> > Cutting/adding/mutating residues at the termini is VERY OFTEN bad for
the
> > folding. Keep in mind that oftentimes having extra residues is bad
> > too.
>> I would have argued that this is rather a question of solubility,
> i.e. "sticky ends" of a protein aggregate? Can you give some examples?
Sorry, but no :) These proteins are related to my current proprietary work
and I can't disclose them without risking to be fired. I would agree that in
many cases the problem lies in the solubility, but not always. Specifically,
when you're truncating a transmembrane domain from a cytosolic catalytic
domain, there is a significant risk of misfolding if the cut is not
accurate. I wish I could really share the examples, but I can't.
> Hm. If you don't cut enough, you get loose termini, which don't
> interfere with folding (because this is the near-native sequence), but
> inhibit crystallization. If you cut too much, you get a problem because
> you cut beyond the "terminus" and deleted a residue that is in the bulk
> of the structure. That's how I see it..
This makes sense, however let's not forget other likely (parallel)
scenarios: imagine that you have left a few extra hydrophobic (or
mixed-type) residues at the N-terminus - chances are that they will tend to
aggregate and assume non-native conformations shortly after their emergence
from the ribosome. This can create a 'nucleus of misfolding' if you wish,
which will drag the rest of the sequence into a free energy hole from which
it may never climb out. With the C-terminal residues, the situation is not
as severe but there are still possible problems with sequences that do not
fold spontaneously and require chaperonins and related molecules.
Best regards,
A.G.E.
