Visualized heterooligomeric subunit structures of 817 human cellular proteins by correlating native protein 2D maps with protein interaction databases.

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.