Characterization of protein folding by dominant reaction pathways.
We assess the reliability of the recently developed approach denominated dominant reaction pathways (DRP) by studying the folding of a 16 residue beta-hairpin, within a coarse-grained Go-type model. We show that the DRP predictions are in quantitative agreement with the results of molecular dynamics simulations performed in the same model. On the other hand, in the DRP approach, the computational difficulties associated with the decoupling of time scales are rigorously bypassed. The analysis of the important transition pathways supports a picture of the beta-hairpin folding, in which the reaction is initiated by the collapse of the hydrophobic cluster.
Dipartimento di Fisica Università degli Studi di Trento, Trento, Italy. faccioli@science.unitn.it
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D003198:Computer Simulation; D008958:Models, Molecular; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
D011506:Proteins