Berlin 2005 – scientific programme

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AKB: Biologische Physik

AKB 90: Protein Folding and Molecular Dynamics

AKB 90.5: Talk

Wednesday, March 9, 2005, 15:00–15:15, TU H2013

All Atom Protein Structure Prediction with Stochastic Optimization Methods — •Wolfgang Wenzel, Thomas Herges, Alexander Schug, and Abhinav Verma — Forschungszentrum Karlsruhe, Institut für Nanotechnologie, Postfach 3640, 76021 Karlsruhe

The prediction of protein tertiary structure remains one of the outstanding problems in biophysical chemistry. According to the thermodynamic hypothesis, the native conformation of a protein can be predicted as the global optimum of its free energy surface with stochastic optimization methods[1] orders of magnitude faster than by direct simulation of the folding process.

We have recently developed an all-atom free energy forcefield (PFF01)[2] which implements a minimal thermodynamic model based on physical interactions. With this forcefield we were able to predictively fold the 20 amino acid trp-cage protein[3], the 40 amino-acid HIV accessory protein[4], the 36 amino-acid villin headpiece and the 60 amino acid bacterial ribosomal protein[5] using various stochastic optimization methods. We will disccuss advantages and limitations of these methods with respect to further improvements of this approach to in-silico all-atom protein strcuture prediction.

[1] W. Wenzel, K. Hamacher, PRL 59, 3003 (1999) [2] T. Herges, W. Wenzel, Biophys. J. 87, 3100 (2004) [3] A. Schug, W. Wenzel, PRL 91, 158102, 2003, EPL 67, 307 (2004) [4] T. Herges, W. Wenzel, PRL (in press) [5] A. Schug, W. Wenzel, JACS (in press)