Possible conformation of interferons: a prediction based on amino acid composition and sequence

Using the method of estimation of alpha-helical and beta-folded types of secondary structure from amino acid composition, it has been established that interferons contain about 60-70% of alpha-helices and not more than 10-20% of beta-structure. The same result was obtained using empirical and stereochemical rules for the prediction of protein secondary structure of amino acid sequence. The hydrophobic clusters on the surfaces of the alpha-helical segments were determined. Using the method for packing of alpha-helical segments into the globule suggested by Efimov, and taking into account the disulfide bond arrangement in leucocyte interferon, two alternative globular conformations with prevailing alpha-helix were obtained. The analysis of these conformations shows an anomalous distribution of charged amino acid residues conserved in the primary structure of leucocyte and fibroblasts interferons. Nine positively charged amino acid residues are concentrated in one site on the surface of protein globule. It is possible that this site is responsible for some general biological activity of the interferons.