dorsal/arxiv
View SchemaFolding Trp-cage to NMR resolution native structure using a coarse-grained model
| Authors | Feng Ding, Sergey V. Buldyrev, Nikolay V. Dokholyan |
|---|---|
| Categories | |
| ArXiv ID | physics/0405134 |
| URL | https://arxiv.org/abs/physics/0405134 |
| DOI | 10.1529/biophysj.104.046375 |
Abstract
We develop a coarse-grained protein model with a simplified amino acid interaction potential. We perform discrete molecular dynamics folding simulations of a small 20 residue protein - Trp-cage - from a fully extended conformation. We demonstrate the ability of the Trp-cage model to consistently reach conformations within 2angstrom backbone root-mean-square distance (RMSD) from the corresponding NMR structures. The minimum RMSD of Trp-cage conformations in the simulation can be smaller than 1.00angstrom. Our findings suggest that, at least for the case of Trp-cage, a detailed all-atom protein model with a physical molecular mechanics force field is not necessary to reach the native state of a protein. Our results also suggest that the success folding Trp-cage in our simulations and in the reported all-atom molecular mechanics simulations studies may be mainly due to the special stabilizing features specific to this miniprotein.
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"abstract": "We develop a coarse-grained protein model with a simplified amino acid\ninteraction potential. We perform discrete molecular dynamics folding\nsimulations of a small 20 residue protein - Trp-cage - from a fully extended\nconformation. We demonstrate the ability of the Trp-cage model to consistently\nreach conformations within 2angstrom backbone root-mean-square distance (RMSD)\nfrom the corresponding NMR structures. The minimum RMSD of Trp-cage\nconformations in the simulation can be smaller than 1.00angstrom. Our findings\nsuggest that, at least for the case of Trp-cage, a detailed all-atom protein\nmodel with a physical molecular mechanics force field is not necessary to reach\nthe native state of a protein. Our results also suggest that the success\nfolding Trp-cage in our simulations and in the reported all-atom molecular\nmechanics simulations studies may be mainly due to the special stabilizing\nfeatures specific to this miniprotein.",
"arxiv_id": "physics/0405134",
"authors": [
"Feng Ding",
"Sergey V. Buldyrev",
"Nikolay V. Dokholyan"
],
"categories": [
"physics.bio-ph",
"cond-mat.other",
"cond-mat.soft",
"cond-mat.stat-mech",
"physics.comp-ph",
"q-bio.OT"
],
"doi": "10.1529/biophysj.104.046375",
"title": "Folding Trp-cage to NMR resolution native structure using a coarse-grained model",
"url": "https://arxiv.org/abs/physics/0405134"
},
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