divergent sequences (superfamily heterodimers). We predict that significant fraction of heterodimers evolved from homodimers with the negative design evolutionary pressure applied against promiscuous homodimer formation. This is achieved through the formation of highly specific contacts formed by charged residues as demonstrated both in model and real superfamily heterodimers
{
"annotation_id": "05e99820-cca1-4d38-bf60-0d80dc7caf66",
"date_created": "2026-03-02T18:01:35.517000Z",
"date_modified": "2026-03-02T18:01:35.517000Z",
"file_hash": "128f328d299fcc858f8e38f8d3f43c6b2987cbc5272cd5c8d0b66606a1c0c85a",
"private": false,
"record": {
"abstract": "We study statistical properties of interacting protein-like surfaces and\npredict two strong, related effects: (i) statistically enhanced self-attraction\nof proteins; (ii) statistically enhanced attraction of proteins with similar\nstructures. The effects originate in the fact that the probability to find a\npattern self-match between two identical, even randomly organized interacting\nprotein surfaces is always higher compared with the probability for a pattern\nmatch between two different, promiscuous protein surfaces. This theoretical\nfinding explains statistical prevalence of homodimers in protein-protein\ninteraction networks reported earlier. Further, our findings are confirmed by\nthe analysis of curated database of protein complexes that showed highly\nstatistically significant overrepresentation of dimers formed by structurally\nsimilar proteins with highly divergent sequences (superfamily heterodimers). We\npredict that significant fraction of heterodimers evolved from homodimers with\nthe negative design evolutionary pressure applied against promiscuous homodimer\nformation. This is achieved through the formation of highly specific contacts\nformed by charged residues as demonstrated both in model and real superfamily\nheterodimers",
"arxiv_id": "q-bio/0609048",
"authors": [
"D. B. Lukatsky",
"B. E. Shakhnovich",
"J. Mintseris",
"E. I. Shakhnovich"
],
"categories": [
"q-bio.BM"
],
"title": "Structural similarity enhances interaction propensity of proteins",
"url": "https://arxiv.org/abs/q-bio/0609048"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "dfb82391-f9c8-4a4a-9562-31816190d50a",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}