You work for a pharmaceutical company’s basic science division. Your lab has identified a small molecule inhibitor of your favorite protein (YFP). Your job now is to isolate this protein for structural studies.
You decide to recombinantly express YFP in bacteria for large scale isolation of the protein. Your supervisor suggests using a Glutathione-S-Transferase (GST) pulldown with TEV protease treatment.
The GST pulldown is a well-established method for protein purification but often generates false-positives.
How will you assay that the product of this pulldown is pure and what are the proper controls?