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

Abstract

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 βI-turn, stabilized by the H₈ amide proton to the F₅ carbonyl hydrogen bond, was found for the F₅P₆S₇H₈ sequence, whereas two γ-turns, centred around the E₁₅ and I₁₈ residues respectively, were found in the C-terminal part of the peptide. In the whole crown folded structure of the peptide, the Y₄, F₅, H₈, F₉ and F₁₀ aromatic side chains are situated on one side with the E₁₃, E₁₅, T₁₇ and C₂₀ side chains on the other. This 3D structure resembles and could mimic the binding site of an antibody.