Tag-Based Pull-Down Assay

Protein-protein interactions play a crucial role in diverse biological processes. As obligate intracellular parasites, plant viruses live and reproduce in living cells and recruit host proteins through protein-protein interactions to complete their infection process. Elucidation of the protein-protein interaction network between viruses and hosts can advance knowledge in the viral infection process at the molecule level and facilitate the development of novel antiviral technologies. One of the most classic and widely used methods to discover or confirm novel protein interactions in plant cells is the pull-down assay. For plant virology research, this method begins with the expression of a tagged viral protein (such as GST- or His-tagged) as "bait" in model plant species such as Nicotiana benthamiana. The expressed "bait" protein is purified by affinity agarose resin (e.g., glutathione or cobalt chelate) followed by a series of washes. Finally, the "bait"-"prey" protein complexes are subjected to mass spectrometry or immunoblotting analysis. In this chapter, we describe a practical protocol of the tag-based pull-down assay and discuss solutions to some common problems associated with this assay.