dorsal/arxiv
View SchemaCooperativity and the origins of rapid, single-exponential kinetics in protein folding
| Authors | P. F. N. Faisca, K. W. Plaxco |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0611062 |
| URL | https://arxiv.org/abs/q-bio/0611062 |
| Journal | Protein Science 15, 1608-1618 (2006) |
Abstract
The folding of naturally occurring, single domain proteins is usually well-described as a simple, single exponential process lacking significant trapped states. Here we further explore the hypothesis that the smooth energy landscape this implies, and the rapid kinetics it engenders, arises due to the extraordinary thermodynamic cooperativity of protein folding. Studying Miyazawa-Jernigan lattice polymers we find that, even under conditions where the folding energy landscape is relatively optimized (designed sequences folding at their temperature of maximum folding rate), the folding of protein-like heteropolymers is accelerated when their thermodynamic cooperativity enhanced by enhancing the non-additivity of their energy potentials. At lower temperatures, where kinetic traps presumably play a more significant role in defining folding rates, we observe still greater cooperativity-induced acceleration. Consistent with these observations, we find that the folding kinetics of our computational models more closely approximate single-exponential behavior as their cooperativity approaches optimal levels. These observations suggest that the rapid folding of naturally occurring proteins is, at least in part, consequences of their remarkably cooperative folding.
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"abstract": "The folding of naturally occurring, single domain proteins is usually\nwell-described as a simple, single exponential process lacking significant\ntrapped states. Here we further explore the hypothesis that the smooth energy\nlandscape this implies, and the rapid kinetics it engenders, arises due to the\nextraordinary thermodynamic cooperativity of protein folding. Studying\nMiyazawa-Jernigan lattice polymers we find that, even under conditions where\nthe folding energy landscape is relatively optimized (designed sequences\nfolding at their temperature of maximum folding rate), the folding of\nprotein-like heteropolymers is accelerated when their thermodynamic\ncooperativity enhanced by enhancing the non-additivity of their energy\npotentials. At lower temperatures, where kinetic traps presumably play a more\nsignificant role in defining folding rates, we observe still greater\ncooperativity-induced acceleration. Consistent with these observations, we find\nthat the folding kinetics of our computational models more closely approximate\nsingle-exponential behavior as their cooperativity approaches optimal levels.\nThese observations suggest that the rapid folding of naturally occurring\nproteins is, at least in part, consequences of their remarkably cooperative\nfolding.",
"arxiv_id": "q-bio/0611062",
"authors": [
"P. F. N. Faisca",
"K. W. Plaxco"
],
"categories": [
"q-bio.BM"
],
"journal_ref": "Protein Science 15, 1608-1618 (2006)",
"title": "Cooperativity and the origins of rapid, single-exponential kinetics in protein folding",
"url": "https://arxiv.org/abs/q-bio/0611062"
},
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