I am continuing to try and understand the domain architecture of the huntingtin protein. In a bid to validate my previous limited proteolysis/mass spectrometry experiment, I wanted to see if I could get similar proteolytically stable fragments by digesting my remaining aliquot (courtesy of the generous Stefan Kochanek and Bin Huang) of full-length huntingtin protein with a different enzyme, chymotrypsin, instead of trypsin. Using an orthogonal enzyme with a different cleavage specificity is a good way to validate the regions of protein which are truly accessible to proteolytic enzymes which therefore likely represent less structured regions of the huntingtin protein and are possibly linker regions between the more structured domains of the protein.
In an eager attempt to see what, if any, fragments are proteolytically stable, I stained the gel for too short a period of time, so it is back in the silver-coomassie stain overnight. However, some bands are visible (wahey!) around 100 kDa and 120 kDa so I am very hopeful as to what I will see tomorrow! You can read all about the details and see a picture of the gel on Zenodo. More on this in the morning.