Virotrap: Abducting Protein Complexes from Mammalian Cells

Cell lysis is an inevitable step in classical affinity purification - mass spectrometry (AP-MS) strategies to map intracellular protein interactions. Cell homogenization implies a drastic change of the protein complex environment which strongly impedes comprehensive analysis. Complementary lysis conditions, in situ crosslinking strategies and proximal labeling techniques have been recently developed to address part of this problem. We here demonstrate the use of a viral particle sorting approach as an alternative lysis-free method. By fusing a bait protein to the HIV-1 GAG protein, we show that interaction partners of the bait protein become trapped within virus-like particles (VLPs) that bud from mammalian cells. This so-called Virotrap approach obviates the need for cell homogenization and preserves the protein complexes during purification. Using an efficient VLP enrichment protocol, Virotrap allows the detection of known binary interactions as well as MS-based identification of novel protein partners. In addition, we show the identification of stimulus-dependent interactions and demonstrate trapping of protein partners for small molecules. Virotrap constitutes an elegant complementary approach to the current arsenal of MS-based methods to study protein complexes.