dorsal/arxiv
View SchemaFolding thermodynamics of model four-strand antiparallel beta-sheet proteins
| Authors | Hyunbum Jang, Carol K. Hall, Yaoqi Zhou |
|---|---|
| Categories | |
| ArXiv ID | physics/0106019 |
| URL | https://arxiv.org/abs/physics/0106019 |
| DOI | 10.1016/S0006-3495(02)75428-3 |
Abstract
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed for different sizes of the bias gap g, an artificial measure of a model protein's preference for its native state. The thermodynamic transition temperatures are obtained by calculating the squared radius of gyration, the root-mean-squared pair separation fluctuation, the specific heat, the internal energy of the system, and the Lindemann disorder parameter. In spite of the simplicity, the protein-like heteropolymers have shown a complex set of protein transitions as observed in experimental studies. Starting from high temperature, these transitions include a collapse transition, a disordered-to-ordered globule transition, a folding transition, and a liquid-to-solid transition. These transitions strongly depend on the native-state geometry of the model proteins and the size of the bias gap. A strong transition from the disordered globule state to the ordered globule state with large energy change and a weak transition from the ordered globule state to the native state with small energy change were observed for the large gap models. For the small gap models no native structures were observed at any temperature, all three beta-sheet proteins fold into a partially-ordered globule state which is geometrically different from the native state. For small bias gaps at even lower temperatures, all protein motions are frozen indicating an inactive solid-like phase.
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"abstract": "The thermodynamic properties for three different types of off-lattice\nfour-strand beta-sheet protein models interacting via a hybrid Go-type\npotential have been investigated. Discontinuous molecular dynamic simulations\nhave been performed for different sizes of the bias gap g, an artificial\nmeasure of a model protein\u0027s preference for its native state. The thermodynamic\ntransition temperatures are obtained by calculating the squared radius of\ngyration, the root-mean-squared pair separation fluctuation, the specific heat,\nthe internal energy of the system, and the Lindemann disorder parameter. In\nspite of the simplicity, the protein-like heteropolymers have shown a complex\nset of protein transitions as observed in experimental studies. Starting from\nhigh temperature, these transitions include a collapse transition, a\ndisordered-to-ordered globule transition, a folding transition, and a\nliquid-to-solid transition. These transitions strongly depend on the\nnative-state geometry of the model proteins and the size of the bias gap. A\nstrong transition from the disordered globule state to the ordered globule\nstate with large energy change and a weak transition from the ordered globule\nstate to the native state with small energy change were observed for the large\ngap models. For the small gap models no native structures were observed at any\ntemperature, all three beta-sheet proteins fold into a partially-ordered\nglobule state which is geometrically different from the native state. For small\nbias gaps at even lower temperatures, all protein motions are frozen indicating\nan inactive solid-like phase.",
"arxiv_id": "physics/0106019",
"authors": [
"Hyunbum Jang",
"Carol K. Hall",
"Yaoqi Zhou"
],
"categories": [
"physics.bio-ph",
"physics.comp-ph",
"q-bio"
],
"doi": "10.1016/S0006-3495(02)75428-3",
"title": "Folding thermodynamics of model four-strand antiparallel beta-sheet proteins",
"url": "https://arxiv.org/abs/physics/0106019"
},
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