Predicted secondary structure and hydrophobic cores of T-cell (TCGF or IL-2) and platelet-derived growth factors as well as of transforming protein p28sis of simian sarcoma virus are similar to those of interferons

Estimation of a content of secondary structures from amino acid composition of IL-2 (TCGF), PDGF and transforming protein p28sis of simian sarcoma virus by means of the previously suggested nomograms (V.P. Zav'yalov and A.I. Denesyuk (1982) Immunol. Lett. 4, 7-14) allowed us to conclude that a dominant secondary structure of these proteins should be alpha-helix. Its content in PDGF and p28sis was estimated to be approximately equal to 50%, and that in IL-2 to be 50-65%. The content of beta-pleated structure in PDGF and p28sis does not exceed 10%, and that in IL-2 is found to be 20-30%. In all the proteins investigated five alpha-helical segments can be distinguished, of which one of the surfaces contains clusters of bulky hydrophobic side chains. As the number of alpha-helical segments satisfying the principles of packing into a hydrophobic core as well as the overall length of a polypeptide chain of IL-2 and PDGF coincided with those for IFNs, it was decided to arrange alpha-helices of these proteins into a globular structure by analogy with IFNs (V.P. Zav'yalov and A.I. Denesyuk (1984) Doklady Akad Nauk S.S.S.R. 275, 242-246). In consequence, identical side chains of amino acid residues were found at 9 out of 29 positions in hydrophobic cores of IFN-beta and IL-2, p28sis (PDGF), respectively. Thus the homology of hydrophobic cores of the proteins compared is greater than 30%. Probability of chance coincidences of amino acid residues in the hydrophobic cores of p28sis (PDGF) and IFN-beta is found to be 0.03, and that deduced from comparison of IL-2 and IFN-beta is 0.05.(ABSTRACT TRUNCATED AT 250 WORDS)