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Nucleic Acids Research, 1984, Vol. 12, No. 1Part1 243-255
© 1984

MAIN-FRAME COMPUTERS

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

Jiri Novotny and Charles Auffray*

Molecular and Cellular Laboratory, Massachusetts General Hospital and Harvard Medical School Boston, MA 02114 *Department of Biochemistry and Molecular Biology, Harvard University Cambridge, MA 02138, USA

Received August 5, 1983. 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 histocompalibility 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 ß2 of class II) and the ß2-microglobulin domain are predicted to consist of seven anti-parallel ß-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 ß-sheet with one of its faces being covered by {alpha}-helices and/or structureless segments ("open face sandwiches").


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