Assessing Spectral Simulation Protocols for the Amide I Band of Proteins
Assessing Spectral Simulation Protocols for the Amide I Band of Proteins
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DOI：
10.1021/acs.jctc.6b00420
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发表时间：
2016-08-01
影响因子：
5.5
通讯作者：
Jansen, Thomas L. C.
中科院分区：
文献类型：
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作者：
Cunha, Ana V.;Bondarenko, Anna S.;Jansen, Thomas L. C.
我们提出了一项针对蛋白质酰胺I带的光谱模拟协议的基准研究。酰胺I带由于信号强度大、对氢键高度敏感、具有二级结构基序等特点，在蛋白质红外光谱中得到了广泛的应用。因此，这条带在许多蛋白质结构功能关系的研究中被证明是有价值的。我们使用两个共同的力场，结合几个静电映射和耦合模型，对光谱模拟协议进行基准测试。实验结果与实验的线性吸收和二维红外光谱相比较，验证了这三种研究良好的蛋白质。我们发现二维红外光谱对模拟协议比线性吸收更敏感，并报告了最好的模拟协议。这些发现表明，仍有改进现有蛋白质酰胺I带模型的空间。
We present a benchmark study of spectral simulation protocols for the amide I band of proteins. The amide I band is widely used in infrared spectroscopy of proteins due to the large signal intensity, high sensitivity to hydrogen bonding, and secondary structural motifs. This band has, thus, proven valuable in many studies of protein structure function relationships. We benchmark spectral simulation protocols using two common force fields in combination with several electrostatic mappings and coupling models. The results are validated against experimental linear absorption and two-dimensional infrared spectroscopy for three well-studied proteins. We find two-dimensional infrared spectroscopy to be much more sensitive to the simulation protocol than linear absorption and report on the best simulation protocols. The findings demonstrate that there is still room for ideas to improve the existing models for the amide I band of proteins.