[ccp4bb] Postdoctoral position at the NIH

[Anirban Banerjee]

Dear all,

There is an open postdoctoral position in my lab. We are interested in the
structure and function of  integral membrane enzymes that catalyze protein
lipidation (Science, 2018, 359, eaao6326; PNAS., 2022 Feb
15;119(7):e2022050119) and transporters of transition metal ions (J Biol
Chem. 2018;293(10):3819-3828; PNAS, 2019,116,17775-17785).  We combine
structural techniques such as cryoEM and macromolecular crystallography
with biophysical and biochemical methods such as reconstitution based
assays, high resolution light microscopy and small molecule screening to
ask mechanistic questions. We are also increasingly becoming invested in
structure inspired cell biological questions.

The candidates should hold a Ph.D. degree, be author of at least one first
author publication and have a strong background in biochemistry or
structural biology. Experience with basic molecular biology, protein
expression, purification and biochemical characterization are required.
Prior experience in membrane protein biochemistry or cryoEM will be added
advantages.

Interested candidates can send an e-mail to anirban.baner...@nih.gov with a
CV and a summary of previous research experience and future interests.

The NIH is dedicated to building a diverse community in its training and
employment programs.
Please help spread the word to interested candidates.

Thanks,

Anirban

>



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Re: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

[Diana Tomchick]

I would say that in a small survey (~5-6) of bacterial enzymes from our lab, 
AlphaFold2 predicted exactly the constructs that were discovered by limited 
proteolysis and/or sequence alignment for currently unpublished structures.

It’s a useful tool but I’ve also had two cases where it incorrectly predicted 
the sequences of helices in a helical bundle—frameshift errors in the sequence, 
which were confirmed by SeMet SAD data. Caveat emptor.

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)




On Apr 4, 2022, at 2:06 PM, Scott Classen 
mailto:sclas...@lbl.gov>> wrote:


EXTERNAL MAIL

Hello CCP4,

Has anyone successfully used the available ML/AI protein folding tools to guide 
crystallization construct design? Maybe you had a protein or domain that was 
resistant to crystallization efforts and the folding algorithms  predicted some 
loops or termini that were disordered? Then you trimmed or modified them in 
some way to aid in crystallization? Or if you haven’t done this yourself, are 
you aware of anyone who has?

Thanks,
Scott


~~
Scott Classen, Ph.D.
ALS-ENABLE
TomAlberTron Beamline 8.3.1
SIBYLS Beamline 12.3.1
Advanced Light Source
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
MS6R2100
Berkeley, CA 94720
mobile 510.206.4418
desk 510.495.2697
beamline 510.495.2134
~~




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The future of medicine, today.



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Re: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

[David Briggs]

Hi Scott,

I've used AF2 order/disorder prediction (based up pLDDT score) to decided upon 
construct boundaries. We turned a non-expressing construct into a reasonably 
well expressing construct based on the AF2 prediction.

It's part of my construct design process now.

HTH,

Dave

--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs

From: CCP4 bulletin board  on behalf of Scott Classen 

Sent: Monday, April 4, 2022 8:06:38 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide 
crystallization?


External Sender: Use caution.

Hello CCP4,

Has anyone successfully used the available ML/AI protein folding tools to guide 
crystallization construct design? Maybe you had a protein or domain that was 
resistant to crystallization efforts and the folding algorithms  predicted some 
loops or termini that were disordered? Then you trimmed or modified them in 
some way to aid in crystallization? Or if you haven’t done this yourself, are 
you aware of anyone who has?

Thanks,
Scott


~~
Scott Classen, Ph.D.
ALS-ENABLE
TomAlberTron Beamline 8.3.1
SIBYLS Beamline 12.3.1
Advanced Light Source
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
MS6R2100
Berkeley, CA 94720
mobile 510.206.4418
desk 510.495.2697
beamline 510.495.2134
~~




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The Francis Crick Institute Limited is a registered charity in England and 
Wales no. 1140062 and a company registered in England and Wales no. 06885462, 
with its registered office at 1 Midland Road London NW1 1AT



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Re: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

[John R. Walker]

It may also be useful to look at homologues of the protein of interest, as
sometimes Alphafold shows very different domain arrangements despite close
sequence similarity.

John

On Mon, Apr 4, 2022 at 3:17 PM Andrew Lovering 
wrote:

> Hi Scott
> We have obtained a structure of a flexible clamshell like fold only after
> using a disulphide mutant to lock the domains based on a Rosetta Fold model.
> Interestingly, Alphafold put the very same residues further apart
> (probably a relevant "open" pose)
>
> Andy
>
> --
>
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Re: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

[Edward Snell]

Dear Scott,

Fabulous question. I think a lot of people are thinking about this quite deeply 
right now but our experience with single acylation and charge ladder work 
(unpublished) was that even a single amino acid charge change had a profound 
impact on crystallization outcome in the 1,536 conditions we probe. We use 
microbatch currently which is more static than vapor diffusion where the 
dynamics add another layer of complexity to the process. It could well be a 
beautiful application of ML/AI and there is a lot of interest in this here but 
even our database (~20 million images and a diverse chemical and protein 
landscape) may not be large enough for the learning process.

We had good experience in the ML/AI area automating image analysis and now 
routinely using this (with help from Google Brian - 
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0198883) but 
it required data from multiple generous sources in the community – both 
academic and industry.

(Unapologetic and shameless plug for the National Crystallization Center (get a 
crystal) at http://getacrystal.org where we use this).

I would love to add any good links in this area to our structural biology 
resources page - Structural Biology Resources | Hauptman-Woodward Medical 
Research Institute 
(buffalo.edu).
Best,

Eddie


Edward Snell Ph.D.

President and CEO | Hauptman-Woodward Medical Research Institute
Director | NSF BioXFEL Science and Technology Center
Professor, Materials Design and Innovation | University at Buffalo, SUNY

p: +1 716 898 8631 | f: +1 716 898 8660
e: esn...@hwi.buffalo.edu
skype: eddie.snell

Hauptman-Woodward Medical Research Institute
700 Ellicott Street | Buffalo, NY 14203-1102
hwi.buffalo.edu


[hwi-logo-primary-horizontal]




From: CCP4 bulletin board  On Behalf Of Scott Classen
Sent: Monday, April 4, 2022 3:07 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide 
crystallization?

Hello CCP4, Has anyone successfully used the available ML/AI protein folding 
tools to guide crystallization construct design? Maybe you had a protein or 
domain that was resistant to crystallization ef
Warning! This message was sent from outside your organization and we were 
unable to verify the sender.

sophospsmartbannerend
Hello CCP4,

Has anyone successfully used the available ML/AI protein folding tools to guide 
crystallization construct design? Maybe you had a protein or domain that was 
resistant to crystallization efforts and the folding algorithms  predicted some 
loops or termini that were disordered? Then you trimmed or modified them in 
some way to aid in crystallization? Or if you haven’t done this yourself, are 
you aware of anyone who has?

Thanks,
Scott

~~
Scott Classen, Ph.D.
ALS-ENABLE
TomAlberTron Beamline 8.3.1
SIBYLS Beamline 12.3.1
Advanced Light Source
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
MS6R2100
Berkeley, CA 94720
mobile 510.206.4418
desk 510.495.2697
beamline 510.495.2134
~~



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Re: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

[Joel Sussman]

The PROSS (Protein Repair One-Stop Shop) at: 
https://pross.weizmann.ac.il/step/pross-terms
was used to both express and be able to crystallize human acetylcholinesterase 
in E. coli, which prior to using PROSS had been impossible.

See paper:

Goldenzweig, A., Goldsmith, M., Hill, S. E., Gertman, O., Laurino, P., Ashani, 
Y., Dym, O., Unger, T., Albeck, S.,
Prilusky, J., Lieberman, R. L., Aharoni, A., Silman, I., Sussman, J. L., 
Tawfik, D. S., & Fleishman, S. J. (2016).
Automated structure- and sequence-based design of proteins for high bacterial 
expression and stability.
Molecular Cell, 63(2), 337–346. https://doi.org/10.1016/j.molcel.2016.06.012

and Proteopedia's Interactive 3D Complement (I3DC) page:

https://proteopedia.org/w/Journal:Molecular_Cell:1

Best regards
Joel

-
Prof. Joel L. Sussman   
joel.suss...@weizmann.ac.il
Dept. of Chemical and Structural Biologytel: +972  (8) 934 6309  
www.weizmann.ac.il/~joel
Weizmann Institute of Science   fax: +972  (8) 934 6312  
proteopedia.org
Rehovot 76100 ISRAELmob: +972 (50) 510 9600
-


On 4 Apr 2022, at 22:06, Scott Classen 
mailto:sclas...@lbl.gov>> wrote:

Hello CCP4,

Has anyone successfully used the available ML/AI protein folding tools to guide 
crystallization construct design? Maybe you had a protein or domain that was 
resistant to crystallization efforts and the folding algorithms  predicted some 
loops or termini that were disordered? Then you trimmed or modified them in 
some way to aid in crystallization? Or if you haven’t done this yourself, are 
you aware of anyone who has?

Thanks,
Scott


~~
Scott Classen, Ph.D.
ALS-ENABLE
TomAlberTron Beamline 8.3.1
SIBYLS Beamline 12.3.1
Advanced Light Source
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
MS6R2100
Berkeley, CA 94720
mobile 510.206.4418
desk 510.495.2697
beamline 510.495.2134
~~




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[ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

[Andrew Lovering]

Hi Scott
We have obtained a structure of a flexible clamshell like fold only after using 
a disulphide mutant to lock the domains based on a Rosetta Fold model.
Interestingly, Alphafold put the very same residues further apart (probably a 
relevant "open" pose)

Andy



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[ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

[Scott Classen]

Hello CCP4,

Has anyone successfully used the available ML/AI protein folding tools to guide 
crystallization construct design? Maybe you had a protein or domain that was 
resistant to crystallization efforts and the folding algorithms  predicted some 
loops or termini that were disordered? Then you trimmed or modified them in 
some way to aid in crystallization? Or if you haven’t done this yourself, are 
you aware of anyone who has?

Thanks,
Scott 


~~
Scott Classen, Ph.D.
ALS-ENABLE
TomAlberTron Beamline 8.3.1
SIBYLS Beamline 12.3.1
Advanced Light Source
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
MS6R2100
Berkeley, CA 94720
mobile 510.206.4418
desk 510.495.2697
beamline 510.495.2134
~~




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[ccp4bb] Postdoc and Higher Scientific Officer positions available at the Institute of Cancer Research London UK

[Rob Van Montfort]

The Institute of Cancer Research (ICR), London, is one of the world’s most 
influential cancer research institutes, with an outstanding record of 
achievement dating back more than 100 years. We provided the first convincing 
evidence that DNA damage is the basic cause of cancer, laying the foundation 
for the now universally accepted idea that cancer is a genetic disease. Today, 
The ICR leads the world at isolating cancer-related genes and discovering new 
targeted drugs for personalised cancer treatment. Together with our hospital 
partner The Royal Marsden, we are rated in the top four centres for cancer 
research and treatment worldwide. As well as being a world-class institute, we 
are a college of the University of London. We came top in the league table of 
university research quality compiled from the Research Excellence Framework 
(REF 2014). The ICR is committed to attracting, developing and retaining the 
best minds in the world to join us in our mission – to make the discoveries 
that defeat cancer.


The Cancer Research UK Cancer Therapeutics Unit (CTU), within the Division of 
Cancer Therapeutics, is a multidisciplinary 'bench to bedside' centre, 
comprising around 200 staff dedicated to the discovery and development of novel 
therapeutics for the treatment of cancer. The CTU’s exciting goal is to 
discover high quality small molecule drug candidates and to progress these to 
clinical trial. All the scientific disciplines are in place to make this 
possible, including medicinal chemistry, biology, structural biology, assay 
scientists, drug metabolism and clinical specialists. This is an exciting and 
fast-moving research setup and offers the opportunity to work within a 
multi-disciplinary environment using state-of-the-art techniques and equipment.

A postdoctoral training fellow (PDTF) and a Higher Scientific Officer (HSO) 
position are available in Dr Rob van Montfort’s Hit Discovery and Structural 
Design Team within the CTU as part of our new Centre for protein degradation 
(See: 
https://www.icr.ac.uk/news-archive/new-centre-targets-undruggable-cancers-after-major-donation).

The Post-doc (position ID185) will be involved in the structure determination 
of protein complexes by cryo-electron microscopy (cryoEM) as part of a CTU 
research programme focused on targeted protein degradation. The postholder will 
be responsible for sample preparation, structure determination by cryoEM and 
subsequent structural analysis of protein complexes. The successful candidate 
will be an integral member of a multidisciplinary project team within the CTU 
at the ICR Sutton site, and will interact closely with biologists, 
computational chemists, medicinal chemists assay scientists and structural 
biologists. The successful candidate will also be part of the Division of 
Structural Biology, located in Chelsea, in which the structural biologists in 
Dr van Montfort’s team are embedded, and will have access to its state-of-the 
art cryoEM facilities. These include an in-house Glacios and 30% direct access 
to a Titan KRIOS located at the Francis Crick Institute. Both microscopes are 
equipped with Falcon III detectors and volta phase plates (VPP). In addition, 
we have excellent access to the electron bioimaging Centre (eBIC) at the 
Harwell Science and Innovation campus, Didcot, UK. The postholder will be 
expected to work across the two sites in Chelsea, London and Sutton, Surrey.
The starting salary for the PDTF position ID185 will be in the range £38,607 to 
£40,902 p.a. inclusive (based on previous postdoctoral experience).
The Higher Scientific Officer (position ID184) will be responsible for 
establishing biophysical assays such as Surface Plasmon Resonance (SPR), 
Thermal Shift Assay (TSA) and ligand-based NMR (LO-NMR) to characterise these 
protein targets and their protein-protein and protein-ligand interactions. The 
successful candidate will be an integral member of a multidisciplinary project 
team and will interact closely with the biologists, computational chemists, 
medicinal chemists and structural biologists to help progress our drug 
discovery projects from hit finding to clinical trial.
The starting salary for the HSO position ID184 will be in the range £32,000 to 
£44,400 p.a. inclusive (based on previous experience).

Both posts are offered on a fixed term contract of 2 years. Informal enquiries 
to rob.vanmontf...@icr.ac.uk or 
yann-vai.lebi...@icr.ac.uk.
Please DO NOT send your application to Dr van Montfort or Dr Le Bihan, but 
apply via the e-recruitment system on our website 
www.icr.ac.uk.


Closing date for both positions:  24 April 2022



Dr. Rob van Montfort
Reader in Structural Biology and Cancer Drug Discovery
Team Leader Hit Discovery and Structural Design
Divisions of Cancer Therapeutics and Structural Biology
The Institute of Cancer Research
15 Cotswold Road
Sutton SM2 5NG
UK

[ccp4bb] reproducibility workshop on April 7th

[Wladek Minor]

Please look at IRRMC (proteindiffraction.org) meeting WEB page:

https://bioreproducibility.org/media/irrmc_conference/

If you are interested, please register to the meeting. Please note that  
meeting is a part of the US National Committee for Crystallography 
workshop series on
exploring structural database use in crystallography. So, you have an 
opportunity to register to other meetings but please remember that our 
is IRRMC meeting.


Meeting start on 11:00 EST (East Coast), 8:00 PST(West Coast), 15:00 UK 
time, 16:00 European time and 12:00am Tokyo time (sorry).


Best regards

Wladek

--
Dr. Wladek Minor
Harrison Distinguished Professor
Department of Molecular Physiology and Biological Physics
Phone: 434-243-6865
Fax: 434-243-2981
http://minorlab.org


US-mail address:
Department of Molecular Physiology and Biological Physics
University of Virginia
PO Box 800736, Charlottesville, VA 22908-0736

Fed-Ex address:
Department of Molecular Physiology and Biological Physics
1340 Jefferson Park Avenue
University of Virginia
Charlottesville, VA 22908






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[ccp4bb] Calculation of translational efficiency

[Ankita Singla]

Hi everyone,
I have a bacteria that has a dormant phase and an active phase in its
biphasic life cycle. It secretes a specific stress response protein "rpoS."
I wish to show that the accumulation of this protein during the dormancy
lifecycle (so early dormancy to late dormancy) is at the level of protein
stability and not because of changes in translational efficiency.
I am not well versed with pulse chase experiments but if anyone can help
me, please let me know. Or if there is any other way of proving this point.
Thank you

Have a beautiful day
Ankita Singla
(she/her/hers)
Ph.D. Candidate/ Deptt. of Physics and Astronomy
University of Utah, U.S.A



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Re: [ccp4bb] Off topic - gene toxic for expression strains

[Artem Evdokimov]

Hi there,

Somehow I've missed the original email :) Sorry!

There are options for expressing really toxic genes, some of which have
already been mentioned and others perhaps not:

1. tight regulation of expression (promoter, repressor, other regulatory
elements, or a combination thereof). Beyond using araBAD, xylose promoter,
rhamnose promoter, etc. there is one more thing that can be done, which is
quite old school: phage induction. Yes, it means what it says - you add
actual phage to the otherwise normal E.coli and the phage brings
polymerase. This way there is no tangible expression except leakage which
for T7 is close to non-existent.

2. change expression to a different organism: Bacillus, Pseudomonas or
insect/mammalian cells

3. counter-expression of antisense RNA from a weaker promoter: this method
is not exactly easy, but it does work -- you need a weak promoter (e.g.
unmodified lac or trp) that would drive expression of antisense RNA.
Easiest way to go about this is to put the antisense promoter on the 3' end
of the gene, facing 'backwards'. Then, during induction, the sense-strand
promoter is much more active and the sense RNA will win over the antisense.

Good luck!

Artem

P.S. if you use 2% glucose in the media be prepared to fight acidification
and the accumulation of Acetate in the spent medium, both of which can be a
problem - sometimes severe - for 'weaker' E. coli strains. Strongly
buffered medium is a must.
- Cosmic Cats approve of this message


On Mon, Apr 4, 2022 at 9:16 AM Nikolay Dobrev <
nikolay.dob...@embl-hamburg.de> wrote:

> Hi Andy,
> just to follow up on Christian suggestion, which is exactly the way to go.
>
> In case you are using an already pET based vector, simply try BL21-AI (
> https://www.thermofisher.com/order/catalog/product/C607003), which has
> the T7 RNA polymerase under arabinose promoter should do the trick.
> Also, 2% Glucose is a must in this kind of situation.
> I have been dealing with several toxic proteins (from the family of
> restriction enzymes :) ) and BL21-AI was a way to go.
> Please also have a look if your pET backbone has the extra copy of the
> lacI, which makes a difference in leakage expression.
>
> As a sum up:
> 1) try BL21-AI (for the induction of the target protein you will need both
> Arabinose (T7 RNA pol induction) and IPTG for the T7 promoter)
> 2) or BL21 with pLysS or pLysE
> both simple keep 2 % Glucose and also directly from trafo goto liquid
> culture in parallel of the plating approach.
>
> Let me know if you need any further tips.
>
>
> *Nikolay Dobrev *
> Postdoctoral Fellow @ Wilmanns group
> EMBL Hamburg, c/o DESY, Building 25A,
> Notkestraße 85, 22607 Hamburg, Germany
> T +49 40 89902 165 | M +49 173 684 0532
> twitter.com/emblevents | facebook.com/embl.org |
> youtube.com/user/emblmedia
> Visit www.embl.org/events for a complete list of all EMBL events.
>
>
> On 04/04/2022 10:32 AM Christian Roth  wrote:
>
>
> Hi Andy,
> have you tried another promotor? Arabinose is much tighter, just to be
> sure that it is really not leaking.
>
> Cheers
> Christian
>
>
> On Mon, Apr 4, 2022 at 10:20 AM Andrew Lovering 
> wrote:
>
> Dear Board,
>
>
>
> Perhaps off-topic, but in the wider scope it’s relevant to many on here.
>
>
>
> We have a gene that we are able to clone, and propagate in DH5a etc
> non-expression cells (hence nucleotide sequence is non-toxic)
>
>
>
> But, when we attempt to transfer to an expression strain we get no
> colonies
>
>
>
> We have tried pLemo, Glucose addition, 30 degrees, C41/C43 and still no joy
>
>
>
> We’d welcome any suggestions here – it’s a fun protein
>
>
>
> Thanks
>
> Andy
>
> --
>
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Re: [ccp4bb] Off topic - gene toxic for expression strains

[Nikolay Dobrev]

Hi Andy,
just to follow up on Christian suggestion, which is exactly the way to go.

In case you are using an already pET based vector, simply try BL21-AI 
(https://www.thermofisher.com/order/catalog/product/C607003), which has the T7 
RNA polymerase under arabinose promoter should do the trick.
Also, 2% Glucose is a must in this kind of situation.
I have been dealing with several toxic proteins (from the family of restriction 
enzymes :) ) and BL21-AI was a way to go.
Please also have a look if your pET backbone has the extra copy of the lacI, 
which makes a difference in leakage expression.

As a sum up:
1) try BL21-AI (for the induction of the target protein you will need both 
Arabinose (T7 RNA pol induction) and IPTG for the T7 promoter)
2) or BL21 with pLysS or pLysE 
both simple keep 2 % Glucose and also directly from trafo goto liquid culture 
in parallel of the plating approach.

Let me know if you need any further tips.


Nikolay Dobrev 
Postdoctoral Fellow @ Wilmanns group
EMBL Hamburg, c/o DESY, Building 25A,
Notkestraße 85, 22607 Hamburg, Germany
T +49 40 89902 165 | M +49 173 684 0532
twitter.com/emblevents https://twitter.com/emblevents 
|http://facebook.com/embl.org  | http://youtube.com/user/emblmedia
Visit http://www.embl.org/events  for a complete list of all EMBL events.



> On 04/04/2022 10:32 AM Christian Roth  wrote:
> 
> 
> Hi Andy,
> have you tried another promotor? Arabinose is much tighter, just to be 
> sure that it is really not leaking.
> 
> Cheers
> Christian
> 
> 
> On Mon, Apr 4, 2022 at 10:20 AM Andrew Lovering  mailto:a.lover...@bham.ac.uk > wrote:
> 
> > > 
> > Dear Board,
> > 
> >  
> > 
> > Perhaps off-topic, but in the wider scope it’s relevant to many on 
> > here.
> > 
> >  
> > 
> > We have a gene that we are able to clone, and propagate in DH5a etc 
> > non-expression cells (hence nucleotide sequence is non-toxic)
> > 
> >  
> > 
> > But, when we attempt to transfer to an expression strain we get no 
> > colonies
> > 
> >  
> > 
> > We have tried pLemo, Glucose addition, 30 degrees, C41/C43 and 
> > still no joy
> > 
> >  
> > 
> > We’d welcome any suggestions here – it’s a fun protein
> > 
> >  
> > 
> > Thanks
> > 
> > Andy
> > 
> > 
> > 
> > -
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> > 
> > > 
> 
> -
> 
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[ccp4bb] Postdoc position @ MPI NAT, Goettingen

[Sonja Lorenz]

Dear colleagues,

my group is looking to hire a motivated postdoc with experience in cell 
biology, a keen interest in proteomics, and the ability to communicate with 
structural biologists. 
It would be fantastic if you could forward the ad below to suitable candidates 
and/or circulate it within your institutes.

Many thanks for your help and best wishes,
Sonja Lorenz
Independent Group Leader
Ubiquitin Signaling Specificity
Max Planck Institute for Multidisciplinary Sciences
Am Fassberg 11
37077 Goettingen
Germany


——
Max Planck Institute for Multidisciplinary Sciences, Göttingen/Germany

The Max Planck Institute for Multidisciplinary Sciences in Göttingen is an 
internationally leading research institute of exceptional scientific breadth. 
The largest institute of the Max Planck Society, it comprises more than 40 
research groups and employs around 1,000 people from over 50 nations.

The research group Ubiquitin Signaling Specificity (Dr. Sonja Lorenz) invites 
applications for a position as

Postdoc (f/m/d)
– Cell biology of ubiquitin ligase complexes –

Our lab aims to understand how ubiquitin − a single, small protein − achieves 
specificity in regulating virtually all aspects of eukaryotic cell biology. A 
major key lies in the action of ubiquitin ligases, the most diversified class 
of enzymes of the ubiquitin system. The immense potential of ubiquitin ligases 
as therapeutic targets is illustrated by the clinical efficacy of thalidomide 
and derivatives in the treatment of hematologic malignancies. However, progress 
towards rationally manipulating these enzymes has been impeded largely by our 
insufficient understanding of their integration into macromolecular complexes 
and the associated structural and functional consequences. We aim to identify 
and characterize macromolecular complexes of ubiquitin ligases to decipher the 
molecular basis of their specificities in substrate recognition and ubiquitin 
chain formation. To this end, we combine chemical-biological, biochemical, cell 
biological, and structural approaches with a particular focus on cryo-electron 
microscopy.

We have a fully-funded postdoc position available for a talented individual to 
uncover cellular ubiquitin ligase assemblies implicated in neurodevelopmental 
disorders.

Your profile:

You have a PhD or equivalent degree in a relevant subject area, such as cell 
and molecular biology, biochemistry or biomedicine.
You have a proven track record in molecular cloning and cell biology, 
specifically in one or more of the following techniques: Crispr/Cas9-mediated 
gene editing, RNA interference, cell fractionation, co-IP, immunofluorescence, 
and live-cell imaging.
Additional experience in neuronal cell culture and/or proteomics will be 
beneficial.
You are curiosity-driven and eager to interact with biochemists and structural 
biologists.
 You are passionate about science and keen to establish creative new approaches 
to tackle challenging protein complexes.
You are self-motivated and independent, and enjoy being part of an 
international, multidisciplinary team.

About us:

We are an independent research group at the Max Planck Institute for 
Multidisciplinary Sciences, one of Germany’s premier research campuses with 
leading-edge infracture in all fields of structural and cell biology. We are a 
highly international and interdisciplinary team, funded by the Max Planck 
Society, the German Research foundation, and the EMBO YIP. The historic city of 
Goettingen, located in the center of Germany, offers great outdoor and cultural 
opportunities, a bustling student scene, and an impressive scientific heritage.

Position details:

The position should be filled as soon as possible, but the exact start date is 
flexible. The position is initially for 2 years with the possibility of 
extension. Payment and benefits are based on the TVöD guidelines.

The Max Planck Society is committed to increasing the number of individuals 
with disabilities in its workforce and therefore encourages applications from 
such qualified individuals. The Max Planck Society strives for gender and 
diversity equality. We welcome applications from all backgrounds.

Application:

Please submit your application including cover letter (explaining background 
and motivation), CV, transcripts, and publication record by e-mail as a single 
PDF file to the email address below. Review of applications will begin 
immediate. Informal inquiries are also welcome.

ausschreibung26...@mpibpc.mpg.de 
Max Planck Institute for Multidisciplinary Sciences
Research Group „Ubiquitin Signaling Specificity“
Dr. Sonja Lorenz
Am Fassberg 11
37077 Göttingen
Germany

Twitter @SLorenzLab

Lab Homepage: https://www.mpinat.mpg.de/lorenz 



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[ccp4bb] Extended registration deadline: Approaches for in cellulo structural biology with X-rays from May 16th to 17th 2022 in Hamburg

[Margret Fischer]

*Extended registration deadline*

Dear all,

We are pleased to announce our 2-dayspractical workshop on */Approaches 
for in cellulo structural biology with X-rays /*from *May **16^th **to 
**17**^th **2022*in Hamburg, Germany.


The workshop will provide practical on-site training on the 
followingresearch topics and technical approaches:


 * Eukaryotic cell systems for applications in structural biology
 * Intracellular protein folding and crystallization
 * Detection and characterization of protein crystals
 * Fluorescence-activated cell sorting (FACS) techniques for
   applications in structural biology
 * Present and future opportunities in advanced X-ray crystallography
 * Sample delivery techniques for X-ray data experiments

The training will be carried out at the relevant infrastructures 
operated by the *European Molecular Biology Laboratory (EMBL)* on the 
DESY Hamburg-Bahrenfeld research campus and by the *European X-ray Free 
Electron Laser in Schenefeld*, near Hamburg.


Application for the workshop isopen here 
 and the *deadline for 
application **has been extended till April 10th 2022*. Successful 
candidates will be informed during the first week after the deadline.


The event will be heldas an in-person workshop.

Best regards,

on behalf of the organizing committee

Jan Blaha (EMBL Hamburg), Lars Redecke (University of Lübeck/DESY), 
Ekaterina Round (European XFEL), Sihyun Sung (EMBL Hamburg), Matthias 
Wilmanns (EMBL Hamburg)



*Vanya Opalchenska*
European Molecular Biology Laboratory
c/o DESY, Notkestrasse 85, bldg. 25A
22607 Hamburg, Germany
Tel.: +49-40-89902-224
Fax.: +49-40-89902-149




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Re: [ccp4bb] Off topic - gene toxic for expression strains

[Christian Roth]

Hi Andy,
have you tried another promotor? Arabinose is much tighter, just to be sure
that it is really not leaking.

Cheers
Christian


On Mon, Apr 4, 2022 at 10:20 AM Andrew Lovering 
wrote:

> Dear Board,
>
>
>
> Perhaps off-topic, but in the wider scope it’s relevant to many on here.
>
>
>
> We have a gene that we are able to clone, and propagate in DH5a etc
> non-expression cells (hence nucleotide sequence is non-toxic)
>
>
>
> But, when we attempt to transfer to an expression strain we get no
> colonies
>
>
>
> We have tried pLemo, Glucose addition, 30 degrees, C41/C43 and still no joy
>
>
>
> We’d welcome any suggestions here – it’s a fun protein
>
>
>
> Thanks
>
> Andy
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>



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Re: [ccp4bb] Coot 1

[Harry Powell - CCP4BB]

Isn’t that what we all say every year on the day after March finishes?

Harry

> On 1 Apr 2022, at 23:46, Paul Emsley  wrote:
> 
> That, for the record, is more or less what Ralf said 18 years ago.
> On 01/04/2022 23:38, Pavel Afonine wrote:
>> It's April 1st today, isn't it? -;)
>> 
>> 
>> On Fri, Apr 1, 2022 at 3:15 AM Paul Emsley  wrote:
>> Coot 1
>> 
>> 18 years after the release of Coot 0 it's time that I actually released 
>> Coot 1.
>> 
> 
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[ccp4bb] Off topic - gene toxic for expression strains

[Andrew Lovering]

Dear Board,

Perhaps off-topic, but in the wider scope it's relevant to many on here.

We have a gene that we are able to clone, and propagate in DH5a etc 
non-expression cells (hence nucleotide sequence is non-toxic)

But, when we attempt to transfer to an expression strain we get no colonies

We have tried pLemo, Glucose addition, 30 degrees, C41/C43 and still no joy

We'd welcome any suggestions here - it's a fun protein

Thanks
Andy



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