A reference dataset for the analyses of membrane protein secondary structures and transmembrane residues using circular dichroism spectroscopy
A reference dataset for the analyses of membrane protein secondary structures and transmembrane residues using circular dichroism spectroscopy
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DOI：
10.1093/bioinformatics/btr234
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发表时间：
2011-06-15
期刊：
影响因子：
5.8
通讯作者：
Wallace, B. A.
中科院分区：
文献类型：
--
作者：
Abdul-Gader, Ali;Miles, Andrew John;Wallace, B. A.
动机：基于圆二色谱(CD)和同步辐射圆二色谱(SRCD)数据对蛋白质二级结构的经验分析依赖于由相关蛋白质光谱组成的参考数据集的可用性，这些参考数据集的晶体结构已经确定。结果：建立了一个新的参考数据集MP180，其中包含了30个膜蛋白的光谱，这些蛋白质的二级结构和折叠空间被所有已知的膜蛋白结构所覆盖。此外，还创建了一个混合的可溶性和膜蛋白数据集SMP180，其中包括98个可溶性蛋白质谱(SP)和MP180谱。与仅使用可溶性蛋白质的数据集相比，使用SMP180对膜和可溶性蛋白质二级结构的计算都有显著改进。SMP180数据集还可以确定跨膜残留物的百分比，从而增强了以前可以从CD光谱学获得的信息。
Motivation: Empirical analyses of protein secondary structures based on circular dichroism (CD) and synchrotron radiation circular dichroism (SRCD) spectroscopic data rely on the availability of reference datasets comprised of spectra of relevant proteins, whose crystal structures have been determined. Datasets comprised of only soluble proteins have not proven suitable for analysing the spectra of membrane proteins.Results: A new reference dataset, MP180, has been created containing the spectra of 30 membrane proteins encompassing the secondary structure and fold space covered by all known membrane protein structures. In addition a mixed soluble and membrane protein dataset, SMP180, has been created, which includes 98 soluble protein spectra (SP) plus the MP180 spectra. Calculations of both membrane and soluble protein secondary structures using SMP180 are significantly improved with respect to those produced, using soluble protein-only datasets. The SMP180 dataset also enables determination of the percentage of transmembrane residues, thus enhancing the information previously obtainable from CD spectroscopy.