omega-amino acids in peptide design. Crystal structures and solution conformations of peptide helices containing a beta-alanyl-gamma-aminobutyryl segment

Insertion of achiral omega-amino acids into peptide sequences results in replacement of scissile peptide bonds by proteolytically stable C-C bonds. This provides a convenient means of creating peptidomimetics. The present study establishes the preservation of helical structures in octa-and undecapeptides with centrally located, P-and gamma-amino acids in the Sequence. X-ray diffraction analyses of single crystals and NMR studies have been used to investigate the extent of perturbations of a regular 3(10)- or alpha-helix by the introduction of (-CH2-)(n) groups into the backbone by the use of the beta-Ala-gamma-Abu segment (beta-Ala = beta-alanine, gamma-Abu = gamma-aminobutyric acid), which is formally homomorphous with a (Gly)3 segment. In crystals, the octapeptide Boc-Leu-Aib-Val-beta-Ala-gamma-Abu-Leu-Aib-Val-OMe (1) and the undecapeptide Boc-Leu-Aib-Val-beta-Ala-gamma-Abu-Leu-Aib-Val-Ala-Leu-Aib-OMe (2) retain their helical motifs with minor bulges. Five new types of 4-->1, 5-->1, and 6-->1 hydrogen bond rings are formed with up to three extra CH2 moieties. Cell parameters for peptide 1 are space group P2(1)2(1)2(1) with a=11.506 (1) Angstrom, b=16.600 (1) Angstrom, c=27.362(1) Angstrom, and R=6.1% for 2696 data measured >4 sigma(F); for the undecapeptide 2, the space group is P2(1) with a=8.605 (3) Angstrom, b=22.806 (4) Angstrom, c=19.014 (3) Angstrom, beta=101.47(2)degrees, and R=7.5% for 3797 data measured >4 sigma(F). Helical conformations in solution are also maintained for peptide 2 as is evident from NMR studies in CDCl3, which suggest that the centrally positioned, flexible beta-Ala-gamma-Abu segment can be comfortably accommodated into helical structures adopting gauche conformations about specific C-C bonds of the poly(methylene) units. Twenty structures for backbone conformations generated from MD simulations using NMR-derived contraints, superpose with a low RMSD value (0.78 +/- 0.05 Angstrom), further indicating that in these peptides the conformational flexibility of the beta-Ala-gamma-Abu segment is limited and confined to largely helical conformations.