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Originally published In Press as doi:10.1074/mcp.T300010-MCP200 on December 9, 2003.
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Molecular & Cellular Proteomics 3:176-182, 2004.
© 2004 by The American Society for Biochemistry and Molecular Biology, Inc.

Technology

Two-dimensional Blue Native/SDS Gel Electrophoresis of Multi-Protein Complexes from Whole Cellular Lysates

A PROTEOMICS APPROACH*

Margarita M. Camacho-Carvajal{ddagger},§, Bernd Wollscheid, Ruedi Aebersold, Viktor Steimle{ddagger},|| and Wolfgang W. A. Schamel{ddagger},**

From the {ddagger} Max Planck-Institute of Immunobiology, Stübeweg 51, 79108 Freiburg, Germany; and Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103-8904

Identification and characterization of multi-protein complexes is an important step toward an integrative view of protein-protein interaction networks that determine protein function and cell behavior. The limiting factor for identifying protein complexes is the method for their separation. Blue native PAGE (BN-PAGE) permits a high-resolution separation of multi-protein complexes under native conditions. To date, BN-PAGE has only been applicable to purified material. Here, we show that dialysis permits the analysis of multi-protein complexes of whole cellular lysates by BN-PAGE. We visualized different multi-protein complexes by immunoblotting including forms of the eukaryotic proteasome. Complex dynamics after {gamma} interferon stimulation of cells was studied, and an antibody shift assay was used to detect protein-protein interactions in BN-PAGE. Furthermore, we identified defined protein complexes of various proteins including the tumor suppressor p53 and c-Myc. Finally, we identified multi-protein complexes via mass spectrometry, showing that the method has a wide potential for functional proteomics.

** To whom correspondence should be addressed: Max Planck-Institut für Immunbiologie, Stübeweg 51, D-79108 Freiburg, Germany. Tel.: (0761) 5108-313; Fax: (0761) 5108-423; E-mail: schamel{at}immunbio.mpg.de


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