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
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