cross-soaking is cool and often works!!!
If your ligand is bound very tight and cant be removed though, maybe
some smart chemistry can help:
http://www.ncbi.nlm.nih.gov/pubmed/19655750
A.
PS yes, yet another self-promotion of won-work if anyone is wondering
... I am in good company with my friends Artem and Girgos ... so ...
its OK!
On Mar 17, 2010, at 21:03, Artem Evdokimov wrote:
It's called cross-soaking and it is a fairly popular technique
especially in the industrial community where we sometimes have to work
with hundreds of ligands.
I've done it on several occasions and mostly have been pretty happy
with the results. Having said this I also would like to point out that
soaking is not always the same as co-crystallization in terms of the
ligand-protein interactions. An extreme case is shown in the paper
below (figure 5):
http://www.iucr.org/cgi-bin/paper?sx5059
PDBID: 2i4g, 2i4h
Cheers,
Artem
On Wed, Mar 17, 2010 at 11:09 AM, Kontopidis George
<gkontopi...@vet.uth.gr> wrote:
Pentapeptide ligand removed from the binding site of the protein
crystal and
replaced with different peptide ligand
Insights into Cyclin Groove Recognition: Complex Crystal Structures
and
Inhibitor Design through Ligand Exchange, Kontopidis, G., et. al.
2003,Structure 11 (12), pp. 1537-1546
George
-----Original Message-----
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Critton, David
Sent: Wednesday, March 17, 2010 6:02 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Soaking to Remove Bound Ligands from Crystals
Dear ccp4bb,
I recently came across a thread from 2007 discussing the removal of
ions/ligands from protein crystals
(https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0705&L=CCP4BB&P=R35929
).
The thread cited a couple of papers (Ray et al. 1991; Schreuder et
al. 1988)
in which crystals were grown in the presence of a given ligand,
then soaked
in conditions containing little (if any) ligand in order to remove
the
ligand from these crystals.
I would like to know if there are any other reports of this method,
especially if any structures were solved from pre- and post-soaked
crystals,
and what kinds of conformational changes (if any) accompany these
kinds of
soaks.
Thank you in advance,
David A. Critton
Graduate Student, Page Laboratory
Department of Molecular Biology, Cell Biology & Biochemistry
Brown University
Providence, RI
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Department of Biochemistry (B8)
Netherlands Cancer Institute,
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