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
schul...@cornell.edu
________________________________
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Palm, Gottfried
<p...@uni-greifswald.de>
Sent: Sunday, March 6, 2022 4:10 AM
To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
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 <CCP4BB@JISCMAIL.AC.UK> On Behalf Of <Shymaa Damfo>
Sent: Saturday, March 5, 2022 12:01
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
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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