Purification and proteomic analysis of 20S proteasomes from human cells

The 20S proteasome is a multicatalytic protein complex present in all eukaryotic cells. Associated to regulatory complexes, it plays a major role in cellular protein degradation and in the generation of Major Histocompatibility Complex (MHC) class I antigenic peptides. In mammalian cells, this symmetrical cylindrical complex is composed of two copies of 14 distinct subunits, three of which possess a proteolytic activity. The catalytic standard subunits can be replaced by immunosubunits to form the immunoproteasome, which possesses different proteolytic efficiencies. Both types of 20S proteasomes can be present in cells in varying distributions. The heterogeneity of 20S proteasome complexes in cells leads to different protein degradation patterns. The characterization of the subunit composition of 20S proteasomes in cells thus represents an important step in the understanding of the effect of the heterogeneity of proteasome complexes on their activity. This chapter describes the use of proteomic approaches to study the subunit composition of 20S proteasome complexes purified from human cells. An immunoaffinity purification method is presented. The separation of all 20S proteasome subunits by 2D gel electrophoresis and the subunit identification by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis and database search are then described. These methods are discussed with the study of 20S proteasomes purified from two human cancer cell lines.