title: 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.
authors.affiliation: Humboldt Universität zu Berlin, Institut für Physik, AG Photobiphysik, Newtonstr. 15, Berlin D-12489, Germany. zheng@physik.hu-berlin.de
authors.forename: Zheng-Wang
authors.initials: ZW
authors.lastname: Qu
authors.forename: Hui
authors.initials: H
authors.lastname: Zhu
authors.forename: Volkhard
authors.initials: V
authors.lastname: May
mesh_terms: D016572:Cyclosporine / Q000737:chemistry*; D006860:Hydrogen Bonding; D008745:Methylation; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D013055:Spectrophotometry, Infrared / Q000379:methods*
chemical_list: D010455:Peptides; D016572:Cyclosporine