Regensburg 2007 – scientific programme
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BP: Fachverband Biologische Physik
BP 4: Protein Structure and Folding
BP 4.6: Talk
Monday, March 26, 2007, 18:45–19:00, H43
Protein structure reconstruction from a vectorial structure representation — •Katrin Wolff1, Michele Vendruscolo2, and Markus Porto1 — 1Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 8, 64289 Darmstadt, Germany — 2Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
We illustrate an approach to reconstruct the folded protein structure from its vectorial representation, a process which is indeed very similar to actual protein folding in the sense that it also employs a 1D quantity to determine the 3D folded structure. This has been prompted by the recent proof that the contact matrix of a protein structure can be reconstructed from its vectorial representation [1], from which the 3D structure can in turn be efficiently recovered [2]. Here, we take one step further and present a reconstruction procedure that uses directly a 3D structure description (the tube model [3]) and a cost function based on the vectorial structure representation. Although no full reconstruction has been achieved yet, the contact matrix overlap to the target structure reaches up to 75%. These simulations are used to investigate the ‘energy landscape’ of this model by means of enhanced sampling techniques including umbrella sampling. They provide a novel approach to investigate protein energy landscapes, which is conceptual different from usually applied Gō-type techniques.
[1] M. Porto et al., Phys. Rev. Lett. 92, 218101 (2004).
[2] M. Vendruscolo et al., Fold. & Des. 2, 295 (1997).
[3] T.X. Hoang et al., Proc. Natl. Acad. Sci. USA 101, 7960 (2004).