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Biophysical Journal 86:1691-1701 (2004)
© 2004 The Biophysical Society

Formation of the Folding Nucleus of an SH3 Domain Investigated by Loosely Coupled Molecular Dynamics Simulations

G. Settanni, J. Gsponer and A. Caflisch

Biochemisches Institut, Universität Zürich, Zürich, Switzerland

Correspondence: Address reprint requests to A. Caflisch, Biochemisches Institut, Universität Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland. Fax: 411-635-6862; E-mail: caflisch{at}bioc.unizh.ch.

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 ß-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 ß-sheet whereas its two hairpins form in a different but consistent way.




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