dorsal/arxiv
View SchemaLoop-closure events during protein folding: Rationalizing the shape of Phi-value distributions
| Authors | Thomas R. Weikl |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0502016 |
| URL | https://arxiv.org/abs/q-bio/0502016 |
Abstract
In the past years, the folding kinetics of many small single-domain proteins has been characterized by mutational Phi-value analysis. In this article, a simple, essentially parameter-free model is introduced which derives folding routes from native structures by minimizing the entropic loop-closure cost during folding. The model predicts characteristic folding sequences of structural elements such as helices and beta-strand pairings. Based on few simple rules, the kinetic impact of these structural elements is estimated from the routes and compared to average experimental Phi-values for the helices and strands of 15 small, well-characterized proteins. The comparison leads on average to a correlation coefficient of 0.62 for all proteins with polarized Phi-value distributions, and 0.74 if distributions with negative average Phi-values are excluded. The diffuse Phi-value distributions of the remaining proteins are reproduced correctly. The model shows that Phi-value distributions, averaged over secondary structural elements, can often be traced back to entropic loop-closure events, but also indicates energetic preferences in the case of a few proteins governed by parallel folding processes.
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"abstract": "In the past years, the folding kinetics of many small single-domain proteins\nhas been characterized by mutational Phi-value analysis. In this article, a\nsimple, essentially parameter-free model is introduced which derives folding\nroutes from native structures by minimizing the entropic loop-closure cost\nduring folding. The model predicts characteristic folding sequences of\nstructural elements such as helices and beta-strand pairings. Based on few\nsimple rules, the kinetic impact of these structural elements is estimated from\nthe routes and compared to average experimental Phi-values for the helices and\nstrands of 15 small, well-characterized proteins. The comparison leads on\naverage to a correlation coefficient of 0.62 for all proteins with polarized\nPhi-value distributions, and 0.74 if distributions with negative average\nPhi-values are excluded. The diffuse Phi-value distributions of the remaining\nproteins are reproduced correctly. The model shows that Phi-value\ndistributions, averaged over secondary structural elements, can often be traced\nback to entropic loop-closure events, but also indicates energetic preferences\nin the case of a few proteins governed by parallel folding processes.",
"arxiv_id": "q-bio/0502016",
"authors": [
"Thomas R. Weikl"
],
"categories": [
"q-bio.BM",
"cond-mat.soft"
],
"title": "Loop-closure events during protein folding: Rationalizing the shape of Phi-value distributions",
"url": "https://arxiv.org/abs/q-bio/0502016"
},
"schema_id": "dorsal/arxiv",
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