dorsal/arxiv
View SchemaGeometrical model for the native-state folds of proteins
| Authors | Trinh X. Hoang, Antonio Trovato, Flavio Seno, Jayanth R. Banavar, Amos Maritan |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0505032 |
| URL | https://arxiv.org/abs/q-bio/0505032 |
| DOI | 10.1016/j.bpc.2004.12.036 |
| Journal | Biophys. Chem. 115 (2005), 289-294 |
Abstract
We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a chain molecule, the geometrical and energetic constraints placed by the hydrogen bonds and sterics, and the role played by hydrophobicity. Within this framework, marginally compact conformations resembling the native state folds of proteins emerge as broad competing minima in the free energy landscape even for a homopolymer. Here we show how the introduction of sequence heterogeneity using a simple scheme of just two types of amino acids, hydrophobic (H) and polar (P), and sequence design allows a selected putative native fold to become the free energy minimum at low temperature. The folding transition exhibits thermodynamic cooperativity, if one neglects the degeneracy between two different low energy conformations sharing the same fold topology.
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"abstract": "We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci.\nUSA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which\nincorporates, in an approximate manner, several key features such as the\ninherent anisotropy of a chain molecule, the geometrical and energetic\nconstraints placed by the hydrogen bonds and sterics, and the role played by\nhydrophobicity. Within this framework, marginally compact conformations\nresembling the native state folds of proteins emerge as broad competing minima\nin the free energy landscape even for a homopolymer. Here we show how the\nintroduction of sequence heterogeneity using a simple scheme of just two types\nof amino acids, hydrophobic (H) and polar (P), and sequence design allows a\nselected putative native fold to become the free energy minimum at low\ntemperature. The folding transition exhibits thermodynamic cooperativity, if\none neglects the degeneracy between two different low energy conformations\nsharing the same fold topology.",
"arxiv_id": "q-bio/0505032",
"authors": [
"Trinh X. Hoang",
"Antonio Trovato",
"Flavio Seno",
"Jayanth R. Banavar",
"Amos Maritan"
],
"categories": [
"q-bio.BM"
],
"doi": "10.1016/j.bpc.2004.12.036",
"journal_ref": "Biophys. Chem. 115 (2005), 289-294",
"title": "Geometrical model for the native-state folds of proteins",
"url": "https://arxiv.org/abs/q-bio/0505032"
},
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