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dc.contributor.authorReyes, Victor E.
dc.contributor.authorPhillips, Lisa
dc.contributor.authorHumphreys, Robert E.
dc.contributor.authorLew, Robert A.
dc.date2022-08-11T08:10:05.000
dc.date.accessioned2022-08-23T16:54:36Z
dc.date.available2022-08-23T16:54:36Z
dc.date.issued1989-08-05
dc.date.submitted2008-08-15
dc.identifier.citationJ Biol Chem. 1989 Aug 5;264(22):12854-8.
dc.identifier.issn0021-9258 (Print)
dc.identifier.pmid2787794
dc.identifier.urihttp://hdl.handle.net/20.500.14038/42538
dc.description.abstractThe 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.
dc.language.isoen_US
dc.relation<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=2787794&dopt=Abstract">Link to Article in PubMed</a>
dc.relation.urlhttp://www.jbc.org/content/264/22/12854.full.pdf+html
dc.subject*Algorithms
dc.subjectAmino Acid Sequence
dc.subjectAnimals
dc.subjectAntigen-Presenting Cells
dc.subject*Antigens
dc.subjectChickens
dc.subjectModels, Molecular
dc.subjectProbability
dc.subject*Protein Conformation
dc.subjectSoftware
dc.subjectStructure-Activity Relationship
dc.subjectSwine
dc.subjectT-Lymphocytes
dc.subjectWhales
dc.subjectLife Sciences
dc.subjectMedicine and Health Sciences
dc.titlePrediction of protein helices with a derivative of the strip-of-helix hydrophobicity algorithm
dc.typeJournal Article
dc.source.journaltitleThe Journal of biological chemistry
dc.source.volume264
dc.source.issue22
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/oapubs/878
dc.identifier.contextkey579767
html.description.abstract<p>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.</p>
dc.identifier.submissionpathoapubs/878
dc.contributor.departmentDepartment of Pharmacology
dc.source.pages12854-8


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