Structure of antibody-bound peptides and retro-inverso analogues. A transferred nuclear overhauser effect spectroscopy and molecular dynamics approach

The three-dimensional structures of the two L-peptides, H-CGGIRGERA-OH, cal led L(A), and H-CGGIRGERG-OH, called L(G), corresponding or close to the IR GERA sequence present in the C-terminal region (residues 130-135) of histon e H3, and their retro-inverso analogues HO-mAreGriGGC-NH2, called RI(mA), a nd HO-mGreGriGGC-NH2, called RI(mG), have been studied by two-dimensional H -1 NMR and molecular dynamics calculations in association with a monoclonal antibody generated against L(A). At 25 degreesC, the affinity constants of the monoclonal antibody with respect to RI(mA) and RI(mG) were 75- and 270 -fold higher than those measured with the homologous L(A) and L(G) peptides , respectively. Due to the spontaneous epimerization of the mA malonic resi due, RI(mA) gave rise to two sets of resonances. With regard to the NH amid e region, one set was similar to that for RI(mG) while the second was simil ar to those for the parent L-peptides L(A) and L(G). The antibody-bound con formations of the two couples of L- and retro-inverso peptides have been an alyzed using molecular modeling calculations based on the transferred NOE i nterproton distances. Folded structures appeared in both cases with a type II' beta -turn in the parent GGIR sequence and a type I' beta -turn in the retro-inverso reGr sequence.