Vibrational analysis of peptides, polypeptides, and proteins. V. Normal vibrations of Β-turns

Abstract

The normal modes have been calculated for Β-turns of types I, II, III, I′, II′, and III′. The complete set of frequencies is given for the first three structures; only the amide I, II, and III modes are given for the latter three structures. Calculations have been done for structures with standard dihedral angles, as well as for structures whose dihedral angles differ from these by amounts found in protein structures. The force field was that refined in our previous work on polypeptides. Transition dipole coupling was included, and is crucial to predicting frequency splittings in the amide I and amide II modes. The results show that in the amide I region, Β-turn frequencies can overlap with those of the Α-helix and Β-sheet structures, and therefore caution must be exercised in the interpretation of protein bands in this region. The amide III modes of Β-turns are predicted at significantly higher frequencies than those of Α-helix and Β-sheet structures, and this region therefore provides the best possibility of identifying Β-turn structures. Amide V frequencies of Β-turns may also be distinctive for such structures.