dorsal/arxiv
View SchemaEffect of finite size on cooperativity and rates of protein folding
| Authors | Maksim Kouza, Mai Suan Li, Edward P. O'Brien Jr., Chin-Kun Hu, D. Thirumalai |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0612039 |
| URL | https://arxiv.org/abs/q-bio/0612039 |
| DOI | 10.1021/jp053770b |
| Journal | J. Phys. Chem. A 110, 671 (2006) |
Abstract
We analyze the dependence of cooperativity of the thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, $N$, using lattice models with side chains,off-lattice Go models and the available experimental data. A dimensionless measure of cooperativity, $\Omega_c$ ($0 < \Omega_c < \infty$), scales as $\Omega_c \sim N^{\zeta}$. The results of simulations and the analysis of experimental data further confirm the earlier prediction that $\zeta$ is universal with $\zeta = 1 +\gamma$, where exponent $\gamma$ characterizes the susceptibility of a self-avoiding walk. This finding suggests that the structural characteristics in the denaturated state are manifested in the folding cooperativity at the transition temperature. The folding rates $k_F$ for the Go models and a dataset of 69 proteins can be fit using $k_F = k_F^0 \exp(-cN^\beta)$. Both $\beta = 1/2$ and 2/3 provide a good fit of the data. We find that $k_F = k_F^0 \exp(-cN^{{1/2}})$, with the average (over the dataset of proteins) $k_F^0 \approx (0.2\mu s)^{-1}$ and $c \approx 1.1$, can be used to estimate folding rates to within an order of magnitude in most cases. The minimal models give identical $N$ dependence with $c \approx 1$. The prefactor for off-lattice Go models is nearly four orders of magnitude larger than the experimental value.
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"abstract": "We analyze the dependence of cooperativity of the thermal denaturation\ntransition and folding rates of globular proteins on the number of amino acid\nresidues, $N$, using lattice models with side chains,off-lattice Go models and\nthe available experimental data. A dimensionless measure of cooperativity,\n$\\Omega_c$ ($0 \u003c \\Omega_c \u003c \\infty$), scales as $\\Omega_c \\sim N^{\\zeta}$. The\nresults of simulations and the analysis of experimental data further confirm\nthe earlier prediction that $\\zeta$ is universal with $\\zeta = 1 +\\gamma$,\nwhere exponent $\\gamma$ characterizes the susceptibility of a self-avoiding\nwalk. This finding suggests that the structural characteristics in the\ndenaturated state are manifested in the folding cooperativity at the transition\ntemperature. The folding rates $k_F$ for the Go models and a dataset of 69\nproteins can be fit using $k_F = k_F^0 \\exp(-cN^\\beta)$. Both $\\beta = 1/2$ and\n2/3 provide a good fit of the data. We find that $k_F = k_F^0\n\\exp(-cN^{{1/2}})$, with the average (over the dataset of proteins) $k_F^0\n\\approx (0.2\\mu s)^{-1}$ and $c \\approx 1.1$, can be used to estimate folding\nrates to within an order of magnitude in most cases. The minimal models give\nidentical $N$ dependence with $c \\approx 1$. The prefactor for off-lattice Go\nmodels is nearly four orders of magnitude larger than the experimental value.",
"arxiv_id": "q-bio/0612039",
"authors": [
"Maksim Kouza",
"Mai Suan Li",
"Edward P. O\u0027Brien Jr.",
"Chin-Kun Hu",
"D. Thirumalai"
],
"categories": [
"q-bio.BM"
],
"doi": "10.1021/jp053770b",
"journal_ref": "J. Phys. Chem. A 110, 671 (2006)",
"title": "Effect of finite size on cooperativity and rates of protein folding",
"url": "https://arxiv.org/abs/q-bio/0612039"
},
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