Most molecular functions depend on defined associations of proteins. Protein-protein interactions may be transient or long-lasting; they may lead to labile assemblies or more stable particles termed protein complexes. Studying protein-protein interactions is of prime importance for understanding molecular functions in cells. The complexome profiling approach allows to systematically analyze protein assemblies of cells or subcellular compartments. It combines separation of intact protein fractions by blue native (BN) polyacrylamide gel electrophoresis (PAGE) and protein identification as well as quantification by mass spectrometry. Complexome profiling has been successfully applied to characterize mitochondrial fractions of plants. In a typical experiment, more than 1000 mitochondrial proteins are identified and assigned to defined protein assemblies. It allows discovering so far unknown protein complexes, studying assembly pathways of protein complexes and even characterizing labile super- and megacomplexes in the >10 mega-Dalton range. We here present a complexome profiling protocol for the straightforward definition of the protein complex inventory of mitochondria or other subcellular compartments from plants.
Keywords: Arabidopsis thaliana; Blue native polyacrylamide gel electrophoresis; Complexome profiling; Mass spectrometry; Plant mitochondria; Respiration; Viscum album.
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