Re: [ccp4bb] Microfocus beamlines (fast-tracks)

[Morgan Milton]

Hi Mariana,

Where are you located? Sector 23 at Argonne National Labs has a minibeam
that goes down to 5 um. APS does rapid request proposals, so you may be
able to get beamtime before the end of the year.


Morgan E. Milton, PhD



On Fri, Oct 5, 2018 at 9:47 AM Mariana Morais 
wrote:

> Dear CCP4 colleagues,
>
>
>
> I have some small protein crystals that would need a microfocus beamline
> to be collected and we have some urgency to collect these data. Do you have
> any information regarding microfocus beamlines that accept fast tracks and
> that allows us to collect remotely? Our aim is to send the crystals and to
> collect before the end of 2018.
>
> I will highly appreciate if anyone could share any information, experience
> or tips!
>
>
>
> Thank you,
>
>
>
> Mariana A. B. Morais
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] 2 crystallography posts available at Evotec

[McEwan, Paul]

Dear All,
There are two senior scientist posts available at Evotec in Abingdon, UK. 
Please do not contact me directly for application, please use the online 
recruitment weblink at the base of this email.




Evotec is a leader in the discovery and development of novel small molecule 
drugs with operational sites in Europe and the US. The Company has built 
substantial drug discovery expertise and an industrialised platform that can 
drive new innovative small molecule compounds into the clinic. In addition, 
Evotec has built a deep internal knowledge base in the treatment of diseases 
related to anti-infective, neuroscience, pain, oncology, inflammation and 
metabolic diseases. Leveraging these skills and expertise the Company intends 
to develop best-in-class differentiated therapeutics and deliver superior 
science-driven discovery alliances with pharmaceutical and biotechnology 
companies.
We are looking for highly motivated individuals for our Abingdon site to work 
as a
Senior Scientist, Structural Biology, X-Ray Crystallography (2 x 12-month 
temporary contract)
Evotec (UK) Ltd is currently seeking to add to our Structural Biology 
Department.  The group works closely with our Discovery Chemistry Department 
and with clients to develop novel small molecule drugs.  The group is at the 
forefront of new science and technology, and is seeking to expand as business 
needs grow.  Our site is located less than 4 miles from Diamond Light Source 
and eBIC national facilities for access to synchrotron radiation and Cryo 
Electron Microscopy respectively to support our high-end analysis of samples.
The position is initially temporary, for 12 months duration, but may become 
permanent dependant on business need.
Required Knowledge, Skills and Abilities:

  *   Expertise in X-ray crystallography from crystal preparation and handling, 
data collection through to analysis of structures
  *   Experience in gene design and protein purification
  *   Self-motivated, enthusiastic, cooperative and reliable
  *   Knowledge of basic laboratory techniques, and understanding of the 
science underlying the techniques and experiments
  *   Experience of working in a laboratory environment
  *   The ability to adapt to changing demands whilst operating under pressure 
to deadlines
  *   The ability to work accurately and with attention to detail
  *   Good interpersonal skills and the ability to work well with other 
scientific staff
  *   The ability to work well independently, and as part of a team
  *   Good organisational and time management skills
  *   Good verbal communication skills
  *   Ability to maintain excellent laboratory records
  *   Computer proficiency
Responsibilities may include:

  *   Supporting a project team by conducting experiments with defined, agreed 
objectives and timelines
  *   Contributing to the design, execution and interpretation of experiments 
in a project team to accomplish project goals
  *   Adapting scientific knowledge to resolve problems encountered in 
achieving defined goals with assistance from line manager or other team members 
to meet internal and project deadlines
  *   Preparing reports of findings, presenting data, and collaborating with 
other scientists at Evotec
  *   Presenting own work at project technical meetings, and department 
technical meetings when required
  *   Demonstrating full command of all techniques and tools required for 
assigned responsibilities within the given project
  *   Ensuring safe working practices of themselves and any direct reports
  *   Complying fully with the company safety policy (including COPs and SOPs) 
when performing experiments
  *   Reading scientific literature relevant to the project
  *   Adhering to Lab Notebook guidelines regarding accurate documentation of 
lab experiments
Desirable Knowledge, Skills and Abilities:

  *   Membrane protein expertise
  *   Cryo-Electron Microscopy sample preparation and data analysis
  *   Fragment based drug discovery
Education and Experience:


  *   PhD in Structural Biology, Biochemistry or related area



https://recruitment.evotec.com/VacancyDetails.aspx?FromSearch=True=QSAukis1tlc==738

best wishes,
Paul..
[cid:image002.png@01D41934.D23B4340]
Paul McEwan, Ph.D.
Principal Scientist, Structural Biology
+44 (0)1235 83 8802  (Direct)
+44 (0)1235 86 3139  (Fax)
paul.mce...@evotec.com
www.evotec.com

Evotec (UK) Ltd.
114 Innovation Drive,
Milton Park, Abingdon
Oxfordshire OX14 4RZ, UK


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Registration number:2674265. 

Re: [ccp4bb] Microfocus beamlines (fast-tracks)

[Isabel Moraes]

Dear Mariana,

I sugest to contact the I24 microfocus beamline at Diamond Light Source  
(https://www.diamond.ac.uk/Instruments/Mx/I24.html)

Best regards,
Isabel

--
Isabel Moraes, PhD
Principal Research Scientist - Structural Biology
National Physical Laboratory (NPL)
Hampton Rd | Teddington | Middlesex | TW11 0LW
---




On 5 Oct 2018, at 14:35, Mariana Morais 
mailto:mariana.abmor...@gmail.com>> wrote:

Dear CCP4 colleagues,

I have some small protein crystals that would need a microfocus beamline to be 
collected and we have some urgency to collect these data. Do you have any 
information regarding microfocus beamlines that accept fast tracks and that 
allows us to collect remotely? Our aim is to send the crystals and to collect 
before the end of 2018.
I will highly appreciate if anyone could share any information, experience or 
tips!

Thank you,

Mariana A. B. Morais



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[ccp4bb] Microfocus beamlines (fast-tracks)

[Mariana Morais]

Dear CCP4 colleagues,



I have some small protein crystals that would need a microfocus beamline to
be collected and we have some urgency to collect these data. Do you have
any information regarding microfocus beamlines that accept fast tracks and
that allows us to collect remotely? Our aim is to send the crystals and to
collect before the end of 2018.

I will highly appreciate if anyone could share any information, experience
or tips!



Thank you,



Mariana A. B. Morais



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[ccp4bb] 2019 Summer intern position at Merck & Co., Inc. Kenilworth, N.J

[Strickland, Corey]

Public



All,


We have the following 2019 summer intern position available.If 
you are interested please apply at  
https://merck.taleo.net/careersection/jobdetail.ftl?job=ADM009828





Sincerely,

Corey


Corey Strickland, Ph.D.
Director, Structural Sciences
Merck Research Labs
K15-ME111
2015 Galloping Hill Road
Kenilworth, NJ 07033








Merck & Co., Inc. Kenilworth, N.J., U.S.A. known as Merck in the United States 
and Canada, is a global health care leader with a diversified portfolio of 
prescription medicines, vaccines and animal health products. The difference 
between potential and achievement lies in the spark that fuels innovation and 
inventiveness; this is the space where Merck has codified its legacy for over a 
century. Merck's success is backed by ethical integrity, forward momentum, and 
an inspiring mission to achieve new milestones in global healthcare.

Merck is on a quest for cures and is committed to being the world's premier, 
most research-intensive biopharmaceutical company. Today, we're doubling down 
on this goal. Merck Research Laboratories is a true scientific research 
facility of tomorrow, and will take Merck's leading discovery capabilities and 
world-class small molecule and biologics R expertise to create breakthrough 
science that radically changes the way we approach serious diseases.



The Structural Sciences group within Merck Research Laboratories located in 
Kenilworth, NJ, is seeking a summer intern. The intern will function as a 
fully-integrated member of a structural biology team, consisting of X-ray 
crystallographers, protein biochemists, and molecular biologists.


The job will involve the crystallization of monoclonal antibodies for drug 
delivery and purification.   The intern will apply various purification methods 
to generate proteins suitable for crystallization.Day-to-day research will 
focus on using techniques in protein biochemistry and biophysics to formulate 
and characterize these samples and setup crystallization experiments.   The 
intern will be responsible for accurate electronic notebook recording, safe 
laboratory practices, and presentation of data and their interpretation to a 
team of scientists. The intern will also attend departmental and team meetings 
to gain a wider perspective on the drug development process in the 
pharmaceutical industry.


We are seeking intern candidates with strong academic performance, 
communication skills, teamwork, and the ability to work in a cross-functional 
environment.


This is a full- time internship position. Housing subsidy is not available as 
part of this program and must be funded 100% by the student.

Qualifications

Education:
* Required: Candidates must be a currently enrolled in a Ph.D. program 
in chemistry, biology, biochemistry, structural biology or related discipline.

Required Experience and Skills:
* Candidates must be available to work full-time for up to (12) 
consecutive weeks beginning in May or June of 2019.
* Candidates must have completed at least (1) year of study toward 
Ph.D. degree by June of 2019.
 Preferred Experience and Skills:
* Candidates should have significant interest in protein 
crystallization and protein structure/function.
* Candidates should understand basic laboratory skills and safe lab 
practices.
* Candidates should have prior research experience such as: molecular 
biology, protein expression & purification, protein characterization using 
biochemical and biophysical techniques and/or protein crystallization

Your role at Merck is integral to helping the world meet new breakthroughs that 
affect generations to come, and we're counting on your skills and inventiveness 
to help make meaningful contributions to global medical advancement. At Merck, 
we're inventing for life.

To apply:
https://merck.taleo.net/careersection/jobdetail.ftl?job=ADM009828



Notice:  This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth,
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for affiliates is available at 
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[ccp4bb] Post-doc positions in Ligand-gated ion channel structure and function, Paris

[Marie Prevost]

Dear all,

Two positions are available in the laboratory of Pierre-Jean Corringer at the 
Institut Pasteur in Paris, France, to investigate the structure and function of 
pentameric ligand-gated ion channels. One position will be focused on the 
structural biology on those receptors by cryo-EM and/or X-ray crystallography, 
the second one on their biophysical properties, mostly by voltage-clamp 
fluorometry.

Details are provided below.

Have a good weekend,

Marie

--

Two positions are available in the laboratory of Pierre-Jean Corringer at the 
Institut Pasteur in Paris, France
(https://research.pasteur.fr/en/team/channel-receptors/)

Our laboratory is looking for two highly motivated post-doctoral fellows with 
strong background and experience in structural biology/biophysics/ion channel 
structure and function. Our lab studies the structure and function of 
pentameric ligand-gated ion channels, with a particular emphasis on 
understanding the structural bases of ion channel gating and regulation by 
small molecules. All projects in the lab are interdisciplinary in nature and 
combine structural techniques with functional approaches, and the two proposed 
positions concern: 1/ voltage-clamp fluorometry, to monitor the ion channel 
gating by electrophysiology concomitant with protein motions by fluorescence in 
physiological conditions and 2/ the structural biology of ion channels in 
complex with small ligands, using both X-ray crystallography and cryo-electron 
microscopy (cryo-EM). Both projects also involve molecular biology, protein 
biochemistry and kinetic modeling. Our lab is fully equipped for molecular 
biology, biochemistry and voltage-clamp fluorometry and has access to the 
renowned platforms of X-ray crystallography and cryo-EM (with a recently 
installed Titan Krios microscope) of the Institut Pasteur in Paris. The 
Institut Pasteur offers a highly dynamic social and scientific environment in 
the heart of Paris.
The successful candidate must have a PhD (or being in the process of completing 
one) in a relevant field with a demonstrated track record of productive 
research, and must be able to work both independently and as part of 
collaborative team. For the voltage-clamp fluorometry project, previous 
experience in fluorescence techniques and/or electrophysiology is highly 
desirable. For the structural biology project, previous experience in cryo-EM 
is highly desirable, as well as experience in protein production in human cell 
lines and X-ray crystallography.
One position opens in January 2019, the other opening around July 2019. 
Post-doc will be funded through an ERC advanced grant for up to five years.

Applications including a cover letter, CV, and the email addresses of two 
references should be sent to:

Pierre-Jean Corringer, pjcor...@pasteur.fr
Channel-Receptors Unit 
Neuroscience Department
Institut Pasteur, Paris



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[ccp4bb] AW: [ccp4bb] [Offtopic] Protein stain in Coomassie Blue dyes

[Hughes, Jon]

hi,
as a comment to zhijie's question, the biggest problem with marion bradford's 
"protein" assay is that it measures the SDS concentration too! therefore, where 
it would be most useful – that is in quantifying the total protein in an 
SDS-treated gel sample – it cannot be used! the amido-black method is far 
better, at least as far as i know. does anyone know why it's seldom used? our 
protocol is below if anyone's interested.
best
jon

Amido-Black assay.
Dilute 10µl of the clarified protein extract (also in SDS sample buffer) to 
200µl with water, add 600µl Amido-Black reagent, mix and incubate at RT for 
5min.  Centrifuge for 5min at 13krcf.  Discard the supernatant and wash the 
pellet twice in 500µl Acid-MeOH [10%(v/v) HAc in MeOH].  The final supernatant 
should be colourless.  Dissolve the pellet in 1ml 1M NaOH (warm if necessary) 
and assay at 615nm.

Amido-Black reagent
Stock = 0.13g Amido-Black 10B (Merck) + 1ml HAc + 9ml MeOH.  Stir well then 
filter.  Stable at 4°C indefinitely.  To use, dilute 1ml of this stock in 50ml 
Acid-MeOH. Stable upto 1 week at 4°C. Calibrate with a dilution series of a 
"standard" protein such as BSA.


Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Alex Lee
Gesendet: Freitag, 5. Oktober 2018 05:37
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] [Offtopic] Protein stain in Coomassie Blue dyes

Hi All,

Thanks for all of your inputs!

Alex

On Thu, Oct 4, 2018 at 7:31 PM Zhijie Li 
mailto:zhijie...@utoronto.ca>> wrote:
Hi,

At high concentration (1-2%) the published saturating SDS:protein binding ratio 
is about 1.4:1 by weight, that is roughly one SDS molecule per two aa on 
average. It is dense but  not that dense to prevent any further interaction.  
More importantly, as a quite hydrophilic small molecule SDS should have no 
trouble dissociating from the peptide when its in-solution concentration drops 
(therefore you can use SDS gel bands for MS). With common procedure, during 
staining the SDS should partially fall off( especially if the gel is heated), 
and partially remain with the protein in the gel, depending on: how hydrophobic 
the protein is, how low the environmental SDS concentration becomes, how much 
organic solvent there is in the solution, etc.. The coomassie should simply 
find whatever hydrophobic/positively charged patch to bind and aggregate. 
Besides, coomassie-R is probably slightly more hydrophobic than SDS so it is 
capable of competing SDS off if necessary. (The even less hydrophobic Coomassie 
G250 definitely binds protein in the presence of detergents - that how Blue 
Native gel works for membrane proteins) Finally, since the only thing you are 
looking for is some deeper blue to indicate the presence of protein, even if 
SDS did prevent dye binding to some extent, your gel still will work. This is 
different from when you want to use the dye to do some quantitative work such 
as the Bradford assay. It would be interesting to know the effect of detergents 
on Bradford.

Zhijie



On Oct 4, 2018, at 9:26 PM, Alex Lee 
mailto:alexlee198...@gmail.com>> wrote:
Dear All,

I am thinking that in an SDS-PAGE experiment, if protein samples are boiled in 
SDS containing loading dye, and supposedly SDS interacts with proteins, why the 
Coomassie Blue dyes could still interact with and stain the proteins?  I am 
thinking SDS is covering the proteins, making no room for the Coomassie Blue 
dyes interaction.  I'd appreciate it if any input from this forum.

Alex



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Re: [ccp4bb] [Offtopic] Protein stain in Coomassie Blue dyes

[mesters]

Hi Alex,


the binding of Coomassie Brilliant Blue R to proteins roughly correlates 
with the number of positive charges (about 1.5-3 dye molecules/charge; 
JBC 216, 9976-9980) whereas the SDS is thought to bind/align to the 
protein backbone during/after heat denaturation (roughly 1 SDS per 2 
amino acids). Because of the correlation to charge, the intensity of a 
band on a gel is not a good indicator of protein concentration at all. 
One or the other odd protein binds the dye so poorly that a negative 
glass-clear band as compared to the slightly blue background of the gel 
after destaining can be observed.


SDS is not fully wrapping/enveloping the unfolded protein, by binding to 
the backbone it just prevents the refolding and by binding in a relative 
stable ratio to the protein backbone (roughly 1 SDS per 2 amino acids), 
induces a relative stable mass-charge distribution (a property that 
nucleic acids own by nature) making the separation on a molecular sieve 
solely based on mass possible in the first place. However, very basic, 
acidic or post-translationally modified proteins will run differently on 
SDS-PAGE than your average protein (and marker proteins).



Jeroen



 Am 05.10.18 um 03:24 schrieb Alex Lee:

Dear All,

I am thinking that in an SDS-PAGE experiment, if protein samples are 
boiled in SDS containing loading dye, and supposedly SDS interacts 
with proteins, why the Coomassie Blue dyes could still interact with 
and stain the proteins?      I am thinking SDS is covering the 
proteins, making no room for the Coomassie Blue dyes interaction.  I'd 
appreciate it if any input from this forum.


Alex



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--
Dr.math. et dis. nat. Jeroen R. Mesters
Deputy, Senior Researcher & Lecturer
Program Coordinator /Infection Biology/ 



Institute of Biochemistry, University of Lübeck
Ratzeburger Allee 160, 23538 Lübeck, Germany
phone: +49-451-31013105 (secretariate -31013101)
fax: +49-451-31013104

http://jobs.zeit.de/image-upload/logo_10564.jpg
http://www.biochem.uni-luebeck.de 
http://www.eine-stadt-sieht-gelb.de 
http://www.uni-luebeck.de/studium/studiengaenge/infection-biology
http://www.iobcr.org 

Visiting Professorship in Biophysics, University of South Bohemia (CZ)
President of the International Organization for Biological 
Crystallization (IOBCr)

--
If you can look into the seeds of time and tell which grain will grow 
and which will not, speak then to me who neither beg nor fear 
(Shakespeare's Macbeth, Act I, Scene 3)

--
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It is invariably the case that high resolution X-ray structures show 
significantly better agreement with solution observables such as 
coupling constants, 13C chemical shifts, and proton chemical shifts, 
than the corresponding NMR structures, including the very best ones. 
Hence, in most cases, a high-resolution crystal structure (< 2.0 Å)will 
provide a better description of the structure in solution than the 
corresponding NMR structure  (Kuszewski, Gronenborn & Clore, 1996, 
Protein Science 5:1067-80)

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