COMPARISON OF ACTUAL AND RANDOM-POSITIONING-MODEL DISTRIBUTIONS OF PEPTIDE SCAVENGING AND T-CELL-PRESENTED SITES IN ANTIGENIC PROTEINS

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.