Structural and computational investigations of the conformation of antigenic peptide fragments of human polymorphic epithelial mucin

Human polymorphic epithelial mucins (PEM) are complex glycoproteins that are associated with breast and ovarian carcinomas. The PEM core protein consists of variable numbers of a tandem repeat sequence which contains a short antigenic hydrophilic region (Pro¹-Asp-Thr-Arg-Pro-Ala-Pro⁷). High-field n.m.r. studies undertaken on antigenic 20- and 11-amino acid fragments of the PEM core protein in dimethyl sulphoxide have identified a type-I β-turn to be present in the region Pro¹-Asp-Thr-Arg⁴. This region includes and overlaps the identified type-I (Asp²-Thr-Arg⁴) and type-II (Arg⁴-Pro-Ala⁶) epitopes of anti-PEM monoclonal antibodies. The studies indicate that the β-turn is stabilized by the presence of a salt-bridge interaction between Asp-2 and Arg-4. In order to probe the conformations accessible to the PEM peptides a computational study was undertaken independently on the peptide Pro-Asp-Thr-Arg-Pro using a modified Metropolis Monte Carlo algorithm. This study identified the n.m.r.-observed salt-bridge type-I β-turn as the major low-energy conformer. These results suggest that this structural motif may be involved in the immune recognition of PEM.