Does prediction of epitopes from the primary structure of a protein represent the epitope in the native structure? A study using cobrotoxin.

In contrast to observations made with S. aureus V8 protease-digest hydrolysates, the antigenic structures of reduced and S-carboxymethylated (RCM)-cobrotixin were notably affected following hydrolysis of RCM-cobrotoxin with chymotrypsin. The peptide separated from the V8 protease-digest hydrolysates with a sequence at positions 22-38 of cobrotoxin exhibited a nearly equal reactivity toward the anti-RCM-cobrotoxin antibodies as RCM-cobrotoxin. Chymotryptic cleavage on this segment caused a precipitous drop in the antigenicity of RCM-cobrotoxin. Alternatively, the N-terminal and C-terminal regions of RCM-cobrotoxin encompassed other antigenic determinants which exhibited low reactivities toward anti-RCM-cobrotoxin antibodies. The epitope structures of RCM-cobrotoxin are in line with those predicted from the hydrophobicity profile of cobrotoxin, but the notably immunoreactive region in the C-terminal region of native toxin molecule (Ref. 1) cannot be predicted from analysis of its primary structure. Moreover, RCM-cobrotoxin had a superior reactivity toward anti-RCM-cobrotoxin antibodies than cobrotoxin did. These results indicate that the epitope structures in RCM-cobrotoxin and cobrotoxin are different.