Hello, The short answer is 'yes'. If you can use both methods :) The issue with limited proteolysis lies in the questionable state of the full-length protein - if the stuff is nasty and misfolded, then fagments generated by proteolytic digest aren't going to be meaningful. On the other hand if you have a small amount of decent quality full-length protein, digest can be extremely useful. Deuterium exchange is a nice technique if one of your friends is an altruistic mass-spectroscopist :)
Purely theoretical methods are limited as well, especially if you're working with a bunch of unknown domains in a sequence that has low identity with anything that has associated structures. And in the end, even for known structures (or very similar ones) truncation can generate surprises - both positive and negative ones. Artem >Hi: >I am following this with interest. Nice and useful info. >My question is: how do you "chop the protein into useful hunks"? >Using some domain identifying software or using limited proteolysis? >Thanks >Subbu
