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首页> 外文期刊>Biopolymers: Original Research on Biomolecules and Biomolecular Assemblies >Vibrational spectroscopic characteristics of secondary structure polypeptides in liquid water: Constrained MD simulation studies
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Vibrational spectroscopic characteristics of secondary structure polypeptides in liquid water: Constrained MD simulation studies

机译：液态水中二级结构多肽的振动光谱特性：受约束的MD模拟研究

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摘要

Using the constrained MD simulation method in combination with quantum chemistry calculation, Hessian matrix reconstruction, and fragmentation approximation methods, we established a computational scheme for numerical simulations of amide I IR absorption, vibrational circular dichroism (VCD), and 2D IR photon echo spectra of peptides in solution. Six different secondary structure peptides, i.e., alpha-helix, 3(10)-helix, pi-helix, antiparallel and parallel beta-sheets, and polyproline II (P-II), are considered, and the vibrational characteristic features in their linear and nonlinearspectra in the amide I band region are discussed. Isotope-labeling effects on IR and VCD spectra are notable only for alpha- and pi-helical peptides due to the strong vibrational couplings between two nearest neighboring amide 1 local oscillators. The amplitudes of difference 2D IR spectra are shown to be strongly dependent on both the extent of mode delocalization and the relative orientation of local mode transition dipoles determined by secondary structure. (c) 2006 Wiley Periodicals, Inc.
机译：通过将约束MD模拟方法与量子化学计算，Hessian矩阵重建和碎片近似方法相结合，我们为酰胺I IR吸收，振动圆二色性（VCD）和二维IR光子回波光谱的数值模拟建立了计算方案。溶液中的肽。考虑了六种不同的二级结构肽，即α-螺旋，3（10）-螺旋，pi-螺旋，反平行和平行β-折叠和聚脯氨酸II（P-II），并且它们的线性振动特征讨论了酰胺I带区域的非线性光谱。同位素标记对IR和VCD光谱的影响仅对α和pi螺旋肽尤为明显，这是因为两个最近的相邻酰胺1本地振荡器之间存在强烈的振动耦合。差分二维红外光谱的幅度显示出强烈依赖于模式离域的程度和由二级结构确定的局部模式跃迁偶极子的相对取向。 （c）2006年Wiley Periodicals，Inc.

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