Berlin 2005 – scientific programme

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DY: Dynamik und Statistische Physik

DY 21: Statistical Physics in Biological Systems

DY 21.5: Talk

Saturday, March 5, 2005, 09:30–09:45, TU H2032

The dynamical lattice model of proteins — •Frank Dressel and Sigismund Kobe — Institut für Theoretische Physik, TU Dresden, D-01062 Dresden, Germany

Lattice models are used to investigate the energy landscape, folding properties and thermodynamics of proteins. The main disadvantage of such up to now considered rigid models is the disability to characterize the real structure. We propose a model, which is more appropriate to deal with biological conformations. The real positions of the amino acids are dynamically simulated using fixed bond lengths between the atoms and an angle distribution taken from Ramachandran plots. Data of the pairwise interactions between the amino acids are based on results of biological investigations [1]. The exact ground state (energy and conformation) is calculated using methods of optimization algorithms with respect to the global energy. Results for different proteins up to a chain length of 40 amino acids are obtained. The comparison with experimentally found biological structures [2] are in good accordance with respect to the secondary structure elements. As an example we discuss the Alzheimer‘s disease amyloid A4 peptide (residues 1-40).

[1] R. I. Dima, G. Settanni, C. Micheletti, J. R. Banavar, A. Maritan, J. Chem. Phys. 112 (2000) 9151.

[2] H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne: The Protein Data Bank. Nucleic Acids Research 28 (2000) 235.