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BP: Fachverband Biologische Physik

BP 26: Posters II

BP 26.7: Poster

Thursday, February 28, 2008, 17:00–19:30, Poster A

Restrained Protein Folding Dynamics in the Tube Model — •Katrin Wolff¹, Michele Vendruscolo², and Markus Porto¹ — ¹Institut für Festkörperphysik, Technische Universität Darmstadt, Germany — ²Department of Chemistry, University of Cambridge, UK

The study of protein folding dynamics through all-atom molecular dynamics requires significant computational efforts, and coarse-grained models are therefore of great interest. Here, we use the tube model [1], which has been shown to be computationally very effective in reproducing the folding behaviour of proteins [1,2,3]. In order to drive the folding dynamics towards a specific protein structure, we augment the energy function with a term based on a structural profile. For single-domain proteins, this structural profile has been shown to contain sufficient information to reconstruct the contact map of the target structure [4]. When directly applied to folding, the use of the structural profile is conceptually very different from the use of the contact map, since the latter would result in a Gō-type model. By contrast, the structural profile entries contain global information about the protein structure rendering this approach similar to the actual protein folding process [5]. We show that by adopting this strategy we are able to fold several small to medium-size single-domain proteins.

[1] T.X. Hoang et al., Proc. Natl. Acad. Sci. USA 101, 7960 (2004).

[2] T.X. Hoang et al., Proc. Natl. Acad. Sci. USA 103, 6883 (2006).

[3] S. Auer et al., Phys. Rev. Lett. 99, 178104 (2007).

[4] M. Porto et al., Phys. Rev. Lett. 92, 218101 (2004).

[5] K. Wolff, M. Vendruscolo, and M. Porto, submitted.