Roles of native topology and chain-length scaling in protein folding: A simulation study with a Go-like model

被引:308
作者
Koga, N
Takada, S [1 ]
机构
[1] Kobe Univ, Grad Sch Sci & Technol, Kobe, Hyogo 6578501, Japan
[2] PRESTO, Japan Sci & Technol, Kobe, Hyogo 6578501, Japan
关键词
contact order; folding rate; transition state; phi-value; denatured state;
D O I
10.1006/jmbi.2001.5037
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
We perform folding simulations on 18 small proteins with using a simple and G (o) over bar -like protein model and analyze the folding rate constants, characteristics of the transition state ensemble, and those of the denatured states in terms of native topology and chain length. Near the folding transition temperature, the folding rate k(F) scales as k(F) similar to exp(-c RCO N-0.6) where RCO and N are the relative contact order and number of residues, respectively. Here the topology RCO dependence of the rates is close to that found experimentally (k(F) similar to exp(-c RCO)), while the chain length N dependence is in harmony with the predicted scaling property (k(F) similar to exp(-c N-2/3)). Thus, this may provides a unified scaling law in folding rates at the transition temperature, k(F) similar to exp(-c RCO N-2/3). The degree of residual structure in the denatured state is highly correlated with RCO, namely, proteins with smaller RCO tend to have more ordered structure in the denatured state. This is consistent with the observation that many helical proteins such as myoglobin and protein A, have partial helices, in the denatured states. The characteristics of the transition state ensemble calculated by the current model, which uses native topology but not sequence specific information, are consistent with experimental phi -value data for about half of proteins. (C) 2001 Academic Press.
引用
收藏
页码:171 / 180
页数:10
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