Title of article :
Roles of native topology and chain-length scaling in protein folding: A simulation study with a Gō-like model
Author/Authors :
Nobuyasu Koga، نويسنده , , Atsuo Tamura and Shoji Takada، نويسنده ,
Issue Information :
روزنامه با شماره پیاپی سال 2001
Abstract :
We perform folding simulations on 18 small proteins with using a simple Gō-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 kF scales as kF ∼ exp(−c RCO N0.6) 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 (kF ∼ exp(−c RCO)), while the chain length N dependence is in harmony with the predicted scaling property (kF ∼ exp(−c N2/3)). Thus, this may provides a unified scaling law in folding rates at the transition temperature, kF ∼ exp(−c RCO N2/3). 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 φ-value data for about half of proteins.
Keywords :
contact order , folding rate , transition state , ?-value , denatured state
Journal title :
Journal of Molecular Biology
Journal title :
Journal of Molecular Biology