在蛋白质二级结构定义和蛋白质FTIR光谱之间寻找更好的匹配,Analytical Chemistry

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在蛋白质二级结构定义和蛋白质FTIR光谱之间寻找更好的匹配
Analytical Chemistry ( IF 6.7 ) Pub Date : 2020-12-17 , DOI: 10.1021/acs.analchem.0c03943
Joëlle De Meutter ₁ , Erik Goormaghtigh ₁

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从高分辨率结构获得蛋白质二级结构的含量需要定义和涉及各种参数的阈值，这些参数通常是氢键能或长度/角度和骨架φ/ψ角。当前使用了几种定义，它们会对二级结构的内容产生深远的影响。傅里叶变换红外（FTIR）光谱对分子几何形状有其自身的敏感性。因此，重要的是选择一组与此灵敏度相匹配的定义。在这里，我们使用了由92种蛋白质组成的新蛋白质组，这些蛋白质专为光谱方法的校准而设计。在高通量过程中已从蛋白质微阵列获得了光谱。已使用根据不同定义确定的71种结构测试了根据FTIR光谱改善二级结构预测的潜力。本文证明了不同的二级结构定义会导致二级结构含量发生较大变化，鉴于蛋白质FTIR光谱，这种变化并不等同。预测品质因数ζ可以提高约。通过选择适当的定义集，可达到20–50％。结果还表明，目前广泛用于评估蛋白质二级结构含量的蛋白质二级结构字典（DSSP）算法是处理FTIR光谱的理想选择。本文证明了不同的二级结构定义会导致二级结构含量发生较大变化，鉴于蛋白质FTIR光谱，这种变化并不等同。预测品质因数ζ可以提高约。通过选择适当的定义集，可达到20–50％。结果还表明，目前广泛用于评估蛋白质二级结构含量的蛋白质二级结构字典（DSSP）算法是处理FTIR光谱的理想选择。本文证明了不同的二级结构定义会导致二级结构含量发生较大变化，鉴于蛋白质FTIR光谱，这种变化并不等同。预测品质因数ζ可以提高约。通过选择适当的定义集，可达到20–50％。结果还表明，目前广泛用于评估蛋白质二级结构含量的蛋白质二级结构字典（DSSP）算法是处理FTIR光谱的理想选择。

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Searching for a Better Match between Protein Secondary Structure Definitions and Protein FTIR Spectra

Obtaining protein secondary structure content from high-resolution structures requires definitions and thresholds for the various parameters involved, typically hydrogen bond energy or length/angle and backbone φ/ψ angles. Several definitions are currently used and can have a profound impact on secondary structure content. Fourier transform infrared (FTIR) spectroscopy has its own sensitivity to molecular geometry. It is, therefore, important to select a set of definitions that matches this sensitivity. Here, we used a new protein set consisting of 92 proteins designed for the calibration of spectroscopic methods. Spectra have been obtained from protein microarrays in a high throughput process. The potential for improving secondary structure predictions from FTIR spectra has been tested using 71 structures determined according to different definitions. The paper demonstrates that different secondary structure definitions result in large variations in secondary structure content that are not equivalent in view of the protein FTIR spectra. The prediction quality factor ζ can be improved by ca. 20–50% by selecting an adequate definition set. The results also indicate that the dictionary of secondary structure of proteins (DSSP) algorithm, which is currently widely used to evaluate protein secondary structure content, is a good choice when dealing with FTIR spectra.

更新日期：2021-01-26

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