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Analysis of Vibrational Circular Dichroism Spectra of Peptides: a Generalised Coupled Oscillator Approach of a Small Peptide Model Using VCDtools

DOI:10.1021/acs.jpcb.9b11261 期刊:The Journal of Physical Chemistry B 出版年份:2020 更新时间:2025-09-19 17:13:59
摘要: Vibrational Circular Dichroism (VCD) is one of the major spectroscopic tools to study peptides. Nevertheless, a full understanding of what determines the signs and intensities of VCD bands of these compounds in the amide I and amide II spectral regions is still far from complete. In the present work we study the origin of these VCD signals using the General Coupled Oscillator (GCO) analysis, a novel approach that has recently been developed. We apply this approach to the ForValNHMe model peptide in both α-helix and β-sheet configurations. We show that the intense VCD signals observed in the amide I and amide II spectral regions essentially have the same underlying mechanism, namely, the through-space coupling of electric dipoles. The crucial role played by intra-molecular hydrogen bonds in determining VCD intensities is also illustrated. Moreover, we find that contributions to the rotational strengths considered to be insignificant in standard VCD models may have sizable magnitudes and can thus not always be neglected. In addition, the VCD robustness of amide I and II modes has been investigated by monitoring the variation of the rotational strength and its contributing terms during linear transit scans and by performing calculations with different computational parameters. From these studies -and in particular the decomposition of the rotational strength made possible by the GCO analysis- it becomes clear that one should be cautious when employing measures of robustness as proposed previously.
作者: Mark A. J. Koenis,Lucas Visscher,Wybren J. Buma,Valentin P. Nicu
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To study the origin of VCD signals in the amide I and amide II spectral regions of peptides using the General Coupled Oscillator (GCO) analysis.

The study concludes that the intense VCD signals in the amide I and amide II spectral regions of peptides are primarily due to the through-space coupling of electric dipoles, as revealed by the GCO analysis. Intra-molecular hydrogen bonds play a crucial role in determining VCD intensities. The research highlights the importance of considering contributions to rotational strengths that are often neglected in standard VCD models and cautions against the uncritical use of robustness measures for VCD signs.

The study focuses on a small model peptide, ForValNHMe, which may not fully represent the complexity of larger peptides and proteins. The analysis is based on computational models, and the results may vary with different computational parameters. The robustness of VCD signs is sensitive to the relative orientation of molecular fragments, which can be influenced by small structural variations.

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