dorsal/arxiv
View SchemaAll-atom ab initio folding of a diverse set of proteins
| Authors | Jae Shick Yang, William W. Chen, Jeffrey Skolnick, Eugene I. Shakhnovich |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0611086 |
| URL | https://arxiv.org/abs/q-bio/0611086 |
Abstract
Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here, we show successful all-atom ab initio folding of a representative diverse set of proteins, using a minimalist transferable energy model that consists of two-body atom-atom interactions, hydrogen-bonding, and a local sequence energy term that models sequence-specific chain stiffness. Starting from a random coil, the native-like structure was observed during replica exchange Monte Carlo (REMC) simulation for most proteins regardless of their structural classes; the lowest energy structure was close to native- in the range of 2-6 A root-mean-square deviation (RMSD). Our results demonstrate that the successful all-atom folding of a protein chain to its native state is governed by only a few crucial energetic terms.
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"abstract": "Natural proteins fold to a unique, thermodynamically dominant state. Modeling\nof the folding process and prediction of the native fold of proteins are two\nmajor unsolved problems in biophysics. Here, we show successful all-atom ab\ninitio folding of a representative diverse set of proteins, using a minimalist\ntransferable energy model that consists of two-body atom-atom interactions,\nhydrogen-bonding, and a local sequence energy term that models\nsequence-specific chain stiffness. Starting from a random coil, the native-like\nstructure was observed during replica exchange Monte Carlo (REMC) simulation\nfor most proteins regardless of their structural classes; the lowest energy\nstructure was close to native- in the range of 2-6 A root-mean-square deviation\n(RMSD). Our results demonstrate that the successful all-atom folding of a\nprotein chain to its native state is governed by only a few crucial energetic\nterms.",
"arxiv_id": "q-bio/0611086",
"authors": [
"Jae Shick Yang",
"William W. Chen",
"Jeffrey Skolnick",
"Eugene I. Shakhnovich"
],
"categories": [
"q-bio.BM"
],
"title": "All-atom ab initio folding of a diverse set of proteins",
"url": "https://arxiv.org/abs/q-bio/0611086"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "83cac6d9-00ba-4edb-b1ff-ba34abf58cfc",
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