Torii Hajime
Department of Chemistry, School of Education, Shizuoka University, 836 Ohya, Shizuoka 422-8529, Japan.
J Phys Chem B. 2008 Jul 24;112(29):8737-43. doi: 10.1021/jp801364s. Epub 2008 Jun 26.
Amide I infrared (IR) spectral features are studied, by using the density functional theoretical method, for two untypical (but possibly rather prevalent) structures inspired from those recently suggested for amyloids: a structure consisting of loop regions in the (alpha L, alpha R) conformation stacked to form an alpha-sheet, and a structure involving some main-chain peptide groups (of any residues) and some side-chain amide groups of glutamine and asparagine residues closely located with each other. The amide I vibrational (off-diagonal) coupling constants are examined by extracting them from the calculated Cartesian-based force constants with the average partial vector method and by comparing them with those estimated on the basis of the transition dipole coupling mechanism. It is suggested that the amide I IR band characteristic of the alpha-sheet conformation in dry environment (without hydrogen bonding to solvent water molecules) is located in a high-frequency region (approximately >1670 cm(-1), somewhat higher than that of alpha-helix), because of the dependence of the diagonal (uncoupled) frequency and the off-diagonal coupling constant on the Phi and Psi dihedral angles. It is also shown that the amide I vibrations of the closely located peptide and amide groups are strongly coupled through-space with each other, and in the presence of this type of strong vibrational coupling, a noticeable change in the IR intensity upon (13)C=O substitution may occur even for a mode that arises mainly from an unsubstituted group and is not much shifted in frequency. The meaning of these results in the interpretation of observed amide I spectral profiles, especially the possible usefulness of IR spectroscopic measurements for detecting those untypical structures in the process of amyloid formation, is also discussed.
采用密度泛函理论方法，研究了两种受近期提出的淀粉样蛋白结构启发的非典型（但可能相当普遍）结构的酰胺I红外（IR）光谱特征：一种由处于（αL，αR）构象的环区域堆叠形成α-片层的结构，以及一种涉及一些主链肽基团（任何残基）和一些谷氨酰胺和天冬酰胺残基的侧链酰胺基团彼此紧密相邻的结构。通过平均部分向量法从计算得到的基于笛卡尔坐标的力常数中提取酰胺I振动（非对角）耦合常数，并将其与基于跃迁偶极耦合机制估算的耦合常数进行比较来对其进行研究。结果表明，在干燥环境中（不与溶剂水分子形成氢键），α-片层构象特征的酰胺I红外带位于高频区域（约>1670 cm⁻¹，略高于α-螺旋），这是由于对角（未耦合）频率和非对角耦合常数对Φ和Ψ二面角的依赖性。还表明，紧密相邻的肽基团和酰胺基团的酰胺I振动通过空间强烈相互耦合，并且在存在这种强振动耦合的情况下，即使对于主要由未取代基团产生且频率变化不大的模式，（¹³）C=O取代时红外强度也可能发生明显变化。还讨论了这些结果在解释观察到的酰胺I光谱轮廓中的意义，特别是红外光谱测量在检测淀粉样蛋白形成过程中那些非典型结构方面可能的有用性。
