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 phi and psi,
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 phi and psi 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.Comment: 23 pages, 9 figure
