As Mark says, structure solution of smallish peptides is not usually as
easy as one might expect. A number of the small (say up to 50 residue)
peptides in the PDB were solved by direct methods, but these require
native data to 1.2A or (preferably) better. If sulfur is present in the
molecule, SAD is a good choice and does not require such a very high
resolution, but you need highly redundant data, so a high symmetry space
group helps. If even one Met is present in the sequence, since you are
synthesizing the peptides anyway, you can replace it with selenomethionine.
George
On 11/10/2011 09:15 PM, mjvdwo...@netscape.net wrote:
Hans,
Most natural toxins from snakes, scorpions etc are 50+/-some peptides.
And quite a few of those have been studied and crystallized (see pdb
for a list). Having worked on one of these structures as a graduate
student, I can share my experience:
- Purification is harder than you would think. You are talking about <
10kD, usually around 5kD. Many methods (size exclusion, even
concentration over a simple membrane) don't work as easily as you
would like.
- I did not have much of a problem crystallizing (i.e. no worse than
other proteins, maybe even a little easier)
- Crystals tend to diffract well (maybe better than average)
- Structures can be hard to solve; MIR is very difficult because ions
tend to not go into such crystals easily (because the molecules are
small and tightly packed?); MR is hard because (again) it does not
work very well on very small systems
- Crystallization is not necessarily purification - if you have a
mixture of peptides to start with, it may be harder to crystallize, or
not: you might get a crystal that is a (random-ish) mixture.
- If you have more than two cysteines in your sequence (natural toxins
typically do), the additional problem is to get the correct folding
and disulphide bridges; alternatively it is very hard to discriminate
between correctly and incorrectly linked disulphides
Finally:
These sequence should be small enough for NMR. That may or may not
answer your questions, but it avoids your original question.
Mark
-----Original Message-----
From: H. Raaijmakers <hraaijmak...@xs4all.nl>
To: CCP4BB <CCP4BB@JISCMAIL.AC.UK>
Sent: Thu, Nov 10, 2011 8:16 am
Subject: [ccp4bb] crystallization of synthetic peptides
Dear crystallographers,
Because of the low cost and speed of synthesizing 40- to 60-mer peptides,
I wonder whether anyone has (good or bad) experiences crystalizing such
peptides. In literature, I've found up to 34-mer synthetic coiled coils,
but no other protein class. I can imagine that a protein sample with a few
percent "random deletion mutants" mixed into it won't crystallize easily,
but has anyone actually tried?
cheers,
Hans
