Re: [ccp4bb] Measuring angles between domains

2021-11-12 Thread Ishan Rathore
Hi Kyle

I have used this pymol plugin to measure the angle between domains

https://pymolwiki.org/index.php/Angle_between_domains

Regards
Ishan


On Sat, Nov 13, 2021, 12:35 AM Kyle Gregory <
3632e92fcc15-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear CCP4 bulletin board,
>
> I have two domains connected by a helix and I want to measure tilt angles
> between domains, for comparison purposes to other structures of the same
> protein.
>
> Does anyone have any tools they'd recommend?
>
> Kind regards,
> Kyle
>
>
>
> --
>
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[ccp4bb] Measuring angles between domains

2021-11-12 Thread Kyle Gregory
Dear CCP4 bulletin board,

I have two domains connected by a helix and I want to measure tilt angles 
between domains, for comparison purposes to other structures of the same 
protein.

Does anyone have any tools they'd recommend?

Kind regards,
Kyle





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[ccp4bb] Announcement 9th International BioXFEL Conference

2021-11-12 Thread Erin Uppington
Dear Colleagues,

The NSF BioXFEL Science and Technology Center is pleased to announce our 9th 
Annual International Conference Feb 8-10, 2022 chaired by Tonya Kuhl, UC-Davis, 
and Thomas Grant, UB.  Registration is now open.  The meeting is currently 
virtual but we are investigating the potential for a hybrid format.

There are opportunities to be considered for a short talk by submitting an 
abstract by December 1st.  Details can be found on our conference web page.

For the most up to date information check our CONFERENCE 
SITE and REGISTER 
HERE

Confirmed Speakers:

Robert Buecker (CSSB-Hamburg)

Sarah
 Bowman (HWI)

Henry Chapman (DESY)

Ahmad Hozzeinedeh (UWM)

Hyotcheryl Ihee (KAIST)

Richard Kirian (ASU)

J. Mia Lahey-Rudolph (Lubeck)

Filipe Maia (PSI)

Valerio Mariani ((SLAC)

Fivos Perakis (Stockholm)

Megan Shelby (LLNL)

Jason Stagno (NIH)

Pablo Villaneuva-Perez (Lund)

Nadia Zatsepin (LaTrobe)

Jian-Min Zuo (U of IL-Urbana Champagne)

Best,

Erin Uppington, MBA

Foundation Administrator | Hauptman-Woodward Medical Research Institute
Managing Director | NSF BioXFEL Science and Technology Center

p: +1 716 898 8610 | f: +1 716 898 8660
e: eupping...@hwi.buffalo.edu

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


[hwi-logo-primary-horizontal]






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Re: [ccp4bb] High-order oligomers vs robust crystals - references?

2021-11-12 Thread Edwin Pozharski
One could use PISA to get a rough distribution of oligomerization states of
proteins in the PDB and compare bacterial vs mammalian... there always will
be a question though of whether any bias is inherent in proteins or driven
by crystallizability itself.

Personally, I always though that bacterial proteins crystallize better
because they express better and are more stable.  All of this is hand
waiving on my part, of course.

---
I don't know why the sacrifice didn't work. The science seemed so solid.
Julien XIII, Lord of the Lemurs

On Fri, Nov 12, 2021 at 9:52 AM Frank von Delft 
wrote:

> Hello all
>
> Two decades ago, I remember (!) much talk about a reason that bacterial
> proteins crystallize "more easily" is that they tend to come as
> oligomers (dimers and up), and that this internal symmetry made them
> happier to crystallize.
>
> Did anybody ever publish hard evidence?  Or even, is there a primary
> citation for the idea?
>
> Thanks
> Frank
>
> 
>
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Re: [ccp4bb] High-order oligomers vs robust crystals - references?

2021-11-12 Thread Georg Mlynek

Hi,

hard evidence I could not find. I once cited "An approach to 
crystallizing proteins by synthetic symmetrization" for a publication on 
a rescue strategy in crystallization. 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1637565/


They reference to a Phd thesis from 2003.

And one idea why it should work is related to "Why protein crystals 
favour some space-groups over others"


https://www.nature.com/articles/nsb1295-1062

Br, Georg.



Am 2021-11-12 um 3:52 PM schrieb Frank von Delft:

Hello all

Two decades ago, I remember (!) much talk about a reason that 
bacterial proteins crystallize "more easily" is that they tend to come 
as oligomers (dimers and up), and that this internal symmetry made 
them happier to crystallize.


Did anybody ever publish hard evidence?  Or even, is there a primary 
citation for the idea?


Thanks
Frank



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Re: [ccp4bb] [External] [ccp4bb] High-order oligomers vs robust crystals - references?

2021-11-12 Thread Dom Bellini - MRC LMB

Hi Frank,

Once we could not crystallize a monomer protein, but we knew the 
structure of a homolog dimer. We made some educated guessed mutations to 
dimerize our monomer target, which were based on the structure of the 
dimeric homolog. Perhaps evidence or perhaps just luck? :-)


https://pubmed.ncbi.nlm.nih.gov/22868772/

BW,

D

On 12/11/2021 14:58, Srivastava, Dhiraj wrote:
Recently there were few articles where synthetic symmetrization was 
used to enhance the crystallizability. proteins used were MBP, 
lysozyme and GFP to name a few. you can search for it. one of them is -

https://www.sciencedirect.com/science/article/pii/S0969212615002890


A Suite of Engineered GFP Molecules for Oligomeric Scaffolding 

Applications ranging from synthetic biology to protein crystallization 
could be advanced by facile systems for connecting multiple proteins 
together i…

www.sciencedirect.com



Dhiraj

*From:* CCP4 bulletin board  on behalf of Frank 
von Delft 

*Sent:* Friday, November 12, 2021 8:52 AM
*To:* CCP4BB@JISCMAIL.AC.UK 
*Subject:* [External] [ccp4bb] High-order oligomers vs robust crystals 
- references?

Hello all

Two decades ago, I remember (!) much talk about a reason that bacterial
proteins crystallize "more easily" is that they tend to come as
oligomers (dimers and up), and that this internal symmetry made them
happier to crystallize.

Did anybody ever publish hard evidence?  Or even, is there a primary
citation for the idea?

Thanks
Frank



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--
Dom Bellini, Xray Crystallography Facility (1S205)
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge CB2 0QH
Phone 01223 267839



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Re: [ccp4bb] [External] [ccp4bb] High-order oligomers vs robust crystals - references?

2021-11-12 Thread Srivastava, Dhiraj
Recently there were few articles where synthetic symmetrization was used to 
enhance the crystallizability. proteins used were MBP, lysozyme and GFP to name 
a few. you can search for it. one of them is -
https://www.sciencedirect.com/science/article/pii/S0969212615002890

[https://ars.els-cdn.com/content/image/1-s2.0-S0969212615002890-fx1.jpg]
A Suite of Engineered GFP Molecules for Oligomeric 
Scaffolding
Applications ranging from synthetic biology to protein crystallization could be 
advanced by facile systems for connecting multiple proteins together i…
www.sciencedirect.com


Dhiraj

From: CCP4 bulletin board  on behalf of Frank von Delft 

Sent: Friday, November 12, 2021 8:52 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [External] [ccp4bb] High-order oligomers vs robust crystals - 
references?

Hello all

Two decades ago, I remember (!) much talk about a reason that bacterial
proteins crystallize "more easily" is that they tend to come as
oligomers (dimers and up), and that this internal symmetry made them
happier to crystallize.

Did anybody ever publish hard evidence?  Or even, is there a primary
citation for the idea?

Thanks
Frank



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[ccp4bb] High-order oligomers vs robust crystals - references?

2021-11-12 Thread Frank von Delft

Hello all

Two decades ago, I remember (!) much talk about a reason that bacterial 
proteins crystallize "more easily" is that they tend to come as 
oligomers (dimers and up), and that this internal symmetry made them 
happier to crystallize.


Did anybody ever publish hard evidence?  Or even, is there a primary 
citation for the idea?


Thanks
Frank



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[ccp4bb] Senior Scientist, Structural Biology position at Sanofi US - Boston area

2021-11-12 Thread Kothe, Michael /US
We are seeking a Scientist to join our Boston-area structural biology group 
conducting drug design research in diverse therapeutic areas. Our group 
integrates with multidisciplinary project teams to accelerate drug discovery on 
innovative and challenging targets using x-ray crystallography and cryo-EM. To 
expand the latter, a state-of-the-art facility is under construction at our new 
2022 Cambridge campus. The successful candidate will generate structure-grade 
protein, and use such protein for structural studies using cryo-EM or 
crystallography in order to drive drug-design workflows. Significant experience 
with single-particle cryo-EM data generation and processing is desired. The 
successful candidate will work closely with members of the Structural Biology, 
Biochemistry and Biophysics teams, as well as members of the therapeutic area 
groups, and must be an enthusiastic team player with excellent communication 
skills and must bring curiosity and a desire to make an impact in the workplace.

Basic Qualifications:
PhD in Biochemistry or a related field (Biology, Cell Biology, Biotechnology, 
etc.) and 3+ years of experience in protein expression, purification and 
cryo-EM studies, or BS degree and 8+ years of relevant experience.

Preferred Qualifications:
Extensive track record with purification and structure determination of 
challenging proteins, (e.g., membrane proteins, complexes, etc.) by cryo-EM or 
crystallography. Hands-on operation of high-end cryo-electron microscopes, 
extensive familiarity with EM data processing suites. Industrial experience.


If interested, please apply using this link:
https://sanofi.wd3.myworkdayjobs.com/SanofiCareers/job/Waltham-MA/Senior-Scientist---Structural-Biology_R2621212-1


--
Michael Kothe
Senior Principal Scientist
Structural Biology, Sanofi R
153 Second Avenue
Waltham MA 02451





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Re: [ccp4bb] simulation of structural changes in the protein

2021-11-12 Thread Edwin Pozharski
Any molecular dynamics simulation would have a temperature parameter.
GROMACS is free and easy to use. And do find a computational biology expert
to consult with if this is more than an excercise.

On Wed, Nov 10, 2021, 11:20 PM Dr Muhammad Saleem 
wrote:

> Dear All,
>
> I was wondering if there is any webserver or software to simulate the
> structural changes in the protein at different temperatures?
>
>
> regards,
> Saleem
>
>
>
>
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Tools for measuring RMSD of entire molecule when a single domain is aligned

2021-11-12 Thread Sabine Schneider

Hi Kyle

DynDom gives you the angle of the relative domain movement, which I also 
find a good quantitative measure.


http://dyndom.cmp.uea.ac.uk/dyndom/runDyndom.jsp

Best Sabine

On 12/11/2021 15:13, Edwin Pozharski wrote:
https://pymolwiki.org/index.php/Rms_cur 



On Fri, Nov 12, 2021, 9:05 AM Kyle Gregory 
<3632e92fcc15-dmarc-requ...@jiscmail.ac.uk 
> wrote:


Dear CCP4 bulletin board,

I was wondering if there are any tools to determine the RMSD of
the entire molecule (two domains) when only aligning one domain,
the point i'm trying to make is a variation in domain positioning
relative to one another but I'd like to quantify it. LSQ alignment
in coot reports RMSD for the aligned porition only, as does the
alignment tools on ccp4 cloud (unless i've missed a feature)

Any advice would be greatly appreciated.

Kind regards,
Kyle



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Re: [ccp4bb] Tools for measuring RMSD of entire molecule when a single domain is aligned

2021-11-12 Thread Edwin Pozharski
https://pymolwiki.org/index.php/Rms_cur

On Fri, Nov 12, 2021, 9:05 AM Kyle Gregory <
3632e92fcc15-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear CCP4 bulletin board,
>
> I was wondering if there are any tools to determine the RMSD of the entire
> molecule (two domains) when only aligning one domain, the point i'm trying
> to make is a variation in domain positioning relative to one another but
> I'd like to quantify it. LSQ alignment in coot reports RMSD for the aligned
> porition only, as does the alignment tools on ccp4 cloud (unless i've
> missed a feature)
>
> Any advice would be greatly appreciated.
>
> Kind regards,
> Kyle
>
> --
>
> 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] Tools for measuring RMSD of entire molecule when a single domain is aligned

2021-11-12 Thread Kyle Gregory
Dear CCP4 bulletin board,

I was wondering if there are any tools to determine the RMSD of the entire 
molecule (two domains) when only aligning one domain, the point i'm trying to 
make is a variation in domain positioning relative to one another but I'd like 
to quantify it. LSQ alignment in coot reports RMSD for the aligned porition 
only, as does the alignment tools on ccp4 cloud (unless i've missed a feature)

Any advice would be greatly appreciated.

Kind regards,
Kyle



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[ccp4bb] Postdoctoral Position Available in Leiden

2021-11-12 Thread Zach Armstrong (Leiden University)
Hi All!

The Armstrong lab is recruiting a postdoctoral fellow with extensive experience 
in structural biology for a 3 year, funded project to study human and viral 
enzymes that modify carbohydrates.
A PhD in Biochemistry, Biophysics, Structural Biology (or a related field), 
experience in protein expression and purification, and excellent English 
communication and writing skills are required. Membrane protein experience is a 
plus (but not required).

The Armstrong lab is part of the bio-organic synthesis group within the 
Institute of Chemistry at Leiden University: 
https://www.universiteitleiden.nl/en/science/chemistry

For more information about the position, contact Zach Armstrong : 
z.w.b.armstr...@lic.leidenuniv.nl
to apply see the adverisemenet: https://www.linkedin.com/jobs/view/2786149594/

 
/Zach 



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[ccp4bb] ReNaFoBiS/FRISBI Webinar : Structural Biology Response to Biomedical Threats

2021-11-12 Thread CAVARELLI Jean (VIE)
Dear All, 

You are invited to the December ReNaFoBiS/FRISBI Zoom webinar. 

When: Dec 8, 2021 04:00 PM Paris 

Webinar Speaker Dr. Wladek Minor (Harrison Distinguished Professor, Department 
of Molecular Physiology and Biological Physics, University of Virginia, USA) 

Topic: Structural Biology Response to Biomedical Threats 





Abstract: 

Structural information, mainly derived by X-ray crystallography and 
Cryo-Electron Microscopy, is the quintessential prerequisite for 
structural-guided drug discovery. However, accurate structural information is 
only one information necessary to understand the big picture of medical 
disorders. To provide a rapid response to emerging biomedical challenges and 
threats like COVID-19, we need to analyze medical data in the context of other 
in-vitro and in-vivo experimental results. This approach may revolutionize drug 
discovery, albeit only when these data are combined and analyzed with effective 
data management framework like Advanced Information System proposed in 2017. 
The recently published virusMED system is a blueprint for Advanced Information 
Systems. 
Short CV of Pr Wladek Minor 


Prof. Wladek Minor received his Ph.D. in 1978 from the University of Warsaw in 
Solid State Physics. After moving to the United States in 1985 and working at 
Purdue University, he gradually switched to macromolecular crystallography. He 
joined the University of Virginia faculty in 1995. He was tenured in 1998 and 
promoted to full professor in 2003. In 2016, he became Harrison Distinguished 
Professor of Molecular Physiology and Biological Physics. He has been 
developing experimental protocols and computational methods for neutron 
scattering and X-ray diffraction since graduate school. After starting his 
independent career, he continued developing software within HKL, HKL-2000, and 
HKL-3000. He also worked on advanced solutions to other crystallographic 
problems: (a) Identification and refinement of metals in macromolecular 
structures; (b) Determination and analysis of macromolecular structures related 
to drug transport and drug discovery; (c) Reproducibility, ligand 
identification, and validation in structural biology; (d) Data mining, 
management, and access to primary experimental data; (e) Protocols and tools 
for more reliable structure determination, including the application of AI; (f) 
Analysis of COVID-19 structures and actions necessary to prepare for a possible 
future pandemic. He published more than 230 papers that attracted more than 
47,000 citations. He is a co-author of more than 450 Protein Data Bank 
deposits. Dr. Minor has trained over 110 people that are very successful in 
academia, industry, and medicine. Dr. Minor's research is often reported in 
general media outlets ( [ https://minorlab.org/news | https://minorlab.org/news 
] ), which helps taxpayers understand why investments in basic science are the 
best investments for the country's future. 

Register in advance for this webinar: 
https://us06web.zoom.us/webinar/register/WN_KnjC1dDBRZG4r8F6hQ_-VQ 


After registering, you will receive a confirmation email containing information 
about joining the webinar. 
Best 
Pr Jean Cavarelli 
[ https://www.renafobis.fr/ | https://www.renafobis.fr/ ] 
https://www.renafobis.fr/ 




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