Orientation determination of protein helical secondary structures using linear and nonlinear vibrational spectroscopy.
Orientation determination of protein helical secondary structures using linear and nonlinear vibrational spectroscopy.
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DOI：
10.1021/jp904153z
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发表时间：
2009-09-10
期刊：
影响因子：
--
通讯作者：
Chen Z
中科院分区：
文献类型：
--
作者：
Nguyen KT;Le Clair SV;Ye S;Chen Z
在本文中，我们系统地介绍了使用振动光谱方法，特别是非线性和频生成（SFG）振动光谱，以及红外光谱和拉曼散射等线性振动光谱技术来确定蛋白质螺旋二级结构的方向。可以使用输入激光束和输出信号束的不同偏振组合来收集 SFG 酰胺 I 信号，以测量螺旋酰胺 I 模式的二阶非线性光学磁化率分量，这些分量通过这些螺旋的取向分布与其分子超极化元素相关。根据螺旋的红外跃迁偶极矩和拉曼极化张量，可以计算螺旋的酰胺I模式的分子超极化元素；这些量是通过使用键加和模型分别对肽单元（或氨基酸残基）的各个红外偶极跃迁矩和拉曼极化张量求和来确定的。计算出的螺旋的整体红外跃迁偶极矩和拉曼极化张量可以通过使用偏振红外和偏振拉曼光谱对具有良好排列的螺旋结构的样品的实验数据进行验证。根据推导的 SFG 超极化元素和测量的 SFG 二阶非线性磁化率分量，可以确定有关螺旋结构的方向信息。尽管也可以使用偏振红外或偏振拉曼酰胺 I 信号来测量此类取向信息，但 SFG 的检测限要低得多，当其表面覆盖率远低于单层时，可用于研究螺旋的取向。此外，不同振动光谱技术（例如 SFG 和衰减全反射 - 傅里叶变换红外光谱）的结合，为取向确定提供了更多测量参数，有助于推论更复杂的取向分布。在本文中，我们讨论了两种类型的螺旋：α 螺旋和 3-10 螺旋。然而，这里提出的方向确定方法是通用的，因此也可以应用于研究其他螺旋。还对不同链长的 α 螺旋和 3-10 螺旋结构的 SFG 酰胺 I 超极化成分进行了计算。研究发现，当螺旋达到一定长度时，螺旋中肽单元的数量不应显着改变数据分析。然而，计算表明，当螺旋链较短时，当链长改变时，SFG超极化率成分比例会发生很大变化。由于蛋白质中的 3-10 个螺旋结构可能非常短，因此短 3-10 个螺旋的方向确定需要考虑螺旋中肽单元的数量。
In this paper, we systematically presented the orientation determination of protein helical secondary structures using vibrational spectroscopic methods, particularly the nonlinear Sum Frequency Generation (SFG) vibrational spectroscopy, along with linear vibrational spectroscopic techniques such as infrared spectroscopy and Raman scattering. SFG amide I signals can be collected using different polarization combinations of the input laser beams and output signal beam to measure the second order nonlinear optical susceptibility components of the helical amide I modes, which are related to their molecular hyperpolarizability elements through the orientation distribution of these helices. The molecular hyperpolarizability elements of amide I modes of a helix can be calculated based on the infrared transition dipole moment and Raman polarizability tensor of the helix; these quantities are determined by using the bond additivity model to sum over the individual infrared dipole transition moments and Raman polarizability tensors, respectively, of the peptide units (or the amino acid residues). The computed overall infrared transition dipole moment and Raman polarizability tensor of a helix can be validated by experimental data using polarized infrared and polarized Raman spectroscopy on samples with well-aligned helical structures. From the deduced SFG hyperpolarizability elements and measured SFG second order nonlinear susceptibility components, orientation information regarding helical structures can be determined. Even though such orientation information can also be measured using polarized infrared or polarized Raman amide I signals, SFG has a much lower detection limit, which can be used to study the orientation of a helix when its surface coverage is much lower than a monolayer. In addition, the combination of different vibrational spectroscopic techniques, e.g., SFG and Attenuated Total Reflectance – Fourier Transform Infrared spectroscopy, provides more measured parameters for orientation determination, aiding in the deduction of more complicated orientation distributions. In this paper, we discussed two types of helices: the α-helix and 3–10 helix. However, the orientation determination method presented here is general, and thus can be applied to study other helices as well. The calculations of SFG amide I hyperpolarizability components for α-helical and 3–10 helical structures with different chain lengths have also been performed. It was found that when the helices reach a certain length, the number of peptide units in the helix should not alter the data analysis substantially. It was shown in the calculation, however, that when the helix chain is short, the SFG hyperpolarizability component ratios can vary substantially when the chain length is changed. Because 3–10 helical structures can be quite short in proteins, the orientation determination for a short 3–10 helix needs to take into account the number of peptide units in the helix.
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