We assess the reliability of the recently developed approach denominated dominant reaction pathways (DRP) by studying the folding of a 16 residue β-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 β-hairpin folding, in which the reaction is initiated by the collapse of the hydrophobic cluster.
Faccioli, P. (2008). Characterization of Protein Folding by Dominant Reaction Pathways. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, 112(44), 13756-13764 [10.1021/jp805762d].
Characterization of Protein Folding by Dominant Reaction Pathways
Faccioli, Pietro
2008
Abstract
We assess the reliability of the recently developed approach denominated dominant reaction pathways (DRP) by studying the folding of a 16 residue β-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 β-hairpin folding, in which the reaction is initiated by the collapse of the hydrophobic cluster.
I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
