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Topological Shape and Size of Peptides: Identification of Potential Allele Specific Helper T Cell Antigenic Sites

IR@IICB: CSIR-Indian Institute of Chemical Biology, Kolkata

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Title Topological Shape and Size of Peptides: Identification of Potential Allele Specific Helper T Cell Antigenic Sites
 
Creator Raychaudhury, Chandan
Banerjee, Asok
Bag, Partha
Roy, Syamal
 
Subject Structural Biology & Bioinformatics
 
Description A database of primary sequences of 28 immunogenic peptides, known to elicit T cell response, derived from five different haplotypes was compiled to identify allele specific helper T cell antigenic sites using a rule based graph-theoretical method. The prediction was based on the identification of allele specific patterns in the form of “topological shape and size” present in the peptides. Indices computed from weighted connected graph models of amino acid side chains and peptides were used in this purpose. The system was trained by 10 Ad and 10 non-Ad restricted peptide sequences, assigned actives and inactives, respectively, chosen randomly from the database, and four Ad and four non-Ad restricted sequences were kept as test peptides. This allowed the system to learn about “topological shape and size” specific for Ad restricted peptides from the differences, if any, they had with the inactive peptides in that respect. The system made 100% correct prediction for the training set peptides and misclassified only one inactive peptide of the test set. The system also identified crucial residues for lambda repressor 12-24 and insulin A-chains. This identification also shows that activity related/crucial residues could be located at varying distances from the peptide terminals. To our knowledge, the method is unique of its kind in the literature and may find application in the rational design of synthetic vaccines and other peptides of immunological importance.
 
Publisher American Chemical Society
 
Date 1999
 
Type Article
PeerReviewed
 
Format application/pdf
 
Identifier http://www.eprints.iicb.res.in/683/1/JOURNAL_OF_CHEMICAL_INFORMATION_AND_COMPUTER_SCIENCES__39(_2)_248%2D254;1999[70].pdf
Raychaudhury, Chandan and Banerjee, Asok and Bag, Partha and Roy, Syamal (1999) Topological Shape and Size of Peptides: Identification of Potential Allele Specific Helper T Cell Antigenic Sites. Journal of Chemical Information and Computer Sciences, 39 (2). pp. 248-254.
 
Relation http://dx.doi.org/10.1021/ci980052w
http://www.eprints.iicb.res.in/683/