Conformational Analysis of Macromolecules. III. Helical Structures of Polyglycine and Poly-L-Alanine

A theoretical study of the regular conformations of isolated helices (i.e., with no intermolecular interactions) of polyglycine and poly-L-alanine has been carried out. The energy of each helical conformation was calculated by using semiempirical potential functions for the barriers to internal rotation about single bonds, nonbonded interactions, dipole—dipole interactions between the amide groups, and hydrogen bonding between backbone NH and CO groups. All bondlengths and bond angles were held fixed, and the amide group was fixed in the planar trans conformation. Within the accuracy of the calculations, the right and left-handed α-helical conformations were found to be those of lowest energy for polyglycine. For poly-L-alanine, the right-handed α helix was found to be the most stable conformation. This conformation was stabilized not only by hydrogen bonding and dipole—dipole interactions, but also by the nonbonded interactions; in fact, it is the nonbonded energy which makes the right-handed α helix more stable than the left-handed one in poly-L-alanine, since dipole—dipole interactions and hydrogen bonding stabilize both structures about equally well. The effect of varying the parameters in the semiempirical potential functions was studied, and the results and conclusions of these calculations were compared with calculations made by other investigators and with experimentally determined polypeptide conformations.