[ccp4bb] CBMS Lecture Series - Dr Sibel Yalcin - March 16, 13:30, DST

[Stojanoff, Vivian]

Please join us……



Sidel Yalcin

Yale University



WEDNESDAY, MARCH 16, 13:30 (DST)



"Electrogenetic Control of Bacteria via Protein Nanowires Capable of Ultrafast 
Charge Transport and

Storage for Next-Generation of Bioelectronic Materials and Devices"



Register in advance for this meeting:

  https://bnl.zoomgov.com/meeting/register/vJItc-yvpzsoHF1vnGho1CztnA-wRfHzxI4



Abstract:

Commercial bioelectronic devices to date rely on silicon-based technology. 
Despite decades of effort, current structural, electronic, and optical 
materials remain fundamentally bioincompatible. Synthetic conducting polymers 
are typically stiff and brittle, as well as non-biodegradable, and show poor 
stability and performance due to disorder. We aim to leverage the unique 
ability of bacterial systems to synthesize electronic materials with high 
conductivity and ability to self-repair and replicate. Electrogenetics has 
potential to efficiently control bacterial growth, adhesion, and communication. 
We have found that electric fields can directly control bacterial synthesis of 
nanowires made up of cytochromes OmcS (Cell 2019) and OmcZ (Nature Chem.Bio. 
2020) without any mediators. We have further found that the nanowires are 
translocated to the bacterial surface using pili that serve as a piston to 
secrete cytochromes rather than functioning as nanowires as previously thought.



World Clock: NYC (DST)  13:30;  London 17:30; Paris 18:30; New Delhi 11:00 PM; 
Shanghai 1:30 AM (Thursday); Tokio 2:30 AM (Thursday); Sidney  4:30 am 
Thursday; San Francisco 10:30 AM (PCT)




==



Vivian Stojanoff, PhD

Education, Training, Outreach

User Program

p 1(631) 344 8375

e nsls.lifescien...@gmail.com

w https://www.bnl.gov/ps/lifesciences/



Address:

Center for Biomolecular Structure

National Synchrotron Light Source II

Building 745

Brookhaven National Laboratory

Upton NY 11973







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Re: [ccp4bb] mysterious density

[Diana Tomchick]

Contour the 2Fo-Fc map at lower sigma than 1.3, and see if the resulting 
density looks like MES. As others have said, if there is no specific pocket or 
interactions for the non-sulfonic acid head group, then I would expect that 
density to be weaker or smeared out due to positional disorder.

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 Mar 13, 2022, at 9:19 AM, Amir Khan 
mailto:k...@crystal.harvard.edu>> wrote:


EXTERNAL MAIL

Hi,

I wonder whether anyone can advise on the ‘tadpole’ like density. The head is 
currently a phosphate
and I’ve placed a water in tail, but it obviously looks connected… would 
appreciate any help!

Green density at 5 sigma (Fo-fc), while blue is 2fo-fc at 1.3 sigma.

Crystallization condition is unknown, though it came from sparse matrix 
commercial (either Wizard, Pact Prem, or JCSG+).

Thanks!

Amir



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UT Southwestern

Medical Center

The future of medicine, today.



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Re: [ccp4bb] Ligand occupancy refinement

[Pavel Afonine]

For the record, occupancy refinement scenario you're looking for is
described here:

https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12

Cheers,
Pavel

On Thu, Mar 3, 2022 at 7:09 AM Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello, the ligand needs to be treated as one occupancy group since
> refining individual occupancies would be a case of refining too many
> parameters, unless it was a very fragmentary compound!! It is one keyword
> in refmac, but I can't remember for phenix, sorry! Ta jc
>
>
> Sent from ProtonMail mobile
>
>
>
>  Original Message 
> On 3 Mar 2022, 14:15, Akanksha Tomar < akankshat...@gmail.com> wrote:
>
>
> Hi everyone,
>
> I am trying to refine the occupancy of a bound ligand. After fixing the
> protein model and water I fitted the ligand into it. Currently, I am using
> Phenix Refine with occupancy refinement for individual atoms switched on.
> After the refinement, the overall occupancy of the ligand is 0.7 and the
> RSCC value is 0.86. The resolution of the structure is 2.1 Å.
>
> Now the problem is that the program has assigned different occupancies to
> different atoms of the ligand. For some cases, it has assigned 0
> occupancies to atoms for which there is a clear positive peak.
>
> Why it has been done so and is it acceptable?
>
> Any help would be greatly appreciated.
>
> Thank you.
>
> --
> Best Regards,
> Akanksha Tomar
> Pre-Doctoral Fellow,
> C\o Dr. Arockiasamy Arulandu,
> Membrane Protein Biology Group,
> International Center for Genetic Engineering and Biotechnology,
> New Delhi, India
>
> --
>
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Re: [ccp4bb] Ligand occupancy refinement

[Steven Herron]

Dear Akanksha,

When you re-do the occupancy refinement, don't include a b-factor 
refinement along with the occupancy refinement.  Do them separately. Do 
one, then do the other, and then repeat until convergence.


If your B-factor values are either high or low, the computer will try to 
adjust using occupancy.  If your occupancy values are either high or 
low, then the computer will try to adjust using B-factors. In the end 
you want the best occupancy and b-factor estimates you can get by making 
sure the refinement programs don't get trapped.


Once you have a good estimate, I suggest that you try a few different 
initial occupancy values to make sure you are not trapped in a local 
minimum.  If you start off with a high occupancy, it should move back 
down during the refinement.  If you start off with a low occupancy, then 
it should back up during the refinement. B-Factors should do the same 
thing.


With a large ligand, I suspect that some of the waters will also have 
alternate orientations.  You also might look at the amino acids that 
bind to the ligand to see if there is any alternate conformations.



Best
Steven Herron



On 3/3/2022 8:51 AM, Akanksha Tomar wrote:

Thank you for the suggestions
I will try again by setting the occupancy of the entire ligand to the 
single average occupancy and re-do the refinement with Buster, Phenix 
refine and Remac5 with full positional and B-factor refinement and 
check the B-factor of the neighbouring residues.
The ligand is a 30 atom containing molecule binding at a shallow 
solvent-exposed site.




On Thu, 3 Mar 2022 at 20:38, Wim Burmeister  wrote:

Hello,
at 2.1 A resolution, atomic temperature factors and occupancy are
strongly correlated. So you have to be very careful with the results.
So the best is just to set the inhibitor to the average occupancy
and then to include it into a full positional and B-factor
refinement. You can check whether the result is coherent by
comparing the B-factors of the ligand and of the atoms, which are
in contact with it. If this is not the case, you may want to
adjust the occupancy manually. As ther are also solvent atoms at
the ligand positions, when it is not bound, there is another
source of inaccuracy and theoretically you would have to model the
site with the solvent and an occupancy 1-q and the ligand with an
occupancy q as alternate structures. But nobody does that and it
is not really required.
Best
Wim


*De: *"Akanksha Tomar" 
*À: *"CCP4BB" 
*Envoyé: *Jeudi 3 Mars 2022 15:15:07
*Objet: *[ccp4bb] Ligand occupancy refinement

Hi everyone,

I am trying to refine the occupancy of a bound ligand. After
fixing the protein model and water I fitted the ligand into it.
Currently, I am using Phenix Refine with occupancy refinement for
individual atoms switched on. After the refinement, the overall
occupancy of the ligand is 0.7 and the RSCC value is 0.86. The
resolution of the structure is 2.1 Å.

Now the problem is that the program has assigned different
occupancies to different atoms of the ligand. For some cases, it
has assigned 0 occupancies to atoms for which there is a clear
positive peak.

Why it has been done so and is it acceptable?

Any help would be greatly appreciated.

Thank you.

-- 
Best Regards,

Akanksha Tomar
Pre-Doctoral Fellow,
C\o Dr. Arockiasamy Arulandu,
Membrane Protein Biology Group,
International Center for Genetic Engineering and Biotechnology,
New Delhi, India



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-- 
*Wim Burmeister*

Professor
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs


/ CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
Mobile:  +33 (0) 7 50 49 19 91
website







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[ccp4bb] Scientist in Structural Biology - Halic Lab

[Bilokapic, Silvija]

Scientist in Structural Biology - Halic Lab


This is an exciting opportunity for a self-motivated scientist to join the 
Structural Biology Department at SJCRH in the laboratory of Dr. Mario Halic. 
The Halic lab studies the epigenetic regulation of gene expression using 
genetics, molecular biology, biochemistry, and structural biology approaches.

The ideal candidate will have extensive experience with biochemical 
methodology, cloning procedures, protein tagging and expression in different 
model organisms, protein and macromolecular complexes purification. Candidates 
should be self-motivated problem-solvers with a high level of accuracy 
especially while multitasking. Experience in structural biology is a plus.

In addition to performing experiments and analyzing results, you will have the 
opportunity to collaborate with and train other key members of the lab. You 
will also be responsible for assisting with the maintenance of lab operations 
as necessary. All candidates are expected to have excellent verbal and written 
communication skills, the ability to work independently, and the ability to 
work constructively as a member of a diverse team.

Three (3) years of relevant post-degree work experience is required. Leadership 
or supervisory experience is a plus.

At St. Jude, you will be part of a collaborative, bench-to-bedside environment 
where you can see, firsthand, how your science translates into survival for the 
children we serve.

Apply to be a part of the mission of St. Jude Children's Research Hospital: to 
advance cures, and means of prevention, for pediatric catastrophic diseases 
through research and treatment. Consistent with the vision of our founder Danny 
Thomas, no child is denied treatment based on race, religion or a family's 
ability to pay.

More information about the lab, publications and ongoing projects can be found 
here: https://www.stjude.org/research/labs/halic-lab.html

Applicants should submit CV and cover letter and names and addresses for 3 
references to mario.ha...@stjude.org. Review of applications will begin 
immediately and continue until the position is filled.



Follow us @LabHalic








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[ccp4bb] PhD studentship in time resolved crystallography of multifunctional enzymes using synchrotron and XFEL facilities

[Hough, Michael (DLSLtd,RAL,LSCI)]

Dear all,

We have extended the deadline for the studentship and will now consider 
applications as they are received with no fixed closing dates. I will be very 
grateful if you could pass this on to any potentially interested candidates.





We have a fully funded four year PhD studentship available from October 2022, 
as a joint project between Diamond Light Source (Mike Hough and Robin Owen) and 
the University of Essex (Jonathan Worrall).

The project will involve the application of time resolved crystallography to 
study enzyme reactions and mechanisms in multifunctional heme enzymes. 
Reactions will be followed in crystals using spectroscopic approaches to 
identify appropriate time points and monitor reactions. There will be extensive 
opportunities to use XFEL and synchrotron serial crystallography beamlines and 
to carry out complementary biochemical and spectroscopic work. Work at Diamond 
will primarily be at beamlines VMXi and I24 with around two years of the 
project being based at Diamond. We have an ongoing collaboration with the SACLA 
XFEL and conduct regular experiments there, with other XFEL sources potentially 
be used as required for the project.

Details are available here: 
https://www.diamond.ac.uk/Careers/Students/Studentships/2022-projects/2022-STU0436.html
 where you can also find application details. There is no fixed closing dates 
although shortlisting and interviews will be carried out when suitable 
candidates have been identified.

I'd be grateful if BB members could pass this onto any potentially interested 
candidates and/or advertise locally

Informal enquiries can come to me 
(michael.ho...@diamond.ac.uk), or to either 
Robin Owen (robin.o...@diamond.ac.uk) or 
Jonathan Worrall (jworr...@essex.ac.uk).




Prof Mike Hough

Principal Beamline Scientist - VMXi
Diamond Light Source Ltd
Harwell Science and Innovation Campus



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[ccp4bb] Research Assistant - UCB (UK)

[Leysen Seppe]

Hi everyone

We're looking for a Research Assistant in our Protein Structure & Biophysics 
team. This is a contract position (12 months).
Please see below for a detailed job description. If you currently have the 
right to work in the UK and wish to apply, send your CV and cover letter to 
protein.purificat...@ucb.com

Research Assistant Protein Structure & Biophysics
Role Overview
We are currently looking for a Research Assistant to support the Protein 
Structure & Biophysics department. This department is part of Discovery Science 
and plays a leading role in the biophysical and structural characterisation of 
target proteins to help with the identification of new drug targets and novel 
antibody therapeutics.
The Research Assistant will perform routine laboratory tasks including 
molecular biology, DNA preparation, mammalian cell culture and harvesting, 
membrane preparations, biologics sample aliquoting, inventory management and 
sample distribution for high throughput screening assays. The successful 
candidate will be exposed to a variety of discovery projects and receive 
regular coaching and input from the teams. Being a motivated, diligent and 
attentive individual, you will ensure the smooth running of laboratory 
workflows, work closely with other team members and use excellent communication 
skills to liaise with other departments.
Primary responsibilities:

  *   Molecular biology (cloning, transformations, bacterial cell culture), 
small and large-scale DNA preparation
  *   Small and large scale e.coli protein expression and expression analysis.
  *   Maintenance of mammalian cell lines, small and large scale transfections, 
harvesting of supernatants and cell pellets
  *   Maintenance of insect cells, virus generation and titres, small and large 
scale expression.
  *   Small scale protein purification and analysis
  *   Preparation of cell membranes
  *   Preparation and maintenance of stock and buffer solutions, ordering of 
consumables
  *   Protein aliquoting, maintaining accurate records of sample location using 
Excel and barcode scanning software
  *   Crystallography screen aliquoting and stock maintenance
  *   Responding to regular sample requests, liaising with scientists to ensure 
timely sample delivery
Essential experience:

  *   B.Sc. in Biological Sciences or equivalent
  *   Demonstrable experience in bacterial and mammalian cell culture
  *   Demonstrable experience in handling large numbers of samples
  *   Competent with pipettes (manual, electronic, single and multichannel)
  *   Meticulous, diligent, able to keep accurate records, good organisational 
skills
  *   Ability to communicate clearly and work efficiently in a team
  *   Ability to work well under pressure and respond to changing priorities to 
meet deadlines
  *   Ability to work on several projects in parallel
  *   Computer literate (proficiency in Microsoft Office)
Desirable skills:

  *   Experience working in a GMP/GLP laboratory
  *   Experience with biologics inventory management software (e.g. Mosaic or 
similar)
  *   Experience in protein expression and purification
Seppe Leysen
Principal Scientist
Protein Structure & Biophysics
UCB
216 Bath Road
SL1 3WE
Slough
UK


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[ccp4bb] contract position - Protein Purification Scientist - UCB (UK)

[Leysen Seppe]

Hi everyone

Do you enjoy protein purification, and can you operate an AKTA to run IMAC, IEX 
and SEC protein purifications without supervision? Do you want an opportunity 
to learn about antibody and small molecule drug discovery? Then check out our 
contract position (12 months, starting asap) in our Protein Purification team 
at UCB (Slough, UK). A full job description can be found below.

If you currently have the right to work in the UK and wish to apply, send your 
CV and cover letter to: 
protein.purificat...@ucb.com

Research Scientist - maternity cover - UCB (Slough, UK)
Everything we do starts with a simple question: "How will this make a 
difference to the lives of people living with severe diseases?" And to find the 
answers, we connect globally with patients and their families living with the 
physical and social burdens of severe disease. These connections give us new 
perspectives, drive our innovation, and offer a hope for a new generation of 
therapies that will help to transform lives.
Role overview
The Protein Production Group provides support for all NBE & NCE projects from 
early stage target validation through to those undergoing pre-clinical 
evaluation, by generating recombinant protein reagents for immunization, 
structural studies, assays and compound screening.  All reagents produced 
undergo biophysical analysis in order to enhance our understanding of their 
stability and solubility.  You will be part of the Protein Production Group 
playing a key role in project success by generating high quality protein 
reagents in a timely manner.
The successful candidate will have the opportunity to rapidly impact on a wide 
range of our NBE & NCE projects, and to significantly contribute to the 
progression of these projects into the clinic and beyond.
Primary responsibilities
*   You will be responsible for expressing and purifying high-quality 
recombinant protein reagents to support UCB's novel world-leading antibody and 
NCE drug discovery platforms for a variety of exciting therapeutic projects.
*   You will use your excellent practical skills, communication and team 
working abilities to drive innovative projects forward from the laboratory.
*   You will be responsible for clearly presenting work and engaging in 
discussion in a variety of cross-functional and external collaborator meetings.

Essential experience
Candidates may be fresh PhD holders with relevant experience, or Bachelor/MSc 
degree holders currently working as skilled Research Scientists, within the 
Biopharmaceutical or Pharmaceutical industry.
We are looking for candidates who are fully independent and competent in the 
following skill sets:
*   Molecular Biology (DNA manipulation techniques and use of VNTI and/or 
other DNA analysis software).
*   Protein Expression in E. coli and/or Mammalian cell systems.
*   Protein Purification (Affinity, Ion Exchange, Size Exclusion 
Chromatography, UV-Vis spectroscopy, protein refolding techniques and extensive 
working knowledge of AKTA purification platforms and associated software)
*   Protein Analysis (SDS PAGE, UPLC/HPLC, Western blotting)
*   Molecular Visualisation of proteins (PyMOL or similar).
*   Experience with X-ray crystallography or cryo-EM would be an advantage
*   Ability to work on several projects and conduct experiments in parallel.
*   Proficiency in the use of Microsoft Office.
*   A highly motivated individual with a proven ability to deliver to tight 
timelines.
*   A team player, with good organisational, communication, record keeping 
and inter-personal skills are essential requirements.
*   Presentations within the group and to project teams will also be 
expected.
*   Possess an inquisitive and innovative nature and a passion for 
delivering innovative new medicines for patients suffering with serious disease.

We can offer you the opportunity to rapidly impact on a wide range of our NBE & 
NCE projects, and to significantly contribute to the progression of these 
projects into the clinic and beyond.  Informal and open working environment 
that does not lock scientists into structure and hierarchy.  Freedom to take 
space to pursue your own ideas and make a difference.  Opportunities and 
expectations to develop global visibility and an international reputation as a 
scientist in your field.

Best wishes

Seppe Leysen
Principal Scientist
Protein Structure & Biophysics
UCB
216 Bath Road
SL1 3WE
Slough



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