A program for prediction of protein secondary structure from nucleotide sequence data: application to histocompatibility antigens

A computer program is described which, given a nucleotide or an amino acid sequence, outputs protein secondary structure prediction curves as well as hydrophobicity and charged-residue profiles. The program allows for cumulative averaging of properties (secondary structure propensities, hydrophobicity and charge profiles) from several homologous primary structures, a novel concept shown to improve the predictive accuracy. The use of the program is demonstrated on a set of nucleotide and amino acid sequences from human and murine histocompatibility antigens of class I and II. The last extracellular domains of both class I and II antigens (alpha 3 of class I, alpha 2 and beta 2 of class II) and the beta 2-microglobulin domain are predicted to consist of seven anti-parallel beta-strands, in accord with previous claims of homology between these domains and the constant domains of immunoglobulin chains. The remaining extracellular domains are all proposed to form an anti-parallel, four-stranded beta-sheet with one of its faces being covered by alpha-helices and/or structureless segments ("open face sandwiches").