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[ccp4bb]: High MPD caused unfolding/refolding?
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Has anyone had experience with crystallization in high MPD
(2-methyl-2,4-pentanediol) that causes the protein to unfold or adopt
dramatically different conformation?
I have a 12 KD protein that is six helical bundle when crystallized
in complex with another protein. All homologous proteins are six helical
bundles so I was expecting the same for this protein crystallized by
Unfortunately (or fortunately?) the structure turns out to be a single
long helix that only accounts for ~40% of the protein and the R factor is
down to ~25% at 2.3 A resolution ( no waters added yet). Other than the R
factor, two more things attest to the authenticity of the structure: 1).
The side chains are clearly visible from the experimental map (that's how
I reluctantly started building my model!); 2). I could use the current
model and go back to Amore to solve the structure. Several months ago I
posted a message for the molecular replacement problem in space group
I222/I212121. Now I know why MR could never have worked!
The crystallization conditions is ~50% MPD, ~0.5 M NaCl, pH 8.5 at 4
degrees. The drop was full of precipitations when first setup and it took
more than a month for the crystals to appear. I have run a gel with the
crystals and the protein is intact. Preliminary NMR studies (sorry folks)
indicate that protein solution without MPD contains perfectly packed
helical molecules and added MPD up to 15% messes up the structure
(broadening of peaks and huge aggregates).
Now I am not terribly disappointed for the unfolding of my protein in
high MPD solutions: some proteins are more sensitive to certain chemicals
than others. The puzzle that I am facing is why is the unfolded protein
refold 40% of itself into this long helix while leave the rest disordered?
And what is the role of MPD in this unfold->refold process? This sort of
thing is got to happen rarely since MPD is among the most popular
crystallization reagents around.
Any ideas? Suggestions? References?
Thanks a lot.
Univ. Texas Southwestern Med. Center @ Dallas
Program in Molecular Biophysics
5323 Harry Hines Blvd.
Dallas, TX 75235-9050