Theoretical study on side-chain control of the 14-helix and the 10/12-helix of β-peptides

The conformational features of a series of beta-peptide models 1-11 have been studied by the molecular mechanics MN2* force-field and quantum mechanics methods. The geometries were optimized by the HF/6-31G** method. Energies were evaluated using the B3LYP/6-31G** method including solvent effect (SCIPCM). For the unsubstituted beta-tripeptide model 1, calculations indicate that a 12-membered-ring hydrogen-bonded structure and a 10-membered-ring hydrogen-bonded structure are low in energy. The coupling of these two structures forms the repeating unit for the 20/12-helix, indicating an intrinsic preference of the 10/12-helix for a beta-polypeptide, Indeed, calculations predict that an unsubstituted beta-heptapeptide model 2 favors the 10/12-helix over the 14-helix by 21.4 and 4.8 kcal/mol in the gas phase and methanol solution, respectively. The side;chain effect on the relative preferences of the 14- and the 10/12-helices is analyzed based on torsional and steric effects, and has been rested by the calculations on beta-peptide models 3-11. The methyl groups in (S)-beta(2)/beta(3)-polypeptide 9 and (S)-beta(2)-polypeptide 11 have little torsional and steric effects for right-handed 10/12-helix and left-handed 14-helix, and these beta-peptides are predicted to adopt the intrinsically favored 10/12-helix. On the other hand, (S)-beta(3)-polypeptide 10 prefers to form a left-handed 14-helix in a polar solvent mainly because of torsional effects by three of the methyl groups in the 10/12-helix. The current study can be extended to evaluate the stabilities of the 10/12- and 14-helices for other sequences. For example, the 10/12-helix is predicted to be the accessible conformation for (R)-beta(3)/(S)-beta(3)-, (S)-beta(2)/(R)-beta(2)-, (S)-beta(2)/(R)-beta(3)-, and (R)-beta(3)/(S)-beta(2)-polypeptides.