A non-statistical approach to the prediction of regular structures in proteins by the example of alpha-helices

A new approach to the analysis of regular structures in proteins that is based on the method of molecular mechanics is proposed. The method uses only the information about the amino acid sequence. The alpha-helical conformation was simulated using the ICM program of molecular mechanics. Energy profiles of the sequences in the alpha-helical conformation, spanning the entire polypeptide chain, were plotted for eight proteins from the Protein Data Bank. The regions of each profile that exhibit energy minima were found to correspond to the alpha-helical regions of the real spatial structure of the protein. Twenty-four out of 25 helices were distinctly pronounced, which indicates a rather high accuracy of the prediction. The energy profiles also help reveal the short regions that correspond to 3/10-helices and the turns that include local alpha-helical conformations. Unlike the known statistical methods of prediction, this method makes it possible to establish the physical principles of the formation of alpha-helical conformations. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2002, vol. 28, no. 6; see also http://www.maik.ru.