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Help! How can I look at the conformational changes in proteins?

R. Bryan Sutton sutton at howie.swmed.edu
Thu Mar 21 00:08:07 EST 1996

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.

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