Molecular mechanics investigation of the flexibility of some cyclic peptides

Conformation space near the crystal conformations of proline-containing cyclic octapeptides and cyclic hexapeptides of C2 sequence symmetry, e.g. cyclo-(Gly-Pro-D-Phe)2 and cyclo-(D-Ala-Gly-Pro-D-Phe)2, was explored using molecular mechanics. Conformations found in crystals were energy minimized, distortions were introduced by systematically fixing backbone dihedral angles at individual residues, and nearby energy-minimized conformations were then located. Interatomic distances and dihedral angles were examined in the conformations within a few kilocalories of the most stable conformation. A common form of flexibility was found to involve libration of amide planes. Among the peptides examined, the cyclic hexapeptides were found to have greater freedom than the cyclic octapeptides, and cyclo-(D-Ala-Gly-Pro-D-Phe)2 was found to be more rigid than cyclo-(D-Ala-Gly-Pro-Phe)2.