Conformational analysis of peptide surrogates. Reduced and retro-amide links in blocked alanine and in secondary structures.

Abstract

We have investigated the conformational effects of modifying the amide link of peptides. We studied a reverse amide bond psi [NHCO], a reduced amide bond psi [CH2NH] and a retro-reduced bond psi [NHCH2] as surrogates for the amide link [CONH] in native peptides. A complete search of the conformational space available to residues with these modified links was carried out. The local minima and the rotational barriers were described and compared to the minima of the native residue. The results are compatible with the available observed structural data. These modified links have been incorporated in secondary structure units such as beta turns, alpha helices, and parallel and anti-parallel beta sheets. It was found that a reduced amide link can lead to stabilised beta turns, while the retro modification can be incorporated in stable beta sheets. A significant reduction in the stability of alpha helices is caused by the retro links, while a reduced amide link results in only a small destabilisation.