dorsal/arxiv
View SchemaProtein folding dynamics via quantification of kinematic energy landscape
| Authors | Sëma Kachalo, Hsiao-Mei Lu, Jie Liang |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0601018 |
| URL | https://arxiv.org/abs/q-bio/0601018 |
| DOI | 10.1103/PhysRevLett.96.058106 |
Abstract
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of occupancy of all 802,075 conformations of 16-mers over 7-orders of time span. We find that (i) folding rates of these protein-like sequences of same length can differ by 4-orders of magnitude, (ii) folding rates of sequences of the same conformation can differ by a factor of 190, and (iii) parameters of the native structures, designability, and thermodynamic properties are weak predictors of the folding rates, rather, basin analysis of the kinematic energy landscape defined by the moves can provide excellent account of the observed folding rates.
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"abstract": "We study folding dynamics of protein-like sequences on square lattice using\nphysical move set that exhausts all possible conformational changes. By\nanalytically solving the master equation, we follow the time-dependent\nprobabilities of occupancy of all 802,075 conformations of 16-mers over\n7-orders of time span. We find that (i) folding rates of these protein-like\nsequences of same length can differ by 4-orders of magnitude, (ii) folding\nrates of sequences of the same conformation can differ by a factor of 190, and\n(iii) parameters of the native structures, designability, and thermodynamic\nproperties are weak predictors of the folding rates, rather, basin analysis of\nthe kinematic energy landscape defined by the moves can provide excellent\naccount of the observed folding rates.",
"arxiv_id": "q-bio/0601018",
"authors": [
"S\u00ebma Kachalo",
"Hsiao-Mei Lu",
"Jie Liang"
],
"categories": [
"q-bio.BM",
"cond-mat.soft",
"cond-mat.stat-mech",
"physics.bio-ph",
"physics.chem-ph"
],
"doi": "10.1103/PhysRevLett.96.058106",
"title": "Protein folding dynamics via quantification of kinematic energy landscape",
"url": "https://arxiv.org/abs/q-bio/0601018"
},
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