M. Salomon et al., COMPARISON OF ACTUAL AND RANDOM-POSITIONING-MODEL DISTRIBUTIONS OF PEPTIDE SCAVENGING AND T-CELL-PRESENTED SITES IN ANTIGENIC PROTEINS, Vaccine, 11(10), 1993, pp. 1067-1073
In a peptide with a T cell-presented epitope (T site), a folded struct
ure with a hydrophobic surface, 'the scavenger (S) site', may regulate
transfer to major histocompatibility complex class II molecules. Thre
e procedures which were proposed to identify T sites selected for amph
ipathic helical patterns but not T sites. In testing whether S sites l
ay in or near T sites, we found their linkage was not greater than tha
t generated by a model in which segments of equal length and number to
the S and T sites for each protein were distributed at random. This s
tudy establishes criteria for evaluation of schemes to predict functio
nal motifs in antigenic proteins.