Prediction of the secondary structure and functional sites of major histocompatibility complex molecules

A method for the theoretical prediction of the antigenic determinants and the antigen-interactive receptor sites of immunological proteins from their primary structure would constitute a useful tool for their study. Such a method developed in this laboratory uses hydrophilicity, accessibility, flexibility, and recognition profiles, together with the predicted secondary structure (alpha-helices, beta-sheets, and turns). The secondary structure is determined by a modification of the method of Lim (1974), as described below. A study of human and mouse class I and class II major histocompatibility complex (MHC) antigens, central to the regulation of immune responses and to the phenomenon of graft rejection, was carried out using the above method. Comparison of the predictions with some of the available experimental and theoretical information supports the validity and usefulness of the approach.