Full Text PDF:

PDF icon Settanni04.pdf

G. Settanni; J. Gsponer; A. Caflisch

Journal: Biophys. J.
Year: 2004
Volume: 86
Issue: 3
Pages: 1691-1701
DOI: 10.1016/S0006-3495(04)74238-1
Type of Publication: Journal Article

Computer Simulation; Models, Chemical; Models, Molecular; Motion; Protein Conformation; Protein Folding; src Homology Domains; src-Family Kinases


The experimentally well-established folding mechanism of the src-SH3 domain, and in particular the phi-value analysis of its transition state, represents a sort of testing table for computational investigations of protein folding. Here, parallel molecular dynamics simulations of the src-SH3 domain have been performed starting from denatured conformations. By rescuing and restarting only trajectories approaching the folding transition state, an ensemble of conformations was obtained with a completely structured central β-sheet and a native-like packing of residues Ile-110, Ala-121, and Ile-132. An analysis of the trajectories shows that there are several pathways leading to the formation of the central β-sheet whereas its two hairpins form in a different but consistent way.