I dont think it is necessary to prove what others have said so far, but
if you would like some concrete evidence to support those statements:
we cocrystallized a protein together with a small peptide, producing a
crystal with for molecules in the AU but only one promoter showed clear
density for the bound peptide (crystal contacts played a part in this);
then the construct was shorten a bit and cocrystallized in a different
space group still, by chance, with 4 molecules in the AU, but this time
we could clearly see the peptide bound to all 4 copies. So indeed each
protomer in the AU can be affected differently in the way they bind a
ligand, depending on all causes (and perhaps even more) that people have
already mentioned.
BW,
D
On 06/03/2022 12:38, David J. Schuller wrote:
I think it would be a mistake to generalize.
I have seen a situation in which 1 of 4 sites was occupied, the ligand
was not included in the crystallization solution(which means it must
have been bound beforehand) and the site participated in crystal
contacts. I do not doubt that examples of the opposite causality
exist. And the data I used to make my conclusions in my own example
came from outside the structure itself.
=======================================================================
All Things Serve the Beam
=======================================================================
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
[email protected]
------------------------------------------------------------------------
*From:* CCP4 bulletin board <[email protected]> on behalf of Palm,
Gottfried <[email protected]>
*Sent:* Sunday, March 6, 2022 4:10 AM
*To:* [email protected] <[email protected]>
*Subject:* Re: [ccp4bb] ligand binds to one molecule
Dear all,
I don't think, there is much to add to the statement of Bernhard or
James that different protomers in the asymmetric unit (must) have some
difference in there contacts and therefore often in their
conformation. What it doesn't answer is a chicken or the egg question:
do the different environments in the crystal allow or force different
conformations (e.g. open or closed loops) and/or different (active)
site occupancies or
do different states in an oligomer allow or force crystallization only
in a packing and space group with multiple states?
Latter could be due to an anti-cooperative binding to a dimer. We have
seen this in the dimeric Tet repressor: wt binds the ligand (a
tetracycline) in each monomer of the dimer with one chain in the
asymmetric unit, but some of the mutants bind only one ligand per
dimer (confirmed by ITC, Biochimica et Biophysica Acta, 2020). Despite
the same packing, this forces reduction of space group symmetry from
I422 to P422 (omitting screws).
From the crystal structures alone, I think, one cannot prove what
comes first. From my gut feeling, in most cases multiple states in
solution force multiple states in the crystal - in other words - I
tend to say, multiple states in the crystal are "real" in the sense
they also occur in solution. Does somebody want to comment on this?
Greetings
Gottfried
Am Sonntag, den 06-03-2022 um 00:40 schrieb Bernhard Rupp:
As you stated, you have multiple protomers in the asymmetric unit,
where they are free from
crystallographic symmetry constraints. Generally that means
different local environment for
each protomer. Inspecting the sites in the different protomers
(frequently related by various
non-crystallographic symmetry operations) often can reveal
plausible reasons
for different occupancies. One hydrogen bond more or less for
example can mean a
difference of 4 orders of magnitude in Kd.
Best, BR
-----Original Message-----
From: CCP4 bulletin board <[email protected]> On Behalf Of
<Shymaa Damfo>
Sent: Saturday, March 5, 2022 12:01
To: [email protected] <mailto:[email protected]>
Subject: [ccp4bb] ligand binds to one molecule
Hello all,
In homo-dimeric or homo-oligomeric protein crystal structures,
what would be the reason for having a ligand (chemical compound or
fragment) binds to one molecule and not all molecules in the
asymmetric unit?
I have soaked a fragment that has an affinity of 200 uM to a viral
protein but I can only see it binds to one molecule (we have eight
molecules in the AU). This is was also notable as well in some
published PDB (dimeric protein).
Any suggestions?
Best wishes,
Shymaa
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