Department of Chemistry, Chemical Engineering and Materials, University of L'Aquila, via Vetoio (Coppito 1), 67010 L'Aquila, Italy.
J Phys Chem B. 2012 Mar 15;116(10):3353-60. doi: 10.1021/jp211063x. Epub 2012 Mar 7.
Infrared spectroscopy has long provided a means to estimate the secondary structure of proteins and peptides. In particular, the vibrational spectra of the amide I' band have been widely used for this purpose as the frequency positions of the amide I' bands are related to the presence of specific secondary structures. Here, we calculate the amide I' IR spectra of polylysine in aqueous solution in its three secondary structure states, i.e., α-helix, β-sheet, and random coil, by means of a mixed quantum mechanics/molecular dynamics (QM/MD) theoretical-computational methodology based on the perturbed matrix method (PMM). The computed spectra show a good agreement with the experimental ones. Although our calculations confirm the importance of the excitonic coupling in reproducing important spectral features (e.g., the width of the absorption band), the frequency shift due to secondary-structure changes is also well reproduced without the inclusion of the excitonic coupling, pointing to a role played by the local environment. Concerning the β-conformation spectrum, which is characterized by a double-peak amide I' band due to excitonic coupling, our results indicate that it does not correspond to a generic antiparallel β-sheet (e.g., of the typical size present in native proteins) but is rather representative of extended β-structures, which are common in β-aggregates. Moreover, we also show that the solvent has a crucial role in the shape determination of the β-conformation amide I' band and in particular in the disappearance of the high-frequency secondary peak in the case of small sheets (e.g., 6-stranded).
红外光谱法长期以来一直是估计蛋白质和肽的二级结构的一种手段。特别是酰胺 I'带的振动光谱已被广泛用于此目的，因为酰胺 I'带的频率位置与特定的二级结构的存在有关。在这里，我们通过基于微扰矩阵方法（PMM）的混合量子力学/分子动力学（QM/MD）理论计算方法，计算了在其三种二级结构状态（α-螺旋、β-折叠和无规卷曲）下水溶液中聚赖氨酸的酰胺 I'IR 光谱。计算出的光谱与实验光谱吻合较好。尽管我们的计算证实了激子耦合在再现重要光谱特征（例如吸收带的宽度）方面的重要性，但没有包含激子耦合也能很好地再现由于二级结构变化引起的频率位移，这表明局部环境起着作用。关于β构象光谱，其特征是由于激子耦合而具有双峰酰胺 I'带，我们的结果表明，它不对应于通用的反平行β-折叠（例如，在天然蛋白质中存在的典型大小），而是代表了常见的伸展β-结构，它们在β-聚集物中很常见。此外，我们还表明，溶剂在β构象酰胺 I'带的形状确定中起着关键作用，特别是在小折叠（例如 6 股）的情况下，高频次级峰消失。
