Computational Study of the Vibrational Characteristics of Alpha-Helical Coiled Coils According to Structural Changes

Alpha-helix and α-helical coiled coils are important structural motifs in biology. Compared to other structural motifs, these structures have been more comprehensively studied because they can be easily changed using a few simple structural parameters. In this study, various structures of α-helical coiled coils and α-helices were produced by systematically changing their structural parameters including rise per residue, superhelical radius, and superhelical frequency, after which their vibrational characteristics were theoretically investigated. To explore the changes in their infrared spectrum according to their structural variations, vibrational Hamiltonians for the amide I modes were theoretically constructed, and various spectra were calculated for the density of vibrational states, the phase-correlation factor, the inverse participation ratio, and the magnitude of transition dipole moment. This study proposes various relationships between coupling constants, transition dipole moments, and spectra. Moreover, the peak of the infrared spectrum was shifted to a lower frequency as the superhelical frequency decreased and the superhelical radius increased.