As indicated in Section 38.4, BN-PAGE is beginning to emerge as a universal tool to study stable protein interactions on a large scale. The power of this approach in comparison to other, more focused techniques lies in its experimental simplicity and the broadness of its potential application. Within a single experiment, the subunits of several protein complexes can be separated, ready for subsequent identification. The introduction of BN-PAGE has increased our knowledge of the composition of the respiratory chain considerably. Especially in plants, but also in other organisms, a wealth of additional subunits in individual protein complexes has been found. Additionally, associations of photosynthetic and respiratory complexes into supercomplexes with defined stoichiometry have been discovered using this tool. Apart from their role in the analysis of protein interactions, 2D and 3D BN-PAGE are also proving to be a valuable tools to resolve the individual proteins present in a given membrane. BN-PAGE can act as a good compromise between IEF/SDS-PAGE, which cannot display the majority of hydrophobic proteins, and 1D SDS-PAGE, which can display hydrophobic protein but does not provide sufficient resolution of complex samples. It has been found that the average GRAVY scores of proteins derived from an Ara-bidopsis mitochondria are significantly higher for BN/SDS-PAGE when compared to IEF/SDS-PAGE, but these proteins also feature a wider range of hydrophobicity as indicated by the standard deviation of the GRAVY scores from the mean [46]. However, despite all the successful applications of BN-PAGE, we think that this technique still has not reached its full potential in its wider applications in proteomics and in the analysis of protein interactions in plants. This might be due to certain generic limitations of the system (see Box 38.1 and Section 38.1), but is mainly due to the fact that BN-PAGE is still not as established and widespread as IEF/SDS-PAGE in proteomic laboratories.

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