Eur. Phys. J. D 39, 23-34 (2006)
https://doi.org/10.1140/epjd/e2006-00067-5

Conformational changes in glycine tri- and hexapeptide

Frankfurt Institute for Advanced Studies, Johann Wolfgang Goethe University, Max von Laue Str. 1, 60438 Frankfurt am Main, Germany

Corresponding author: ^a solovyov@fias.uni-frankfurt.de

Received: 6 December 2005
Revised: 24 January 2006
Published online: 4 April 2006

Abstract

We have investigated the potential energy surfaces for glycine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles ϕ and ψ, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of the characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable correspondence of the most prominent minima on the calculated potential energy surfaces to the experimentally measured angles ϕ and ψ for the glycine chains appearing in native proteins. We have also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids.