Ab initio study of alanine polypeptide chains twisting

摘要

We have investigated the potential energy surfaces for alanine chainsconsisting of three and six amino acids. For these molecules we have calculatedpotential energy surfaces as a function of the Ramachandran angles Phi and Psi,which are widely used for the characterization of the polypeptide chains. Theseparticular degrees of freedom are essential for the characterization ofproteins folding process. Calculations have been carried out within ab initiotheoretical framework based on the density functional theory and accounting forall the electrons in the system. We have determined stable conformations andcalculated the energy barriers for transitions between them. Using athermodynamic approach, we have estimated the times of characteristictransitions between these conformations. The results of our calculations havebeen compared with those obtained by other theoretical methods and with theavailable experimental data extracted from the Protein Data Base. Thiscomparison demonstrates a reasonable correspondence of the most prominentminima on the calculated potential energy surfaces to the experimentallymeasured angles Phi and Psi for alanine chains appearing in native proteins. Wehave also investigated the influence of the secondary structure of polypeptidechains on the formation of the potential energy landscape. This analysis hasbeen performed for the sheet and the helix conformations of chains of six aminoacids.