[ccp4bb] ligand bound to only one chain in the crystal

2020-10-27 Thread Christian GALICIA 

Hello,
In our structure only one chain in a crystallographic trimer 
(non-biological) shows a ligand bound to it (with clear density). There 
doesn't seem to be any channels (or lack of them) favoring that specific 
site. Can the community give your opinion on whether this can make the 
presence of the ligand or its biological role questionable, and give any 
examples of similar cases you might be aware of. Thank you.

--
*Christian Galicia*
Post Doctoral Scientist
E-mail: cgali...@vub.be 




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Re: [ccp4bb] ligand bound to only one chain in the crystal

2020-10-27 Thread Weiergräber , Oliver H . 
Dear Christian,

You obviously mean a _non-crystallographic_ trimer -- in a crystallographic 
trimer the protomers (and their ligands) would be identical by definition.
On the other hand, chains related by non-crystallographic symmetry necessarily 
differ in their environments. As a results of nearby lattice contacts, the 
properties (average conformation, dynamics, electrostatics etc.) of the binding 
sites may have become unfavourable for ligand association in two out of three 
chains in your case. This does not by itself question the relevance of the 
binding site (provided there is good biochemical evidence), but it does 
indicate that the ligand is exchanged with the solvent at a rate that is 
sufficient to allow for such lattice effects. In the end, any conclusion from 
the crystalline state with respect to the solution state should be thought of 
as an extrapolation ;-)

Best regards
Oliver

==
  PD Dr. Oliver H. Weiergräber
  Institut für Biologische Informationsprozesse
  IBI-7: Strukturbiochemie
  Tel.: +49 2461 61-2028
  Fax: +49 2461 61-9540
==





From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Christian 
GALICIA [christian.galicia.diaz.sant...@vub.be]
Sent: 27 October 2020 11:19
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] ligand bound to only one chain in the crystal

Hello,
In our structure only one chain in a crystallographic trimer (non-biological) 
shows a ligand bound to it (with clear density). There doesn't seem to be any 
channels (or lack of them) favoring that specific site. Can the community give 
your opinion on whether this can make the presence of the ligand or its 
biological role questionable, and give any examples of similar cases you might 
be aware of. Thank you.
--
Christian Galicia
Post Doctoral Scientist
E-mail: cgali...@vub.be





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[ccp4bb] AW: [ccp4bb] ligand bound to only one chain in the crystal

2020-10-27 Thread Schreuder, Herman /DE 
Dear Christian,
We occasionally observe binding to only one monomer of a multimeric complex. I 
don’t think this invalidates the biological significance of your finding. I 
would superimpose the different monomers to see if they have (slightly) 
different conformations that prevent ligand binding. Also for cocrystallization 
experiments, the presence of or absence of channels is irrelevant. This only 
matters for soaking experiments.

Best,
Herman

Von: CCP4 bulletin board  Im Auftrag von Christian 
GALICIA
Gesendet: Dienstag, 27. Oktober 2020 11:19
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] ligand bound to only one chain in the crystal

Hello,
In our structure only one chain in a crystallographic trimer (non-biological) 
shows a ligand bound to it (with clear density). There doesn't seem to be any 
channels (or lack of them) favoring that specific site. Can the community give 
your opinion on whether this can make the presence of the ligand or its 
biological role questionable, and give any examples of similar cases you might 
be aware of. Thank you.
--
Christian Galicia
Post Doctoral Scientist
E-mail: cgali...@vub.be





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Re: [ccp4bb] ligand bound to only one chain in the crystal

2020-10-27 Thread Barone, Matthias 
Hi Christian
One of our proteins crystallizes always as non-crystallographic dimer. We 
occasionally find inhibitors bound to a second non-canonical site. Usually, the 
inhibitors bound to the second binding sites are sufficiently resolved only on 
one of the protein dimer. In these cases I often fail to place the second 
inhibitor at all and have to leave an unmodeled blob there. To exclude that 
this second binding site is not a crystal artifact, we used NMR HSQC to show 
that chemical shifts perturbations do occur even in solution and low inhibitor 
excess.
Best, Matthias


Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284


From: CCP4 bulletin board  on behalf of Christian 
GALICIA 
Sent: Tuesday, October 27, 2020 11:19:23 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] ligand bound to only one chain in the crystal

Hello,
In our structure only one chain in a crystallographic trimer (non-biological) 
shows a ligand bound to it (with clear density). There doesn't seem to be any 
channels (or lack of them) favoring that specific site. Can the community give 
your opinion on whether this can make the presence of the ligand or its 
biological role questionable, and give any examples of similar cases you might 
be aware of. Thank you.
--
Christian Galicia
Post Doctoral Scientist
E-mail: cgali...@vub.be





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Re: [ccp4bb] ligand bound to only one chain in the crystal

2020-10-27 Thread Ian Tickle 
Hi Christian

I wouldn't worry: if the density is clear that nails it.  You didn't say
whether this is a soak or co-crystallization.  I assume the former since
you mention solvent channels.  In my experience this is much more likely in
the case of soaks, which can often (though not always) be rationalised by
the kinetic effect (different rates of exchange of bound and free ligand
due to different accessibilities), so the time to attain equilibrium can be
much longer than your soaking time, whereas in the case of
co-crystallizations it's obviously pre-equilibrated and determined purely
by the binding affinity.

Even if there are no obvious solvent channels leading from the bulk solvent
to the binding sites, a soaked ligand can still get in (particularly if
high-affinity which prevents it leaving again), because the protein can
"breathe" opening up short-lived channels which close behind the ligand.

Cheers

-- Ian


On Tue, 27 Oct 2020 at 10:29, Christian GALICIA <
christian.galicia.diaz.sant...@vub.be> wrote:

> Hello,
> In our structure only one chain in a crystallographic trimer
> (non-biological) shows a ligand bound to it (with clear density). There
> doesn't seem to be any channels (or lack of them) favoring that specific
> site. Can the community give your opinion on whether this can make the
> presence of the ligand or its biological role questionable, and give any
> examples of similar cases you might be aware of. Thank you.
> --
> *Christian Galicia*
> Post Doctoral Scientist
> E-mail: cgali...@vub.be
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] ligand bound to only one chain in the crystal

2020-10-27 Thread Christian GALICIA 

Hi Matthias,

Thank you for response. Could you provide one or more pdb codes as example?

Best,
Christian


*From:* Barone, Matthias 
*Subject:* [ccp4bb] ligand bound to only one chain in the crystal
*Date:* Tuesday, October 27, 2020, 12:55
*To:* CCP4BB@JISCMAIL.AC.UK; Christian GALICIA


Hi Christian
One of our proteins crystallizes always as non-crystallographic dimer. 
We occasionally find inhibitors bound to a second non-canonical site. 
Usually, the inhibitors bound to the second binding sites are 
sufficiently resolved only on one of the protein dimer. In these cases 
I often fail to place the second inhibitor at all and have to leave an 
unmodeled blob there. To exclude that this second binding site is not 
a crystal artifact, we used NMR HSQC to show that chemical shifts 
perturbations do occur even in solution and low inhibitor excess.

Best, Matthias


Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284


*From:* CCP4 bulletin board  on behalf of 
Christian GALICIA 

*Sent:* Tuesday, October 27, 2020 11:19:23 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] ligand bound to only one chain in the crystal
Hello,
In our structure only one chain in a crystallographic trimer 
(non-biological) shows a ligand bound to it (with clear density). 
There doesn't seem to be any channels (or lack of them) favoring that 
specific site. Can the community give your opinion on whether this can 
make the presence of the ligand or its biological role questionable, 
and give any examples of similar cases you might be aware of. Thank you.

--
*Christian Galicia*
Post Doctoral Scientist
E-mail: cgali...@vub.be 




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Re: [ccp4bb] ligand bound to only one chain in the crystal

2020-10-27 Thread Palm, Gottfried 
Dear all, 

   the tenor seems to be, if you see the ligand in any of the
monomers, that's the mode the ligand binds. We have seen other cases,
though, too. 

Usually the protein I am thinking of (TetR(D)) crystallizes with one
molecules /a.u. In solution it is an obligate dimer. The dimer is
formed by a crystallographic axis. Each chain binds one ligand and for
wt the binding constant is sub uM without noticable cooperativity. For
some mutants we saw breakdown of this crystallographic axis (symmetry
dereases from I4(1)22 to P4(3)2(1)2), though, and now one of the
chains harbored a ligand, the other did not. It took some very careful
measurements to check that these mutants bind the ligand
anticooperatively, i.e. the first chain binds a ligand, the second of
the monomer so much weaker that we couldn't measure it. So, in case of
oligomers, keep cooperativity in mind. 

Greetings
  Gottfried








On Tuesday, 27-10-2020 at 12:57 Ian Tickle wrote:



Hi Christian


I wouldn't worry: if the density is clear that nails it.  You didn't
say whether this is a soak or co-crystallization.  I assume the
former since you mention solvent channels.  In my experience this is
much more likely in the case of soaks, which can often (though not
always) be rationalised by the kinetic effect (different rates of
exchange of bound and free ligand due to different accessibilities),
so the time to attain equilibrium can be much longer than your soaking
time, whereas in the case of co-crystallizations it's obviously
pre-equilibrated and determined purely by the binding affinity.


Even if there are no obvious solvent channels leading from the bulk
solvent to the binding sites, a soaked ligand can still get in
(particularly if high-affinity which prevents it leaving again),
because the protein can "breathe" opening up short-lived channels
which close behind the ligand.


Cheers


-- Ian




On Tue, 27 Oct 2020 at 10:29, Christian GALICIA  wrote:



  Hello, 
  In our structure only one chain in a crystallographic trimer
(non-biological) shows a ligand bound to it (with clear density).
There doesn't seem to be any channels (or lack of them) favoring that
specific site. Can the community give your opinion on whether this can
make the presence of the ligand or its biological role questionable,
and give any examples of similar cases you might be aware of. Thank
you.
-- 
Christian Galicia
Post Doctoral Scientist
E-mail: cgali...@vub.be


 







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[ccp4bb] Beam Time for Macromolecular Crystallography at CHESS: Now Accepting Spring 2021 Proposals

2020-10-27 Thread Aaron Finke 
Dear CCP4BB Members,

The new and fully-upgraded macromolecular crystallography beamline at CHESS, 
FlexX, is now accepting proposals for the Spring 2021 run.

SPRING 2021 RUN: The regular proposal deadline for the Spring 2021 run is Oct. 
28, 2020. However, we will accept late proposals due to Covid, but please 
submit as soon as possible to secure beamtime!

The FlexX station (beamline ID7B2) is the all-new macromolecular 
crystallography station at CHESS. The recently completed CHESS upgrade has 
considerably improved our capabilities in order to meet the the stringent 
demands of users. Current capabilities include:
* undulator source with multilayer monochromator for high flux. 7-14 keV energy 
range. Standard beam sizes available: 100 x 100 um (H x V FWHM) and 10 x 10 um 
microbeam.
* single-axis goniostat, EIGER2 16M detector, BAM2 automounter accepting 
Unipucks
* remote data collection with on-site CHESS staff scientist support (NB: due to 
Covid and occupancy restrictions, physical access for users to CHESS is very 
limited, so remote data collection is highly recommended!)
* we welcome "non-standard" experiments! The staff at CHESS is more than happy 
to work with users who want to perform experiments beyond standard rotation 
cryocrystallography. Interested in trying serial crystallography for 
room-temperature data collection, or microcrystals? High-pressure cryocooling 
for reduced mosaicity? High-pressure crystallography with a diamond anvil cell? 
We can accommodate your needs and more!

Interested? Instructions for submitting a proposal here: 
https://www.chess.cornell.edu/users/new-user-guide

Feel free to contact me with any questions!

Aaron


--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu




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Re: [ccp4bb] ligand bound to only one chain in the crystal

2020-10-27 Thread Navdeep Sidhu 
Dear Christian,

Kleywegt (1996; "Use of Non-crystallographic Symmetry in Protein
Structure Refinement." Acta Cryst D52, 842-857. DOI:
10.1107/S0907444995016477) reported that NCS-related molecules tend to
be similar but differences in ligand binding do sometimes occur (cited
Sevcik et al. 1996 in that paper).

We saw a similar difference (coenzyme absent/present; co-crystallized)
between 2 biologically monomeric NCS-related protein molecules
apparently due to crystal contact differences (Sidhu et al. 2011;
"Structure of a highly NADP+-specific isocitrate dehydrogenase." Acta
Cryst. D67, 856-869. DOI: 10.1107/S0907444911028575).

Best wishes,
Navdeep


---
On 27.10.20 11:19, Christian GALICIA wrote:
> Hello,
> In our structure only one chain in a crystallographic trimer
> (non-biological) shows a ligand bound to it (with clear density). There
> doesn't seem to be any channels (or lack of them) favoring that specific
> site. Can the community give your opinion on whether this can make the
> presence of the ligand or its biological role questionable, and give any
> examples of similar cases you might be aware of. Thank you.
> -- 
> *Christian Galicia*
> Post Doctoral Scientist
> E-mail: cgali...@vub.be 
> 
>  
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 



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[ccp4bb] I24 upgrade webinar

2020-10-27 Thread Owen, Robin (DLSLtd,RAL,LSCI) 
Dear all,

We are proposing to significantly upgrade beamline I24 for Diamond-II to enable 
improved dynamic and microfocus MX.
As part of this we will host a webinar on Tues 3rd November 16:00 – 17:00 GMT. 
The webinar will comprise an introduction and overview from myself followed by 
two short presentations from Andy Doré (Sosei Heptares) and Agata Butryn (UK 
XFEL Hub) showcasing some of the experiments currently possible and what we 
might realise in the future.

Further information and zoom details can be found at the link below

https://www.diamond.ac.uk/Home/Events/2020/Diamond-II-Webinar--I24-KMX-Upgrade-Project.html

Please join if you can.

All the best,
Robin OwenI24 PBS
Mike HoughI24 KMX working group chair




Dr Robin Owen
Principal Beamline Scientist
I24, Microfocus Macromolecular Crystallography
Diamond Light Source, UK
Tel: +44 1235 778522
http://www.diamond.ac.uk/Beamlines/Mx/I24.html


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[ccp4bb] Postdoc Position: Structural biology of RNA/protein complexes

2020-10-27 Thread Yunsun Nam 
Postdoctoral Research Fellow Position Available: Biochemistry and Structural 
Biology of Functional RNAs and RNA/protein Complexes A postdoctoral training 
position is available in the laboratory of Yunsun Nam, in the Cecil H. and Ida 
Green Center for Reproductive Biology Sciences at UT Southwestern Medical 
Center to study the mechanisms of post-transcriptional gene regulation. Our 
laboratory has several exciting projects related to how RNA structure changes 
the destiny of an RNA by altering its function and specific interactions with 
proteins. The goal is to determine how macromolecular recognition and enzymatic 
regulation are accomplished, using biochemistry, structural biology, and cell 
biology. The functional noncoding RNAs and RNA/protein complexes we study are 
relevant for normal development as well as diseases such as cancer, making our 
mechanistic work also valuable for therapeutics research. Postdoctoral scholars 
will have many opportunities to learn the newest methods in protein and nucleic 
acid biochemistry and biophysics, in addition to working in an exciting, 
fast-evolving field in biomedical sciences. We use various approaches, 
including X-ray crystallography, NMR spectroscopy, cryo-electron microscopy 
(cryo-EM), molecular biology, nucleic acid and protein biochemistry, genomics 
with next-generation sequencing, drug discovery, and mammalian cell-based 
studies. The postdoctoral fellow will have ready access to the top of the line 
equipment and resources necessary for the above approaches. Information on the 
UT Southwestern postdoctoral training program and benefits can be found in the 
Postdoc Handbook.

Candidates must hold a Ph.D. and/or M.D. degree. Experience in biochemistry 
(protein or nucleic acids), cell biology, and/or structural biology leading to 
publication in peer-reviewed journals is recommended. Interested individuals 
should send a CV, statement of interests, and a list of three references as a 
single pdf file to the P.I.:

Yunsun Nam, Ph.D (yunsun@utsouthwestern.edu)
Lab Website: www.ynamlab.org

* UT Southwestern Medical Center is committed to an educational and working 
environment that provides equal opportunity to all members of the University 
community. In accordance with federal and state law, the University prohibits 
unlawful discrimination, including harassment, on the basis of: race; color; 
religion; national origin; sex; including sexual harassment; age; disability; 
genetic information; citizenship status; and protected veteran status. In 
addition, it is UT Southwestern policy to prohibit discrimination on the basis 
of sexual orientation, gender identity, or gender expression.



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[ccp4bb] Postdoctoral positions immediately available - University of Minnesota

2020-10-27 Thread Mikael H Elias 
Dear All,

 

Multiple openings for postdoctoral fellows are available at  the University
of  Minnesota,  USA,  Department  of Biochemistry, Molecular  Biology, and
Biophysics, in   the   research   group   of   MikaelElias
(http://www.eliaslab.org/ ) to work on NIH and NSF funded projects.

 

In brief, the projects relate to the microbial signaling mechanism termed
quorum sensing, and ways to interfere with it (known as quorum quenching
strategies). The project involves the use of engineered proteins and other
effectors to investigate the importance of microbial signaling at the
cellular, the microbiome and the organism levels. For more details, see
(https://grantome.com/grant/NIH/R35-GM133487-01  and
https://nsf.gov/awardsearch/showAward?AWD_ID=2020695
 &HistoricalAwards=false) 

 

The ideal candidates  will have strong expertise in one or several of the
following areas: structural biology, protein engineering, bioinformatics,
metabolomics, transcriptomics, next gen sequencing or microbiology. The pay
scale for the positions follow NIH guidelines.

 

Fellows   will   joina   highlystimulating environment,   working
in   theBioTechnology  Institute, and will have outstanding
opportunities on a  research  projects  with  numerous  possible
applications. The University of Minnesota,  founded in 1851, is one of  the
largest university in  the United  States,   and  ranks   amongst  the
most prestigious research  universities in  the  world. The  campus  is
located  in  the  heart  of   the Minneapolis-St Paul   (Twin  Cities)
area,   an enjoyable, affordable  place,  extremely  rich  in cultural
events and natural attractions.

 

The University of Minnesota is an equal opportunity educator and employer.

 

To apply, please send a CV and names for at least two referees to Mikael
Elias: mhel...@umn.edu  

 




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