Deciphering the structural preference encoded in amide-I vibrations of lysine dipeptide in gas phase and in aqueous solutionCai, KC (Cai, Kaicong); Zheng, X (Zheng, Xuan); Hou, YJ (Hou, Yanjun); Chen, F (Chen, Feng); Yan, GY (Yan, Guiyang); Zhuang, DL (Zhuang, Danling)
Spectrochimia acta part A-Molecular and Biomolecular Spectroscopy, 2021, Volume 247, 119066.
Protein's biological function is critically associated with its structural feature, which is encoded in its amino acid sequence. For evaluation of conformational fluctuation and folding mechanism, DFT calculations were performed on the model compound lysine dipeptide (LYSD) in gas phase to demonstrate the correlation between amide-I vibrations and secondary structure. Molecular dynamics simulations were carried out for the structural dynamics of LYSD in aqueous solution. The results show that LYSD tends form C-7eq, C-5, beta, PPII and alpha conformations in the gas phase and primarily presented PPII and alpha conformations in aqueous solution. The obtained amide-I vibrational frequencies of LYSD conformers were assigned, thus build the correlations between amide-I probes and secondary structure of LYSD. These results provide theoretical insights into the structural feature of LYSD through amide-I vibrations, and would shed light on site specific structural prediction of polypeptides. (C) 2020 Elsevier B.V. All rights reserved.
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