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Vibrational spectral signatures of peptide secondary structures: N ‐methylation and side chain hydrogen bond in cyclosporin A
Author(s) -
Qu ZhengWang,
Zhu Hui,
May Volkhard
Publication year - 2011
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21728
Subject(s) - antiparallel (mathematics) , conformational isomerism , chemistry , hydrogen bond , side chain , peptide bond , protein secondary structure , vibrational circular dichroism , peptide , peptide conformation , crystallography , circular dichroism , acetonitrile , infrared spectroscopy , computational chemistry , molecule , physics , organic chemistry , biochemistry , quantum mechanics , magnetic field , polymer
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