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首页> 外文期刊>The journal of physical chemistry, B. Condensed matter, materials, surfaces, interfaces & biophysical >The Amide I Spectrum of Proteins-Optimization of Transition Dipole Coupling Parameters Using Density Functional Theory Calculations
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The Amide I Spectrum of Proteins-Optimization of Transition Dipole Coupling Parameters Using Density Functional Theory Calculations

机译：使用密度函数理论计算的蛋白质蛋白质优化蛋白质优化优化 - 优化转变偶极耦合参数

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摘要

The amide I region of the infrared spectrum is related to the protein backbone conformation and can provide important structural information. However, the interpretation of the experimental results is hampered because the theoretical description of the amide I spectrum is still under development. Quantum mechanical calculations, for example, using density functional theory (DFT), can be used to study the amide I spectrum of small systems, but the high computational cost makes them inapplicable to proteins. Other approaches that solve the eigenvalues of the coupled amide I oscillator system are used instead. An important interaction to be considered is transition dipole coupling (TDC). Its calculation depends on the parameters of the transition dipole moment. This work aims to find the optimal parameters for TDC in three major secondary structures: alpha-helices, antiparallel beta-sheets, and parallel beta-sheets. The parameters were suggested through a comparison between DFT and TDC calculations. The comparison showed a good agreement for the spectral shape and for the wavenumbers of the normal modes for all secondary structures. The matching between the two methods improved when hydrogen bonding to the amide oxygen was considered. Optimal parameters for individual secondary structures were also suggested.
机译：红外光谱的酰胺I区域与蛋白质骨干构象相关，并且可以提供重要的结构信息。然而，对实验结果的解释被阻碍，因为酰胺I光谱的理论描述仍在开发中。量子力学计算，例如，使用密度泛函理论（DFT），可用于研究小型系统的酰胺I光谱，但高计算成本使它们不适用于蛋白质。解决了解决偶联酰胺I振荡器系统的特征值的其他方法。要考虑的重要相互作用是过渡偶极耦合（TDC）。其计算取决于转换偶极矩的参数。这项工作旨在找到三个主要二级结构中TDC的最佳参数：α-螺旋，反平行β-薄片和平行β-薄片。通过DFT和TDC计算之间的比较提出了参数。比较显示了对所有二级结构的频谱形状和常规模式的波数的良好一致性。考虑到与酰胺氧的氢键合时，两种方法之间的匹配得到改善。还提出了各个二级结构的最佳参数。

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