New Techniques for Protein Simulations The Generalized-Ensemble Approach

Article type: Research Article

Authors: Hansmann, Ulrich H.E.^{; 1}

Affiliations: Department of Physics, Michigan Technological University, Houghton, MI 49931, USA. E-mail: [email protected]

Correspondence: [1] The address for manuscript correspondence: Ulrich H.E. Hansmann, Department of Physics, Michigan Technological University, Houghton, MI 49931, USA. E-mail: [email protected]. Fax: 1 906 487 2933. Tel: 1-906-4872909.

Abstract: The energy landscape of proteins and peptides is characterized by a multitude of local minima separated by high energy barriers. Low temperature simulations by canonical molecular dynamics or Monte Carlo will get trapped in configurations corresponding to one of these local minima. We show how this problem can be overcome by new simulation techniques such as generalized-ensemble algorithms. We demonstrate the effectiveness of this approach for the structure prediction of peptides and proteins, and study these molecules from a statistical physics point of view. As an example, we investigated the helix-coil transition through calculating partition function zeros and finite-size scaling analysis. Especially, we were able to determine a set of critical exponents which characterize the coil-helix transition.

Keywords: Generalized-Ensemble Simulations, Protein-Folding Problem, Helix-Coil-Transition

DOI: 10.3233/JCM-2002-21-213

Journal: Journal of Computational Methods in Sciences and Engineering, vol. 2, no. 1-2, pp. 95-103, 2002