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  • Title: Mapping the amide-I vibrations of model dipeptides with secondary structure sensitivity and amino acid residue specificity, and its application to amyloid β-peptide in aqueous solution.
    Author: Cai K, Zheng X, Liu J, Du F, Yan G, Zhuang D, Yan S.
    Journal: Spectrochim Acta A Mol Biomol Spectrosc; 2019 Aug 05; 219():391-400. PubMed ID: 31059891.
    Abstract:
    Vibrational spectroscopy has been known as particularly well-suited for deciphering the polypeptide's structure. To decode structural information encoded in IR spectra, we developed amide-I frequency maps on the basis of model dipeptides to correlate the amide-I frequency of interest to the combination of the calculated secondary structure dependent amide-I frequency by using DFT method and the electrostatic potentials that projected onto the amide unit from the micro-environment within molecular mechanics force field. The constructed maps were applied to model dipeptides and amyloid β-peptide fragment (Aβ25-35). The dipeptide specified map (DS map) and the hybrid map (HYB map) predicted amide-I bands of Aβ25-35 in solution satisfactorily reproduce experimental observation, and indicate the preference of forming β-sheet and random coil structure for Aβ25-35 in D2O just as the results of cluster analysis suggested. These maps with secondary structural sensitivity and amino acid residue specificity open up a way for the interpretation of amide-I vibrations and show their potentials in the understanding of molecular structure of polypeptides in solution.
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