Conformational study of the complementary peptide to a B-cell epitope of the La/SSB autoantigen

Starting from the 20-mer peptide 289-308, one of the experimentally charact erized B-cell epitopes of the La/SSB autoantigen, the complementary peptide cpl(289-308), encoded by the complementary RNA was designed. The conformat ional properties of the cpl(289-308) were investigated in DMSO solution wit h the combined use of NMR data (vicinal coupling constants, NOE effects and temperature coefficient values), molecular modelling calculations of energ y minimization and molecular dynamics. MD calculations led to a folded stru cture in which a betaI-turn, stabilized by the H-8 amide proton to the F-5 carbonyl hydrogen bond, was found for the F5P6S7H8 sequence, whereas two ga mma -turns, centred around the E-15 and I-18 residues respectively, were fo und in the C-terminal part of the peptide. In the whole crown folded struct ure of the peptide, the Y-4, F-5, H-8, F-9 and F-10 aromatic side chains ar e situated on one side with the E-13, E-15, T-17 and Cc side chains on the other. This 3D structure resembles and could mimic the binding site of an a ntibody. (C) 2001 Academic des sciences/Editions scientifiques et medicales Elsevier SAS.