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

摘要

Starting from the 20-mer peptide 289-308, one of the experimentally characterized B-cell epitopes of the La/SSB autoantigen, the complementary peptide cpl(289-308), encoded by the complementary RNA was designed. The conformational properties of the cpl(289-308) were investigated in DMSO solution with the combined use of NMR data (vicinal coupling constants, NOE effects and temperature coefficient values), molecular modelling calculations of energy minimization and molecular dynamics. MD calculations led to a folded structure in which a #beta#I-turn, stabilized by the H_8 amide proton to the F_5 carbonyl hydrogen bond, was found for the F_5P_6S_7H_8 sequence, whereas two #gamma#-turns, centred around the E_15 and I_18 residues respectively, were found in the C-terminal part of the peptide. In the whole crown folded structure of the peptide, the Y_4, F_5, H_8, F_9 and F_10 aromatic side chains are situated on one side with the E_13, E_15, T_17 and C_20 side chains on the other. This 3D structure resembles and could mimic the binding site of an antibody.