dorsal/arxiv
View SchemaLocal Interactions and Protein Folding: A 3D Off-Lattice Approach
| Authors | Anders Irbäck, Carsten Peterson, Frank Potthast, Ola Sommelius |
|---|---|
| Categories | |
| ArXiv ID | physics/9610010 |
| URL | https://arxiv.org/abs/physics/9610010 |
| DOI | 10.1063/1.474357 |
| Journal | J. Chem. Phys. 107 (1997) 273-282 |
Abstract
The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobic and hydrophilic. In absence of local interactions, native structure formation does not occur for the temperatures considered. By including sequence independent local interactions, which qualitatively reproduce local properties of functional proteins, the dominance of a native state for many sequences is observed. As in lattice model approaches, folding takes place by gradual compactification, followed by a sequence dependent folding transition. Our results differ from lattice approaches in that bimodal energy distributions are not observed and that high folding temperatures are accompanied by relatively low temperatures for the peak of the specific heat. Also, in contrast to earlier studies using lattice models, our results convincingly demonstrate that one does not need more than two types of residues to generate sequences with good thermodynamic folding properties in three dimensions.
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"abstract": "The thermodynamic behavior of a three-dimensional off-lattice model for\nprotein folding is probed. The model has only two types of residues,\nhydrophobic and hydrophilic. In absence of local interactions, native structure\nformation does not occur for the temperatures considered. By including sequence\nindependent local interactions, which qualitatively reproduce local properties\nof functional proteins, the dominance of a native state for many sequences is\nobserved. As in lattice model approaches, folding takes place by gradual\ncompactification, followed by a sequence dependent folding transition. Our\nresults differ from lattice approaches in that bimodal energy distributions are\nnot observed and that high folding temperatures are accompanied by relatively\nlow temperatures for the peak of the specific heat. Also, in contrast to\nearlier studies using lattice models, our results convincingly demonstrate that\none does not need more than two types of residues to generate sequences with\ngood thermodynamic folding properties in three dimensions.",
"arxiv_id": "physics/9610010",
"authors": [
"Anders Irb\u00e4ck",
"Carsten Peterson",
"Frank Potthast",
"Ola Sommelius"
],
"categories": [
"physics.chem-ph",
"cond-mat",
"hep-lat"
],
"doi": "10.1063/1.474357",
"journal_ref": "J. Chem. Phys. 107 (1997) 273-282",
"title": "Local Interactions and Protein Folding: A 3D Off-Lattice Approach",
"url": "https://arxiv.org/abs/physics/9610010"
},
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