Vibrational spectral signatures of peptide secondary structures:N-methylation and side chain hydrogen bond in cyclosporin A

Abstract Molecular dynamics simulations are performed to explore important conformations of cyclosporin A, an immunosuppressive cyclic undecapeptide drug, in different media including gas‐phase, chloroform, and acetonitrile. Density functional theory calculations are used to refine the low‐lying conformers and to predict their infrared and vibrational circular dichroism spectra. Vibrational spectral signatures in the important amide II, I, and A regions are identified for typical peptide secondary structures including β‐turn (type II′ or I), antiparallel β‐sheet (flat or twisted), inverse γ‐turn, N ‐methylated peptide bond, and side chain H‐bond. New insights into the spectral signatures of secondary structures especially with N ‐methylation and side chain hydrogen bond are provided, which can be very useful for further peptide conformation analysis in general. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011