Topological Shape and Size of Peptides: Identification of Potential Allele Specific Helper T Cell Antigenic Sites
IR@IICB: CSIR-Indian Institute of Chemical Biology, KolkataView Archive Info
Topological Shape and Size of Peptides: Identification of Potential Allele Specific
Helper T Cell Antigenic Sites
Structural Biology & Bioinformatics
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.
American Chemical Society
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.