dorsal/arxiv
View SchemaThe architecture of the protein domain universe
| Authors | Nikolay V. Dokholyan |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0408006 |
| URL | https://arxiv.org/abs/q-bio/0408006 |
Abstract
Understanding the design of the universe of protein structures may provide insights into protein evolution. We study the architecture of the protein domain universe, which has been found to poses peculiar scale-free properties (Dokholyan et al., Proc. Natl. Acad. Sci. USA 99: 14132-14136 (2002)). We examine the origin of these scale-free properties of the graph of protein domain structures (PDUG) and determine that that the PDUG is not modular, i.e. it does not consist of modules with uniform properties. Instead, we find the PDUG to be self-similar at all scales. We further characterize the PDUG architecture by studying the properties of the hub nodes that are responsible for the scale-free connectivity of the PDUG. We introduce a measure of the betweenness centrality of protein domains in the PDUG and find a power-law distribution of the betweenness centrality values. The scale-free distribution of hubs in the protein universe suggests that a set of specific statistical mechanics models, such as the self-organized criticality model, can potentially identify the principal driving forces of molecular evolution. We also find a gatekeeper protein domain, removal of which partitions the largest cluster into two large sub-clusters. We suggest that the loss of such gatekeeper protein domains in the course of evolution is responsible for the creation of new fold families.
{
"annotation_id": "d5c75d76-4315-43b2-8581-c432f6f5057b",
"date_created": "2026-03-02T18:01:31.875000Z",
"date_modified": "2026-03-02T18:01:31.875000Z",
"file_hash": "da0b3c9224fe194b2bae119cd82dc454987ace1244d338997241469eeed6d03e",
"private": false,
"record": {
"abstract": "Understanding the design of the universe of protein structures may provide\ninsights into protein evolution. We study the architecture of the protein\ndomain universe, which has been found to poses peculiar scale-free properties\n(Dokholyan et al., Proc. Natl. Acad. Sci. USA 99: 14132-14136 (2002)). We\nexamine the origin of these scale-free properties of the graph of protein\ndomain structures (PDUG) and determine that that the PDUG is not modular, i.e.\nit does not consist of modules with uniform properties. Instead, we find the\nPDUG to be self-similar at all scales. We further characterize the PDUG\narchitecture by studying the properties of the hub nodes that are responsible\nfor the scale-free connectivity of the PDUG. We introduce a measure of the\nbetweenness centrality of protein domains in the PDUG and find a power-law\ndistribution of the betweenness centrality values. The scale-free distribution\nof hubs in the protein universe suggests that a set of specific statistical\nmechanics models, such as the self-organized criticality model, can potentially\nidentify the principal driving forces of molecular evolution. We also find a\ngatekeeper protein domain, removal of which partitions the largest cluster into\ntwo large sub-clusters. We suggest that the loss of such gatekeeper protein\ndomains in the course of evolution is responsible for the creation of new fold\nfamilies.",
"arxiv_id": "q-bio/0408006",
"authors": [
"Nikolay V. Dokholyan"
],
"categories": [
"q-bio.MN",
"cond-mat.stat-mech",
"q-bio.BM"
],
"title": "The architecture of the protein domain universe",
"url": "https://arxiv.org/abs/q-bio/0408006"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "6e036256-46e1-482b-820f-f20c4d07122e",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}