Assessment of the amide-I local modes in gamma- and beta-turns of peptides.
The amide-I local modes, mainly the C[double bond, length as m-dash]O stretching vibrations, form the structural basis of femtosecond 2D IR spectroscopy in characterizing backbone structures and dynamics of peptides and proteins. In this work, a density functional theory (DFT) level of computational assessment of the amide-I local modes in oligomers mostly in the turn conformations was carried out. It is shown that local mode properties, including transition frequencies and transition dipole magnitudes and orientations, are slightly conformational dependent. However, the distributions of these properties in the peptide oligomers are narrow and have mean values almost identical to those from an isolated peptide monomer, justifying the prevalent use of a uniform local mode in modeling the 1D and 2D IR spectra. In addition, it is shown that the transition dipole magnitude and orientation of the peptide monomer predicted by the DFT calculations can be well approximated by electrostatic potential-based transition charge schemes, e.g. Merz-Singh-Kollman, CHELP, as well as CHELPG.
Wang
Jianping
J
Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China. jwang@iccas.ac.cn
D000577:Amides / Q000737:chemistry*; D003198:Computer Simulation; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary
D000577:Amides; D010455:Peptides