dorsal/arxiv
View SchemaThe effects of non-native interactions on protein folding rates: Theory and simulation
| Authors | C. Clementi, S. S. Plotkin |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0407023 |
| URL | https://arxiv.org/abs/q-bio/0407023 |
| Journal | Protein Science 2004 13: 1750-1766 |
Abstract
Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free energy barrier. We present an analytic theory to account for the modification on the free energy landscape upon introduction of non-native contacts, added as a perturbation to the strong native interactions driving folding. Our theory predicts a rate-enhancement regime at fixed temperature, under the introduction of weak, non-native interactions. We have thoroughly tested this theoretical prediction with simulations of a coarse-grained protein model, by employing an off-lattice $C_\alpha$ model of the src-SH3 domain. The strong agreement between results from simulations and theory confirm the non trivial result that a relatively small amount of non-native interaction energy can actually assist the folding to the native structure.
{
"annotation_id": "6cb7e38b-f261-4d03-abe8-49c6191210ac",
"date_created": "2026-03-02T18:01:31.873000Z",
"date_modified": "2026-03-02T18:01:31.873000Z",
"file_hash": "edc6f0e914f1beba5d8881e0c7e56e3f44af277272a94a17ff27d2323488d376",
"private": false,
"record": {
"abstract": "Proteins are minimally frustrated polymers. However, for realistic protein\nmodels non-native interactions must be taken into account. In this paper we\nanalyze the effect of non-native interactions on the folding rate and on the\nfolding free energy barrier. We present an analytic theory to account for the\nmodification on the free energy landscape upon introduction of non-native\ncontacts, added as a perturbation to the strong native interactions driving\nfolding. Our theory predicts a rate-enhancement regime at fixed temperature,\nunder the introduction of weak, non-native interactions. We have thoroughly\ntested this theoretical prediction with simulations of a coarse-grained protein\nmodel, by employing an off-lattice $C_\\alpha$ model of the src-SH3 domain. The\nstrong agreement between results from simulations and theory confirm the non\ntrivial result that a relatively small amount of non-native interaction energy\ncan actually assist the folding to the native structure.",
"arxiv_id": "q-bio/0407023",
"authors": [
"C. Clementi",
"S. S. Plotkin"
],
"categories": [
"q-bio.BM"
],
"journal_ref": "Protein Science 2004 13: 1750-1766",
"title": "The effects of non-native interactions on protein folding rates: Theory and simulation",
"url": "https://arxiv.org/abs/q-bio/0407023"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "36710dc8-ec95-4da0-88e9-3a560dd237d6",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}