Please be VERY careful with this particular assay for conformational
change. Not only can a protease sensitive site be uncovered by a
structural change, but also a ligand-less protein CAN be more
"breathe-able" with respect to its liganded strucuture which can have a
more "solid" protease protected structure. Typsin can be very sneakey
if given the chance. This happened to us. Turns out that by X-ray
analysis and by NMR analysis, what was previously thought of as a
"structural change on ligand binding" was actually a firming up of the
fold of the protein. No residues actually changed position to any great
extend. The protease protection is probably a red herring in this case.
There are very well documented examples of protease protection revealing
gross structural changes. Just...PLEASE BE CAREFUL with the
interpretation of this assay.