Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong 510006, China.
Faculty of Science, Ehime University, 2-5 Bunkyo-cho, Matsuyama City 790-0825, Japan.
J Chromatogr B Analyt Technol Biomed Life Sci. 2021 Jan 15;1163:122509. doi: 10.1016/j.jchromb.2020.122509. Epub 2020 Dec 21.
Previously, we have reported on the reconstruction of 4323 native protein 2D maps of human bronchial smooth muscle cells (HBSMC) by combining nondenaturing 2DE, grid gel-cutting, and quantitative LC-MS/MS. In this work, we report on the visualization of the heterooligomeric subunit structures of HBSMC proteins by correlating the native protein 2D maps with the information in protein interaction databases. Image analysis of the 2D maps was employed as the first approach. Each of the native protein 2D maps of 2327 proteins, which had three or more detected squares in the native protein 2D maps, was compared with the 2D maps of the remaining 2326 proteins scoring the degree of overlap in an area around the quantity peak and the protein partner which showed the best score was decided. The protein pairs were examined on their reported interactions referring to protein interaction databases. In order to consider the cases where a protein has multiple functions and the heterooligomeric subunit structures might not be detected from the image analysis, prior database search was employed as the second approach. Each of the 1689 HBSMC proteins, which had five or more detected squares in the native protein 2D maps, was examined on its interactor proteins described in the databases, then the native 2D map was compared with the maps of the interactor proteins to find the overlap which reasonably supported the interaction. Summarizing these examinations, 215 heterooligomeric subunit structures of 817 human cellular proteins could be visualized on the native protein 2D maps.
此前，我们曾报道过通过结合非变性 2-DE、网格胶切割和定量 LC-MS/MS，重建 4323 个人类支气管平滑肌细胞（HBSMC）天然蛋白质 2D 图谱。在这项工作中，我们通过将天然蛋白质 2D 图谱与蛋白质相互作用数据库中的信息相关联，报告了 HBSMC 蛋白质的异源寡聚亚基结构的可视化。通过对 2D 图谱进行图像分析，作为第一种方法。对于在天然蛋白质 2D 图谱中有三个或更多检测到的正方形的 2327 种蛋白质中的每一种蛋白质，将其与其余 2326 种蛋白质的 2D 图谱进行比较，在数量峰和最佳得分的蛋白质伴侣周围的区域中比较重叠程度，并决定最佳得分的蛋白质伴侣。根据蛋白质相互作用数据库，检查这些蛋白质对报道的相互作用。为了考虑蛋白质具有多种功能的情况，并且可能无法从图像分析中检测到异源寡聚亚基结构，因此采用了预先的数据库搜索作为第二种方法。对于在天然蛋白质 2D 图谱中有五个或更多检测到的正方形的 1689 种 HBSMC 蛋白质，检查数据库中描述的其相互作用蛋白，然后将天然 2D 图谱与相互作用蛋白的图谱进行比较，以找到合理支持相互作用的重叠。总结这些检查，在天然蛋白质 2D 图谱上可以可视化 817 个人类细胞蛋白质的 215 个异源寡聚亚基结构。
