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Molecular & Cellular Proteomics 2:1225-1233, 2003.
© 2003 by The American Society for Biochemistry and Molecular Biology, Inc.

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Technology

Identification of Novel Protein-Protein Interactions Using A Versatile Mammalian Tandem Affinity Purification Expression System^*

Matthew Knuesel, Yong Wan, Zhan Xiao^¶, Eric Holinger, Nick Lowe, Wei Wang and Xuedong Liu^,||

From the Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15213-1863, and ^¶ Cancer Research, Abbott Laboratories, Abbott Park, Illinois 60064-6101

Identification of protein-protein interactions is essential for elucidating the biochemical mechanism of signal transduction. Purification and identification of individual proteins in mammalian cells have been difficult, however, due to the sheer complexity of protein mixtures obtained from cellular extracts. Recently, a tandem affinity purification (TAP) method has been developed as a tool that allows rapid purification of native protein complexes expressed at their natural level in engineered yeast cells. To adapt this method to mammalian cells, we have created a TAP tag retroviral expression vector to allow stable expression of the TAP-tagged protein at close to physiological levels. To demonstrate the utility of this vector, we have fused a TAP tag, consisting of a protein A tag, a cleavage site for the tobacco etch virus (TEV) protease, and the FLAG epitope, to the N terminus of human SMAD3 and SMAD4. We have stably expressed these proteins in mammalian cells at desirable levels by retroviral gene transfer and purified native SMAD3 protein complexes from cell lysates. The combination of two different affinity tags greatly reduced the number of nonspecific proteins in the mixture. We have identified HSP70 as a specific interacting protein of SMAD3. We demonstrated that SMAD3, but not SMAD1, binds HSP70 in vivo, validating the TAP purification approach. This method is applicable to virtually any protein and provides an efficient way to purify unknown proteins to homogeneity from the complex mixtures found in mammalian cell lysates in preparation for identification by mass spectrometry.

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