title: Prediction of protein helices with a derivative of the strip-of-helix hydrophobicity algorithm.
abstract: The strip-of-helix hydrophobicity algorithm was devised to identify protein sequences which, when coiled as alpha or 3(10) helices, had one axial, hydrophobic strip and otherwise variably hydrophilic residues. The strip-of-helix hydrophobicity algorithm also ranked such sequences according to an index, the mean hydrophobicity of amino acids in the axial strip. This algorithm well predicted T cell-presented fragments of antigenic proteins. A derivative of this algorithm (the structural helices algorithm (SHA] was tested for the prediction of helices in crystallographically defined proteins. For the SHA, eight amino acid sequences, 2 cycles plus one amino acid in an alpha helix, with strip-of-helix hydrophobicity indices greater than 2.5, were selected with overlapping segments joined. These selections were terminated according to simple "capping rules," which took into account the roles of N-terminal Asn or Pro and C-terminal Gly in the stability of helices. In analyses of 35 crystallographically defined proteins with known alpha and 3(10) helices, the predictions with the SHA overlapped (had overlap indices x greater than or equal to 0.5) with 34% of known helices, touched (had overlap indices 0.5 greater than x greater than 0) or overlapped with 66% of known helices, or were neighboring (came within 6 residues) or touched or overlapped with 82% of known helices. At each level of judging the quality of prediction, the SHA was usually less sensitive (correct predictions/total number of known helices) and more efficient (correct predictions/total number of predictions) than the Chou-Fasman and Garnier-Robson methods. It was simpler in design and calculation. The chemical mechanisms underlying these algorithms appear to apply both to protein folding and to selection of T cell-presented antigenic sequences.
authors: Department of Pharmacology, University of Massachusetts Medical School, Worcester 01655.
authors: V E
authors: VE
authors: Reyes
authors: L
authors: L
authors: Phillips
authors: R E
authors: RE
authors: Humphreys
authors: R A
authors: RA
authors: Lew
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D000938:Antigen-Presenting Cells / Q000276:immunology; D000941:Antigens; D002645:Chickens; D008958:Models, Molecular; D011336:Probability; D011487:Protein Conformation; D012984:Software; D013329:Structure-Activity Relationship; D013552:Swine; D013601:T-Lymphocytes / Q000276:immunology; D014907:Whales
chemical_list: D000941:Antigens