Dipartimento di Scienze Fisiche e Chimiche, University of L'Aquila , via Vetoio (Coppito 1), 67010 Coppito (AQ), Italy.
J Phys Chem B. 2013 Oct 17;117(41):12383-90. doi: 10.1021/jp406708p. Epub 2013 Oct 3.
The amide I' infrared spectrum of a α-helical photoswitchable peptide is calculated here by means of a mixed quantum mechanics/molecular dynamics theoretical-computational methodology based on the perturbed matrix method (PMM). The contribution of specific residues to the total spectrum is also analyzed and the results compared to previous experimental spectroscopic data, obtained by means of site-specific isotope labeling at different residues, resulting in good agreement. One of the residues (Ala7) shows atypical spectroscopic behavior in both the experimental and calculated spectra, i.e., the folded-state amide I' band is shifted to higher frequencies than the unfolded-state one, while the other residues show the opposite behavior. The calculations reveal the origin of this uncommon spectroscopic trend and point to a crucial role of the molecular switch, the presence of which perturbs the conformational sampling of the peptide. Indeed, infrared spectra of the same peptide calculated in the absence of the molecular switch show that the single-residue spectrum of Ala7 does not have any distinguishing feature, resembling the spectra of the other analyzed residues.
本文采用基于微扰矩阵方法（PMM）的混合量子力学/分子动力学理论计算方法，计算了α-螺旋光开关肽的酰胺 I' 红外光谱。还分析了特定残基对总光谱的贡献，并将结果与以前通过在不同残基处进行定点同位素标记获得的实验光谱数据进行了比较，结果吻合较好。一个残基（Ala7）在实验和计算光谱中表现出非典型的光谱行为，即折叠态酰胺 I' 带的频率高于展开态，而其他残基则表现出相反的行为。计算结果揭示了这种不寻常的光谱趋势的起源，并指出分子开关的关键作用，其存在会干扰肽的构象采样。事实上，在不存在分子开关的情况下计算相同肽的红外光谱表明，Ala7 的单残基光谱没有任何特征，类似于其他分析残基的光谱。
