Effect of conformation on the conversion of cyclo-(1,7)-Gly-Arg- Gly-Asp-Ser-Pro-Asp-Gly-OH to its cyclic imide degradation product

The objective of this study was to explain the increased propensity for the conversion of cyclo-(1,7)-Gly-Arg Cly-Asp-Ser-Pro-Asp-Gly-OH (1), a vitron ectin-selective inhibitor, to its cyclic imide counterpart cyclo-(1,7)-Gly- Arg-Gly-Asu-Ser-Pro-Asp-Gly-OH (2). Therefore, we present the conformationa l analysis of peptides 1 and 2 by NMR and molecular dynamic simulations (MD ). Several different NMR experiments, including COSY, COSY-Relay, HOHAHA, N OESY, ROESY, DQF-COSY and HMQC, were used to: (a) identify each proton in t he peptides; (b) determine the sequential assignments; (c) determine the ci s-trans isomerization of X-Pro peptide bond; and (d) measure the NH-HCalpha coupling constants. NOE- or ROE-constraints were used in the MD simulation s and energy minimizations to determine the preferred conformations of cycl ic peptides 1 and 2. Both cyclic peptides 1 and 2 have a stable solution co nformation; MD simulations suggest that cyclic peptide 1 has a distorted ty pe I beta-turn at Arg2-Gly3-Asp4-Ser5 and cyclic peptide 2 has a pseudotype I beta-turn at Ser5-Pro6-Asp7-Gly1. A shift in position of the type I beta -turn at Arg2-Cly3-Asp4-Ser5 in peptide 1 to Ser5-Pro6-Asp7-Gly1 in peptide 2 occurs upon formation of the cyclic imide at the Asp4 residue. Although the secondary structure of cyclic peptide 1 is not conducive to succinimide formation, the reaction proceeds via neighbouring group catalysis by the S er5 side chain. This mechanism is also supported by the intramolecular hydr ogen bond network between the hydroxyl side chain and the backbone nitrogen of Ser5. Based on these results, the stability of Asp-containing peptides cannot be predicted by conformational analysis alone; the influence of anch imeric assistance by surrounding residues must also be considered.