Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
Department of Optics, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic.
Phys Chem Chem Phys. 2018 Feb 14;20(7):4926-4935. doi: 10.1039/c7cp08016f.
Vibrational circular dichroism (VCD) spectroscopy is an excellent method to determine the secondary structure of proteins in solution. Comparison of experimental spectra with quantum-chemical simulations represents a convenient and objective way to extract information on the structure. This has been difficult for such large molecules where approximate theoretical models have to be used. In the present study we applied the Cartesian-coordinate based tensor transfer (CCT) making it possible to extend the density functional theory (DFT) and model spectral intensities of large globular proteins nearly at quantum-chemical precision. Indeed, comparison with experiment provided a better understanding of the dependence of VCD spectral shapes on the geometry, their sensitivity to fine structural details and interactions with the environment. On a model set of globular proteins the simulated spectra correlated well with experimental data and revealed which structural information can (and cannot) be obtained from this kind of spectroscopy. Although the VCD technique has been regarded as being rather insensitive to side-chain variations, we found that the spectra of human and hen lysozyme differing by a few amino acids only are quite distinct. This has been explained by long-distance coupling of the amide vibrations. Likewise, the modeling reproduced some spectral changes caused by protein deuteration even when the protein structure was conserved.
振动圆二色性（VCD）光谱学是一种确定溶液中蛋白质二级结构的极好方法。将实验光谱与量子化学模拟进行比较代表了一种提取结构信息的便捷和客观的方法。对于这种大分子来说，这一直很困难，因为必须使用近似的理论模型。在本研究中，我们应用了基于笛卡尔坐标的张量转移（CCT），使得在密度泛函理论（DFT）和模型光谱强度方面扩展对大型球状蛋白质的研究成为可能，几乎达到了量子化学的精度。实际上，与实验的比较提供了对 VCD 光谱形状对几何形状的依赖性、对精细结构细节的敏感性以及与环境相互作用的更好理解。在一组球状蛋白质模型上，模拟的光谱与实验数据很好地相关，并揭示了可以（和不能）从这种光谱中获得哪种结构信息。尽管 VCD 技术被认为对侧链变化的敏感性较低，但我们发现仅相差几个氨基酸的人溶菌酶和鸡溶菌酶的光谱非常明显。这可以通过酰胺振动的长程耦合来解释。同样，即使在保持蛋白质结构不变的情况下，建模也可以复制由蛋白质氘化引起的一些光谱变化。
