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Effect of finite size on cooperativity and rates of protein folding | | Maksim Kouza
; Mai Suan Li
; Edward P. O’Brien Jr.
; Chin-Kun Hu
; D. Thirumalai
; | | Date: |
21 Dec 2006 | | Journal: | J. Phys. Chem. A 110, 671 (2006) | | Subject: | Biomolecules | | 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 $k_F = k_F^0 exp(-cN^eta)$. Both $eta = 1/2$ 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) $k_F^0 approx (0.2mu s)^{-1}$ 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. | | Source: | arXiv, q-bio/0612039 | | Services: | Forum | Review | PDF | Favorites | |
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