HIV Particles Used as Tool to Capture Native Protein Complexes

Protein purification has been the cornerstone of laboratory research for decades, and in that time, scientists have funneled considerable effort and finances into isolating protein complexes under native conditions. Classical purification techniques require the use of cell lysis chemicals that often disassociate the interactions between complex protein molecules.

Now Belgian scientists from the Flanders Institute for Biotechnology (VIB) and Ghent University (UGent) have developed a viral particle sorting approach for purifying protein complexes under native conditions, which they have dubbed Virotrap. This new method catches a bait protein together with its associated protein partners in virus-like particles that are budded from human cells. Cell lysis is not required using this technique and protein complexes are preserved during purification.

“The first step in a classical study on protein complexes essentially turns the highly organized cellular structure into a big messy soup,” explained lead study author Sven Eyckerman, Ph.D., expert scientist at VIB and lecturer at UGent. “We used the natural process of HIV particle formation to our benefit by hacking a completely safe form of the virus to abduct intact protein machines from the cell.”

The research team took inspiration from virus biology to develop the Virotrap system, as it has been well known that the human immunodeficiency virus (HIV) captures a number of host proteins during its particle formation.

“By fusing a bait protein to the HIV-1 GAG protein, we show that interaction partners become trapped within virus-like particles (VLPs) that bud from mammalian cells,” the authors wrote. “Using an efficient VLP enrichment protocol, Virotrap allows the detection of known binary interactions and MS [mass spectrometry]-based identification of novel protein partners as well. In addition, we show the identification of stimulus-dependent interactions and demonstrate trapping of protein partners for small molecules.”

The findings from this study were published recently in Nature Communications in an article entitled “Trapping Mammalian Protein Complexes in Viral Particles.”

“Virotrap represents a new concept in co-complex analysis wherein complex stability is physically guaranteed by a protective, physical structure,” noted co-senior study author Jan Tavernier, Ph.D., a professor at UGent and VIB group leader. “It is complementary to the arsenal of existing interactomics methods, but also holds potential for other fields, like drug target characterization. We also developed a small molecule-variant of Virotrap that could successfully trap protein partners for small molecule baits.”

The investigators found that by trapping protein complexes in the protective environment of a virus-like shell, the intact complexes are preserved during the purification process. Moreover, they showed that the method was suitable for detection of known binary interactions as well as MS-based identification of novel protein partners.

“Virotrap can also impact our understanding of disease pathways,” remarked Kris Gevaert, Ph.D., a professor at UGent and associate department director at VIB. “We were actually surprised to see that this virus-based system could be used to study antiviral pathways, like Toll-like receptor signaling. Understanding these protein machines in their natural environment is essential if we want to modulate their activity in pathology.”