[ccp4bb] Oleron 2024. There are only few places left

2024-02-22 Thread CAVARELLI Jean (VIE) 
Oleron 2024. 

The RéNaFoBiS Oléron workshop, dedicated to Integrative Structural Biology, 
will take place on the Oléron island (France), from May 30 until June 7, 2024 
The main objective of this workshop is to offer a theoretical and practical 
training in the different techniques used in integrative structural biology 
(X-ray diffraction, small angle X-ray scattering, NMR, electron microscopy, 
sample preparation for structural biology, biophysical methods to study and 
characterize macromolecular interactions). The goals are to explain and 
illustrate, to an audience mainly composed of doctoral students and young 
researchers, the contributions and limitations of each method with a strong 
emphasis on their complementarity/synergies and future developments. The 
official language of the workshop is French but some presentations may be given 
in English, depending on the overall profile of the students. For practicals, 
English and French speaking groups may be organised. 

As the number of places is limited (28 participants), participants will be 
selected on the basis of a CV and a letter of motivation. 
Applications will be examined and validated upon deposition and registration 
will be closed once the maximum number of students has been reached. 

There are only few places left . If you would like to participate, please 
submit your application as soon as possible. 

More details on 

https://ecolebios2024.sciencesconf.org/ 

Best regards 

Dr. Arnaud Poterszman 
Scientific Director Oleron 2024 




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[ccp4bb] OLERON 2024

2024-01-22 Thread CAVARELLI Jean (VIE) 


ReNaFoBiS. Oleron 2024. 

We are pleased to announce the 11th RéNaFoBiS Oléron workshop, dedicated to 
Integrative Structural Biology, that will take place on the Oléron island 
(France), from May 30 until June 7, 2024. 
The main objective of this workshop is to offer a theoretical and practical 
training in the different techniques used in integrative structural biology 
(X-ray diffraction, small angle X-ray scattering, NMR, electron microscopy, 
sample preparation for structural biology, biophysical methods to study and 
characterize macromolecular interactions). The goals are to explain and 
illustrate, to an audience mainly composed of doctoral students and young 
researchers, the contributions and limitations of each method with a strong 
emphasis on their complementarity/synergies and future developments. 

The official language of the workshop is French but some presentations may be 
given in English, depending on the overall profile of the students. For 
practicals, English and French speaking groups may be organised. 

Registration is now open on a specific web site maximum number of participants: 
28). See 


[ https://ecolebios2024.sciencesconf.org/ | 
https://ecolebios2024.sciencesconf.org/ ] 



As the number of places is limited (28 participants), participants will be 
selected on the basis of a CV and a letter of motivation. The deadline for 
applications is March 3, 2024. 
Applications will be examined and validated upon deposition and registration 
will be closed once the maximum number of students has been reached. 

Dr. Arnaud Poterszman 






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[ccp4bb] OLERON 2023.

2022-12-16 Thread CAVARELLI Jean (VIE) 
ReNaFoBiS. Oleron 2023. 

We are pleased to announce the 10th RéNaFoBiS Oléron workshop, dedicated to 
Integrative Structural Biology, that will take place on the Oléron island 
(France), from June the 1st until June the 9th, 2023. 
The main objective of this workshop is to offer a theoretical and practical 
training in the different techniques used in integrative structural biology 
(X-ray diffraction, small angle X-ray scattering, NMR, electron microscopy, 
sample preparation for structural biology, biophysical methods to study and 
characterize macromolecular interactions). 
The goals are to explain and illustrate, to an audience mainly composed of 
doctoral students and young researchers, the contributions and limitations of 
each method with a strong emphasis on their complementarity/synergies and 
future developments. 

The official language of the workshop is French but some presentations may be 
given in English, depending on the overall profile of the students. For 
practicals, English and French speaking groups may be organised. 

Registration is now open on a specific web site maximum number of participants: 
28). See 
[ https://ecolebios2023.sciencesconf.org/ ] 

[ https://ecolebios2023.sciencesconf.org/ | 
https://ecolebios2023.sciencesconf.org/ ] 

As the number of places is limited (28 participants), participants will be 
selected on the basis of a CV and a letter of motivation. The deadline for 
applications is March 1, 2023. 
Applications will be examined and validated upon deposition and registration 
will be closed once the maximum number of students has been reached. 

Jean Cavarelli 
National ReNaFoBiS Coordinator 
http://www.renafobis.fr/ 




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[ccp4bb] ReNaFoBiS/FRISBI/INSTRUCT-ERIC Webinar

2022-03-15 Thread CAVARELLI Jean (VIE) 
Dear All 

You are invited to a Zoom webinar. 
When: Apr 19, 2022 04:00 PM Paris 

Topic : Watching molecules dancing in the cell. 

After a short journey through the evolution of structural biology and the 
present state of the art of crystallography and cryo-EM, 
we will show how the combination of optical methods and cryo-tomography open 
the door to the cell at atomic level. 

Webinar Speaker : 

Dino Moras (UNISTRA, CNRS, IGBMC) 

Dino Moras, emeritus research director at CNRS, is currently “professeur 
conventionné” at the University of Strasbourg. After completing a PhD in 
chemistry in 1971, he moved into structural biology with his research focused 
on the expression of genetic information and its regulation. His major 
contributions include the partition of aminoacyl-tRNA synthetases into two 
classes (1990), the first structure determination of a class II aaRS-tRNA 
complex (1991) and the elucidation of the mechanism of aminoacylation. In the 
field of transcription his focus has been on nuclear receptors of hormones. 
with the first crystal structure of a ligand-binding domain (RXR) in 1995. 
Using an integrative approach, he solved the crystal and solution structures of 
several receptors bound to ligands, DNA and cofactors. 

Register in advance for this webinar: 
[ https://us06web.zoom.us/webinar/register/WN_IXDQtdiVToyUiFDrZhcqRw | 
https://us06web.zoom.us/webinar/register/WN_IXDQtdiVToyUiFDrZhcqRw ] 

After registering, you will receive a confirmation email containing information 
about joining the webinar. 
- 
Jean Cavarelli 
Professor of Structural Biology 
"Structural biology of epigenetic targets" 
Department of Integrated structural biology 
IGBMC,UMR7104 CNRS-UNISTRA, INSERM U 1258 
phone : +33 (0)3 69 48 52 74 




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[ccp4bb] ReNaFoBiS/FRISBI/INSTRUCT-ERIC webinar

2022-02-07 Thread CAVARELLI Jean (VIE) 
Dear All, 

You are invited to a ReNaFoBiS/FRISBI/INSTRUCT-ERIC webinar. 

When: March 1, 2022 04:00 PM Paris 
Topic: New Opportunities for Integrated Structural Biology at 4th generation 
synchrotron sources . 
Webinar Speaker : Dr Andrew THOMPSON (Synchrotron SOLEIL) 


Register in advance for this webinar: 
[ https://us06web.zoom.us/webinar/register/WN_unvGJZCVSOyJRXwHUY-AXg | 
https://us06web.zoom.us/webinar/register/WN_unvGJZCVSOyJRXwHUY-AXg ] 


After registering, you will receive a confirmation email containing information 
about joining the webinar. 

-- 
Andrew Thompson started his career at the SRS daresbury laboratory, working 
with John Helliwell, Colin Nave and Miroslav Papiz on the protein 
crystallography beamlines. 
He then moved to EMBL grenoble oustation, as part of a new collaboration 
between the ESRF and EMBL where he built and operated beamlines BM14 and ID29 
for anomalous phasing measurements in x-ray diffraction. After joining 
synchrotron SOLEIL in 2002, Andrew Thompson constructed and operated the 
Proxima1 facility, moving into a mangerial post in 2014. He is currently 
working on the Proxima1 beamline whilst preparing SOLEIL for the arrival of its 
first 300 kV cryo-electron microscope which is expected in early 2023. 
- 









- 
Jean Cavarelli 
Professor of Structural Biology 
"Structural biology of epigenetic targets" 
Department of Integrated structural biology 
IGBMC,UMR7104 CNRS-UNISTRA, INSERM U 1258 
phone : +33 (0)3 69 48 52 74 




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Re: [ccp4bb] Validation of structure prediction

2022-01-17 Thread CAVARELLI Jean (VIE) 

May be useful if not already mentioned 

Ten things I `hate' about refinement 
Pietro Roversi and Dale E. Tronrud 
https://journals.iucr.org/d/issues/2021/12/00/qt5008/index.html 

- 
Jean Cavarelli 
Professor of Structural Biology 
"Structural biology of epigenetic targets" 
Department of Integrated structural biology 
IGBMC,UMR7104 CNRS-UNISTRA, INSERM U 1258 
phone : +33 (0)3 69 48 52 74 


De: "Jan Dohnalek"  
À: "ccp4bb"  
Envoyé: Lundi 17 Janvier 2022 09:39:33 
Objet: Re: [ccp4bb] Validation of structure prediction 

I think quite a bit of this "inconsistency" with protein structures comes from 
the fact that with our larger globules it is much more true that our model is 
an approximate time and space average of something that could have the ideal 
geometry. 
I.e. the way we are trying to represent the density is actually not that 
appropriate. The only "improvement" to this I think is the multiple model 
approach. 

My 2 c. 

Jan 


On Sat, Jan 15, 2022 at 9:29 PM James Holton < [ mailto:jmhol...@lbl.gov | 
jmhol...@lbl.gov ] > wrote: 




On 1/13/2022 11:14 AM, Tristan Croll wrote: 

BQ_BEGIN
(please don’t actually do this) 


Too late! I've been doing that for years. What happens, of course, is the 
"geometry" improves, but the R factors go through the roof. This I expect comes 
as no surprise to anyone who has played with the "weight" parameters in 
refinement, but maybe it should? What is it about our knowledge of chemical 
bond lengths, angles, and radii that is inconsistent with the electron density 
of macromolecules, but not small molecules? Why do macro-models have a burning 
desire to leap away from the configuration we know they adopt in reality? If 
you zoom in on those "bad clashes" individually, they don't look like something 
that is supposed to happen. There is a LOT of energy stored up in those little 
springs. I have a hard time thinking that's for real. The molecule is no doubt 
doing something else and we're just not capturing it properly. There is 
information to be had here, a lot of information. 

This is why I too am looking for an all-encompassing "geometry score". Right 
now I'm multiplying other scores together: 

score = (1+Clashscore)*sin(worst_omega)*1./(1+worst_rama)*1/(1+worst_rota) 
*Cbetadev*worst_nonbond*worst_bond*worst_angle*worst_dihedral*worst_chir*worst_plane
 

where things like worst_rama is the "%score" given to the worst Ramachandran 
angle by phenix.ramalyze, and worst_bond is the largest "residual" reported 
among all the bonds in the structure by molprobity or 
phenix.geometry_minimization. For "worst_nonbond" I'm plugging the observed and 
ideal distances into a Leonard-Jones6-12 potential to convert it into an 
"energy" that is always positive. 

With x-ray data in hand, I've been multiplying this whole thing by Rwork and 
trying to find clever ways to minimize the product. Rfree is then, as always, 
the cross-check. 

Or does someone have a better idea? 

-James Holton 
MAD Scientist 


On 1/13/2022 11:14 AM, Tristan Croll wrote: 

BQ_BEGIN

Hard but not impossible - even when you *are* fitting to low-res density. See [ 
https://twitter.com/crolltristan/status/1381258326223290373?s=21 | 
https://twitter.com/crolltristan/status/1381258326223290373?s=21 ] for example 
- no Ramachandran outliers, 1.3% sidechain outliers, clashscore of 2... yet 
multiple regions out of register by anywhere up to 15 residues! I never 
publicly named the structure (although I did share my rebuilt model with the 
authors), but the videos and images in that thread should be enough to 
illustrate the scale of the problem. 

And that was *with* a map to fit! Take away the map, and run some MD energy 
minimisation (perhaps with added Ramachandran and rotamer restraints), and I 
think it would be easy to get your model to fool most “simple” validation 
metrics (please don’t actually do this). The upshot is that I still think 
validation of predicted models in the absence of at least moderate-resolution 
experimental data is still a major challenge requiring very careful thought. 

— Tristan 

On 13 Jan 2022, at 18:41, James Holton < [ mailto:jmhol...@lbl.gov | 
jmhol...@lbl.gov ] > wrote: 


BQ_BEGIN

Agree with Pavel. 

Something I think worth adding is a reminder that the MolProbity score only 
looks at bad clashes, ramachandran and rotamer outliers. 

MPscore=0.426∗ln(1+clashscore)+0.33∗ln(1+max(0,rota_out−1))+0.25∗ln(1+max(0,rama_iffy−2))+0.5
 

It pays no attention whatsoever to twisted peptide bonds, C-beta deviations, 
and, for that matter, bond lengths and bond angles. If you tweak your weights 
right you can get excellent MP scores, but horrible "geometry" in the 
traditional bonds-and-angles sense. The logic behind this kind of validation is 
that normally nonbonds and torsions are much softer than bond and angle 
restraints and therefore fertile ground for detecting problems. Thus far, I am 
not aware of any "Grand Unified Score" that

[ccp4bb] CALL FOR APPLICATIONS - GROUP LEADER POSITION IGBMC

2022-01-10 Thread CAVARELLI Jean (VIE) 
Dear All 



We want to draw your attention to a tenure-track team leader position in 
cryogenic Electron Tomography (cryo-ET) which is about to open at IGBMC, and we 
would be grateful if you could disseminate this information to any motivated 
candidate. 




The main focus of this position is to strengthen and develop new research 
directions using cryo-ET, especially -but not exclusively, in situ cellular 
cryo-ET, and dedicated image analysis software. The junior professor will 
develop his own scientific project and consolidate the cryo-ET activities 
initialized by our teams. The position is supported by the Inserm and we are 
therefore particularly interested in attracting scientists with innovative 
research projects related to human health and diseases, and with experience and 
motivation for method optimization and development. 




This tenue-track junior professor position is a new type of academic position 
for France. To attract motivated candidates, the position offers a more 
competitive salary and, after successful evaluation, is converted into a senior 
Directeur de Recherche (DR) position, which is equivalent to a full 
professorship with little teaching duties. This is a more straightforward and 
fast way to obtain a senior position as compared to the regular academic 
carrier that requires a highly selective competition for upgrading to DR. The 
tenure-track period has been initially set to 5 years, but can be shorten upon 
demonstrated scientific performance. 




The junior professor will be immersed in the collaborative, interdisciplinary 
environment of IGBMC, a leading biomedical research centre bringing together 
research groups with interests in cell, molecular and structural biology ( [ 
https://www.igbmc.fr/en/ | link here ] ). The candidate will be supported by 
the cryo-EM platform of the Department of Integrated Structural Biology that 
hosts the French and European Infrastructures for Integrated Structural 
Biology, FRISBI and Instruct-ERIC, respectively [ 
https://www.igbmc.fr/en/plateforms-and-services/platforms/integrated-structural-biology
 | link here ] . It is equipped with cutting-edge instrumentation such as Titan 
Krios and Glacios cryo electron microscopes, and a cryo Focused Ion Beam 
Scanning Electron Microscope (FIB/SEM). The Titan Krios microscope is equipped 
with a Cs corrector, GIF energy filter, K3 camera and phase plates. A CLEM 
module (Leica Microsystems) is available for correlative cryo-fluorescent 
imaging and integrated sample transfer to cryo-FIB/SEM or cryo-TEM. In 
addition, the cryo-EM platform has a suite of associated equipment for sample 
preparation and dedicated computing resources for image processing and 3D 
reconstruction. New investments, in particular a second Titan-like instruments, 
are granted. 




The new group is expected to start in 2023 and will benefit from a start-up 
package. Application instructions can be found at the Inserm eva portal ( [ 
https://eva3-accueil.inserm.fr/sites/eva/appels-a-projets/Pages/default.aspx | 
link here ] ). Interested candidates can contact Prof. M. Eltsov 
(mikhail.elt...@igbmc.fr) or Dr P. Schultz (patrick.schu...@igbmc.fr) for 
further information. We will be happy to answer any questions and assist the 
candidates in framing the project in line with the requirements of call. 







Usefull links : 


IGBMC Web site 


[ https://www.igbmc.fr/en/ | https://www.igbmc.fr/en/ ] 


Intergated Structural Biology Platform 


[ 
https://www.igbmc.fr/en/plateforms-and-services/platforms/integrated-structural-biology
 | 
https://www.igbmc.fr/en/plateforms-and-services/platforms/integrated-structural-biology
 ] 


INSERM Portal 


https://eva3-accueil.inserm.fr/sites/eva/appels-a-projets/Pages/default.aspx 


https://eva3-accueil.inserm.fr/sites/eva/appels-a-projets/cpj/Pages/projets.aspx
 






- 
Jean Cavarelli 
Professor of Structural Biology 
"Structural biology of epigenetic targets" 
Department of Integrated structural biology 
IGBMC,UMR7104 CNRS-UNISTRA, INSERM U 1258 
phone : +33 (0)3 69 48 52 74 




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[ccp4bb] ReNaFoBiS/FRISBI/INSTRUCT-ERIC Webinar

2021-12-13 Thread CAVARELLI Jean (VIE) 
Dear All 

You are invited to a Zoom webinar. 
When: Jan 18, 2022 04:00 PM Paris 

Topic: AlphaFold changes everything: Incorporating predicted models in X-ray 
and Cryo-EM structure determination 

Webinar Speaker : Thomas C Terwilliger (Senior Scientist @New Mexico 
Consortium) 
Tom Terwilliger is a member of the Phenix software development team and 
develops tools and algorithms for X-ray crystallography and cryo-EM 
(http://www.phenix-online.org). He has an AB in Physics from Harvard, a PhD in 
Molecular Biology from UCLA under David Eisenberg, was a Helen Hay Whitney 
Fellow at Berkeley with Daniel Koshland, Jr. and a Presidential Young 
Investigator at the University of Chicago. He is now a Laboratory Fellow at Los 
Alamos National Laboratory and a Senior Scientist at the New Mexico Consortium. 

Register in advance for this webinar: 
https://us06web.zoom.us/webinar/register/WN_NHmWj7dpQbiRDq9gLRThpg 


After registering, you will receive a confirmation email containing information 
about joining the webinar. 
- 
Jean Cavarelli 
Professor of Structural Biology 
"Structural biology of epigenetic targets" 
Department of Integrated structural biology 
IGBMC,UMR7104 CNRS-UNISTRA, INSERM U 1258 
phone : +33 (0)3 69 48 52 74 



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[ccp4bb] ReNaFoBiS/FRISBI Zoom webinar Structural Biology Response to Biomedical Threats

2021-12-07 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 | 
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://frisbi.eu/ | https://frisbi.eu/ ] 


- 
Jean Cavarelli 
Professor of Structural Biology 
"Structural biology of epigenetic targets" 
Department of Integrated structural biology 
IGBMC,UMR7104 CNRS-UNISTRA, INSERM U 1258 
phone : +33 (0)3 69 48 52 74 




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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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[ccp4bb] ReNaFoBiS/FRISBI Webinars

2021-10-07 Thread CAVARELLI Jean (VIE) 
Dear All 

The next two webinars will be given by Dr Amélie LeForestier (CNRS, Université 
Paris-Saclay) 

1. Oct 13, 2021 04:00 PM Paris 
Topic: Cryo electron Tomography 

Register in advance for this webinar: 
https://us06web.zoom.us/webinar/register/WN_5gZHGdeFR0-oxJtY7XALQQ 

2. Nov 10, 2021 04:00 PM Paris 
Topic: Cellular cryo electron microscopy 
Register in advance for this webinar: 
https://us06web.zoom.us/webinar/register/WN_n5PH1yUNSG6jOZ1tJR5c3g 


Amélie Leforestier (DR2 CNRS) is a biophysicist and cryo electron microscopist 
head of the team Structure and dynamics of self-assembled biological objects at 
the Solid state Physics Laboratory (LPS, Université Paris-Saclay). She studied 
biophysics at UPMC (Paris) and obtained a PhD for her work on liquid 
crystalline phases of DNA. Supported by an EMBO fellowship, she joined Jacques 
Dubochets lab in Lausanne, where she discovered cryo electron microscopy 
in the 90s. Back in France, she joined the CNRS at LPS, where she set up a 
cryo-EM lab dedicated to soft matter physics and physics of biological systems. 
Her research interests focus on the architecture of DNA and chromatin 
assemblies in vitro and in situ. 



- 
Jean Cavarelli 
Professor of Structural Biology 
"Structural biology of epigenetic targets" 
Department of Integrated structural biology 
IGBMC,UMR7104 CNRS-UNISTRA, INSERM U 1258 
phone : +33 (0)3 69 48 52 74 




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[ccp4bb] ReNaFoBiS/FRISBI webinar series : Single Particle Cryo-EM : from specimen preparation to data collection

2021-09-08 Thread CAVARELLI Jean (VIE) 
Dear All 

You are invited to a ReNaFoBiS/FRISBI webinar. 

When: Sep 29, 2021 04:00 PM Paris 
Topic: Single Particle Cryo-EM : from specimen preparation to data collection 
Principles and typical workflow of Single Particle cryo-EM from specimen 
preparation to data collection will be presented, including recent advances in 
grid preparation, specimen deposition, and also in data collection with direct 
electron detectors, and ancillary devices. 

Register in advance for this webinar: 
https://us06web.zoom.us/webinar/register/WN_duay_VRkSE2BbfFOVbqXGw 

-- 

Webinar Speaker : Olivier Lambert (DR CNRS, CBMN, Université Bordeaux) 
Olivier Lambert is a structural biologist using cryoEM methods for structure 
determination of protein complexes. He obtained a PhD at the University of 
Tours (1994) for his work on the architecture of several respiratory complexes 
determined by single particle cryoEM. Then, after two postdoctoral stages 
(University of Groningen and Institut Curie in Paris), he got the opportunity 
to develop methods to reconstitute membrane proteins in lipid systems amenable 
to structural EM studies including SPA and tomography. Nowadays as a team 
leader, his research activities are focused on bacterial multidrug efflux pumps 
involved in the antibio-resistance. 

After registering, you will receive a confirmation email containing information 
about joining the webinar. 


- 
Jean Cavarelli 
Professor of Structural Biology 
"Structural biology of epigenetic targets" 
Department of Integrated structural biology 
IGBMC,UMR7104 CNRS-UNISTRA, INSERM U 1258 
phone : +33 (0)3 69 48 52 74 


[ https://frisbi.eu/ | https://frisbi.eu/ ] 
[ https://www.renafobis.fr/ | https://www.renafobis.fr/ ] 





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[ccp4bb] ReNaFoBiS/FRISBI webinar series : Cryo electron Tomography

2021-09-08 Thread CAVARELLI Jean (VIE) 
Dear All 

You are invited to a ReNaFoBiS/FRISBI webinar. 

When: Oct 13 , 2021 04:00 PM Paris 

Topic: Cryo electron Tomography 
Principles and typical workflow of cryo-electron tomography will be presented, 
including: missing information, tilt series acquisition, phase plates and 
energy filtering, tilt series alignment and tomogram reconstruction and 
visualization. 

Register in advance for this webinar: 
[ https://us06web.zoom.us/webinar/register/WN_5gZHGdeFR0-oxJtY7XALQQ | 
https://us06web.zoom.us/webinar/register/WN_5gZHGdeFR0-oxJtY7XALQQ ] 

Webinar Speaker 

Amélie LeForestier (DR2 CNRS, LPS, Université Paris-Saclay) 
Amélie Leforestier is a biophysicist and cryo electron microscopist head of the 
team Structure and dynamics of self-assembled biological objects at the Solid 
state Physics Laboratory (LPS, Université Paris-Saclay). She studied biophysics 
at UPMC (Paris) and obtained a PhD for her work on liquid crystalline phases of 
DNA. Supported by an EMBO fellowship, she joined Jacques Dubochet's lab in 
Lausanne, where she discovered cryo electron microscopy in the 90's. Back in 
France, she joined the CNRS at LPS, where she set up a cryo-EM lab dedicated to 
soft matter physics and physics of biological systems. Her research interests 
focus on the architecture of DNA and chromatin assemblies in vitro and in situ. 


After registering, you will receive a confirmation email containing information 
about joining the webinar. 

- 
Jean Cavarelli 
Professor of Structural Biology 
"Structural biology of epigenetic targets" 
Department of Integrated structural biology 
IGBMC,UMR7104 CNRS-UNISTRA, INSERM U 1258 
phone : +33 (0)3 69 48 52 74 

[ https://frisbi.eu/ | https://frisbi.eu/ ] 
[ https://www.renafobis.fr/ | https://www.renafobis.fr/ ] 




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[ccp4bb] ReNaFoBiS/FRISBI Webinar Series : XFEL

2021-05-04 Thread CAVARELLI Jean (VIE) 

ReNaFoBiS/FRISBI Webinar Series 
Serial Femtosecond Crystallography @ XFELs; current and future prospects for 
structural biology. 
May 12, 2021 04:00 PM (CET, France) 
Jacques-Philippe Colletier (PhD, DR CNRS, Serial Nano-Crystallography team 
(SNaX), IBS, Grenoble, Fran ce) 

Register in advance for this webinar: 
[ https://zoom.us/webinar/register/WN_YQoVAlD4TQKdNTt7ZEBKTA | 
https://zoom.us/webinar/register/WN_YQoVAlD4TQKdNTt7ZEBKTA ] 


After registering, you will receive a confirmation email containing information 
about joining the webinar. 

-- 

Webinar Speaker 
Jacques-Philippe Colletier earned his Ph.D. (2006) in biological 
crystallography and NMR at the University Joseph Fourier (Grenoble, France). 
His Ph.D. in kinetic crystallography, focused on the substrate traffic and 
inhibition in acetylcholinesterase, was prepared at the Institut de Biologie 
Structurale with Dr. Martin Weik. Jacques-Philippe did a first postdoc 
(2006-2007) at the Weizman Institute of Science (Rehovot, Israel), working with 
Profs. Joel Sussman and Israel Silman on the structural dynamics of 
acetylcholinesterase as seen by molecular dynamics simulations. He then joined 
the lab of Prof. David Eisenberg (2007-2009), at the University of California 
in Los Angeles, to work on the structure of the beta-amyloid 
peptide.Jacques-Philippe came back in 2009 to the IBS. Since 2012, his focus 
shifted to static and time-resolved nano crystallography using the ultra bright 
pulses delivered by X-ray Free Electron Laser. 
- 
Jean Cavarelli 
Professor of Structural Biology 
"Structural biology of epigenetic targets" 
Department of Integrated structural biology 
IGBMC,UMR7104 CNRS-UNISTRA, INSERM U 1258 
phone : +33 (0)3 69 48 52 74 



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[ccp4bb] ReNaFoBiS/FRISBI webinar. April 21, 2021 08:00 PM Paris

2021-04-17 Thread CAVARELLI Jean (VIE) 

ReNaFoBiS/FRISBI Webinar. 
Structural biology in industry : the NovAliX perspective 
By Denis Zeyer (CEO NovAliX ), PhD 
April 21, 2021 08:00 PM Paris 

Register in advance for this webinar: 
https://zoom.us/webinar/register/WN_Fq-wVPQaQoSieSwnIHuzdQ 


After registering, you will receive a confirmation email containing information 
about joining the webinar. 

-- 
Webinar Speaker : Denis Zeyer (CEO NovAliX ), PhD 
Denis earned his M.Sc. in biological crystallography and NMR at the Louis 
Pasteur University (Strasbourg, France). His Ph.D. in protein X-ray 
crystallography (with Dr. Jean-Paul Renaud and Dr. Dino Moras at the Institute 
of Genetics and Molecular and Cellular Biology, Strasbourg, France, in 
collaboration with Bristol Myers Squibb).In 2003 Denis built structural biology 
and biophysics groups and launched the research services business of AliX 
pharmaceuticals. In that capacity he has been instrumental in building a sound 
client base including major pharmaceutical companies; establishing a reputation 
for scientific excellence and reliability; and in technical improvements though 
internal and external innovations. Denis was appointed CEO of AliX in 2008 and 
has been CEO of NovAliX since its inception. He has been instrumental in the 
implementation of Novalix’ cryo-electron microscopy platform in 2015 and its 
subsequent development with a strong focus for the use of cryoEM in SBDG. 



- 
Jean Cavarelli 
Professor of Structural Biology 
"Structural biology of epigenetic targets" 
Department of Integrated structural biology 
IGBMC,UMR7104 CNRS-UNISTRA, INSERM U 1258 
phone : +33 (0)3 69 48 52 74 




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[ccp4bb] ReNaFoBiS OLERON 2020. Registration open

2020-01-21 Thread CAVARELLI Jean (VIE) 
ReNaFoBiS. Oleron 2020. 

We are pleased to announce the RéNaFoBiS Oléron workshop, dedicated to 
Integrative Structural Biology, that will take place on the Oléron island 
(France), from June the 12th until June the 19th, 2020. 
The main objective of this workshop is to offer a theoretical and practical 
training in the different techniques used in integrative structural biology 
(X-ray diffraction, small angle X-ray scattering, NMR, cryo-electron 
microscopy, sample preparation for structural biology, biophysical methods to 
study and characterize macromolecular interactions). 
The goals are to explain and illustrate, to an audience mainly composed of 
doctoral students and young researchers, the contributions and limitations of 
each method with a strong emphasis on their complementarity/synergies and 
future developments. 
The official language of the workshop is French but presentations may be given 
in English, depending on the overall profile of the students. 
For practicals, English and French speaking groups may be organised. 

Registration is now open on a specific web site, 
https://ecolebios2020.sciencesconf.org/) (maximum number of participants: 25). 
Applications will be evaluated upon deposition. 
More information on https://ecolebios2020.sciencesconf.org/ 
(see also http://www.renafobis.fr/) 


Jean Cavarelli 
- 
Jean Cavarelli 
Professor of Structural Biology 
"Structural biology of epigenetic targets" 
Department of Integrated structural biology 
IGBMC,UMR7104 CNRS-UNISTRA, INSERM U 1258 
phone : +33 (0)3 69 48 52 74 



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[ccp4bb] ReNaFoBiS National School OLERON 2020

2019-11-13 Thread CAVARELLI Jean (VIE) 

ReNaFoBiS. Oleron 2020. 

We are pleased to announce the 7th RéNaFoBiS Oléron workshop, dedicated to 
Integrative Structural Biology, that will take place on the Oléron island 
(France), from June the 12th until June the 19th, 2020. The main objective of 
this workshop is to offer a theoretical and practical training in the different 
techniques used in integrative structural biology (X-ray diffraction, small 
angle X-ray scattering, NMR, cryo-electron microscopy, sample preparation for 
structural biology, biophysical methods to study and characterize 
macromolecular interactions). The goals are to explain and illustrate, to an 
audience mainly composed of doctoral students and young researchers, the 
contributions and limitations of each method with a strong emphasis on their 
complementarity/synergies and future developments. 
The official language of the workshop is French but presentations may be given 
in English, depending on the overall profile of the students. For practicals, 
English and French speaking groups may be organised. 
Registration will be open on a specific web site starting January 20th, 2020 
(maximum number of participants: 25). 
Applications will be evaluated upon deposition. 
More information on the French Initiative ReNaFoBiS : [ 
http://www.renafobis.fr/ | http://www.renafobis.fr/ ] 
Best regards 
Jean Cavarelli 
National ReNaFoBiS Coordinator 

 

ReNaFoBiS. 7eme École de Biologie Structurale Intégrative 
Oléron – du 12 au 19 juin 2020 

Le réseau RéNaFoBIS organise son école nationale du 12 au 19 juin 2020 à 
Oléron. Cette école propose une formation théorique et appliquée aux 
différentes approches utilisées en biologie structurale (diffraction et 
diffusion des rayons X, RMN, cryo-microscopie, préparations des échantillons en 
vue des études structurales, interactions macromoléculaires). Elle mettra 
l’accent sur l’intégration de plusieurs de ces méthodes pour répondre aux 
grandes questions de la biologie fonctionnelle à l’échelle atomique. 
Pour un public de doctorants ou de jeunes chercheurs, cette formation montrera 
les apports et les limites de chaque méthode et leur complémentarité. Elle 
inclura des sessions théoriques le matin et des travaux pratiques en groupes 
l’après-midi. 
Cette école est ouverte aux techniciens et ingénieurs (domaine académique et 
industriel) dans le cadre de la formation continue. Les conférences seront 
données principalement en français. Les supports des présentations seront en 
anglais, afin de permettre aux participants non-francophones de suivre plus 
facilement. Lors des sessions pratiques (TP), des groupes anglophones pourront 
être proposés si besoin. 
Le site Web spécifique d'inscriptions sera ouvert à partir du 20 janvier 2020 . 
Le nombre de places étant limité (25 participants), les participants seront 
sélectionnés sur la base d'un CV et d'une lettre de motivation. Les dossiers 
seront examinés et validés au fur et à mesure de leur déposition. 
Plus d'informations le site de ReNaFoBiS [ http://www.renafobis.fr/ | 
http://www.renafobis.fr/ ] 
Tres cordialement 
Jean Cavarelli 
Coordinateur National ReNaFoBiS 

- 
Jean Cavarelli 
Professor of Structural Biology 
"Structural biology of epigenetic targets" 
Department of Integrated structural biology 
IGBMC,UMR7104 CNRS-UNISTRA, INSERM U 1258 
phone : +33 (0)3 69 48 52 74 




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[ccp4bb] ReNaFoBiS. Oleron 2019. Registration is now open

2019-01-16 Thread VIE 
ReNaFoBiS. Oleron 2019. Registration is now open

We are pleased to announce the 6th RéNaFoBiS Oléron workshop, dedicated to 
Integrative Structural Biology, that will take place on the Oléron island 
(France), from June the 21th until June the 28th, 2019. The main objective of 
this workshop is to offer a theoretical and practical training in the different 
techniques used in integrative structural biology (X-ray diffraction, small 
angle X-ray scattering, NMR,cryo-electron microscopy, sample preparation for 
structural biology,biophysical methods to study and characterize macromolecular 
interactions). The goals are to explain and illustrate, to an audience mainly 
composed of doctoral students and young researchers, the contributions and 
limitations of each method with a strong emphasis on their complementarity and 
future developments.

The official language of the workshop is French but presentations may be given 
in English, depending on the overall profile of the students. For
practicals, English and French speaking groups may be organised.

Registration is now open on https://ecolebios2019.sciencesconf.org/

Applications will be evaluated upon deposition.

Best regards
Jean Cavarelli
National ReNaFoBiS Coordinator
https://www.renafobis.fr/
--

Jean Cavarelli
Professor of Structural Biology
Tél : +33 (0)3 69 48 52 74
jean.cavare...@unistra.fr
Structural Biology of Epigenetic Targets
Integrated Structural Biology Department
IGBMC. UMR7104 CNRS-UDS, INSERM U964.
F - 67404 Illkirch



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[ccp4bb] OLERON 2019.

2018-11-20 Thread VIE 

ReNaFoBiS. Oleron 2019.

We are pleased to announce the 6th RéNaFoBiS Oléron workshop, dedicated to 
Integrative Structural Biology, that will take place on the Oléron island 
(France), from June the 21th until June the 28th, 2019. The main objective of 
this workshop is to offer a theoretical and practical training in the different 
techniques used in integrative structural biology (X-ray diffraction, small 
angle X-ray scattering, NMR, cryo-electron microscopy, sample preparation for 
structural biology,  biophysical methods to study and characterize 
macromolecular interactions). The goals are to explain and illustrate, to an 
audience mainly composed of doctoral students and young researchers, the 
contributions and limitations of each method with a strong emphasis on their 
complementarity and future developments.

The official language of the workshop is French but presentations may be given 
in English, depending on the overall profile of the students. For practicals, 
English and French speaking groups may be organised.
Registration will be open on a specific web site on January 2019 (maximum 
number of participants: 25).
Applications will be evaluated upon deposition.
More information on the French Initiative ReNaFoBiS : http://www.renafobis.fr/
Best  regards
Jean Cavarelli
National ReNaFoBiS Coordinator

--

Jean Cavarelli
Professor of Structural Biology
Tél : +33 (0)3 69 48 52 74
jean.cavare...@unistra.fr
Structural Biology of Epigenetic Targets
Integrated Structural Biology Department
IGBMC. UMR7104 CNRS-UDS, INSERM U964.
F - 67404 Illkirch



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[ccp4bb] ReNaFoBiS. Oleron 2018. There are only few places left

2018-03-19 Thread VIE 

ReNaFoBiS. Oleron 2018. There are only few places left.

The 5th RéNaFoBiS Oléron workshop, dedicated to Integrative Structural Biology, 
will take place on the Oléron island (France), from June the 1st until June the 
8th, 2018. The main objective of this workshop is to offer a theoretical and 
practical training in the different techniques used in integrative structural 
biology (X-ray diffraction, small angle X-ray scattering, NMR, cryo-electron 
microscopy, sample preparation for structural biology,  biophysical methods to 
study and characterize macromolecular interactions). The goals are to explain 
and illustrate, to an audience mainly composed of doctoral students and young 
researchers, the contributions and limitations of each method with a strong 
emphasis on their complementarity and future developments. Engineers and 
Technicians (public and private sector employers) are welcome.
The official language of the workshop is French but presentations may be given 
in English, depending on the overall profile of the students. For practicals, 
English and French speaking groups may be organised.
Registration is open on the web site:
https://ecolebios2018.sciencesconf.org/

There are only few places left. Deadline for registration: April 9, 2018 
(maximum number of participants: 25)
Applications will be evaluated upon deposition.
More information on the French Initiative ReNaFoBiS : http://www.renafobis.fr/
Best  regards

Jean Cavarelli

National ReNaFoBiS Coordinator


ReNaFoBiS. 5ème École de Biologie Structurale Intégrative
Oléron – du 1 au 8 juin 2018

Il reste quelques places. Inscriptions sur le site 
https://ecolebios2018.sciencesconf.org

Cette cinquième école propose une formation théorique et appliquée aux 
différentes approches utilisées en biologie structurale (diffraction et 
diffusion des rayons X, RMN, cryo-microscopie, préparations des échantillons en 
vue des études structurales, interactions macromoléculaires). Elle mettra 
l’accent sur l’intégration de plusieurs de ces méthodes pour répondre aux 
grandes questions de la biologie fonctionnelle à l’échelle atomique.
Pour un public de doctorants ou de jeunes chercheurs, cette formation montrera 
les apports et les limites de chaque méthode et leur complémentarité. Elle 
inclura des sessions théoriques le matin et des travaux pratiques en groupes 
l’après-midi.
Cette école est ouverte aux techniciens et ingénieurs (domaine académique et 
industriel) dans la cadre de la formation continue. Les conférences seront 
données principalement en français. Les supports des présentations seront en 
anglais, afin de permettre aux participants non-francophones de suivre plus 
facilement. Lors des sessions pratiques (TP), des groupes anglophones pourront 
être proposés si besoin.
Dépôt des dossiers avant le 9 avril 2018.
Le nombre de places étant limité (25 participants), les participants seront 
sélectionnés sur la base d'un CV et d'une lettre de motivation. Les dossiers 
seront examinés et validés au fur et à mesure de leur déposition.
Plus d'informations sur le site de l'école 
https://ecolebios2018.sciencesconf.org et sur le site  de ReNaFoBiS  
http://www.renafobis.fr/
Tres cordialement

Jean Cavarelli
Coordinateur National ReNaFoBiS


--

Jean Cavarelli
Professor of Structural Biology
Tél : +33 (0)3 69 48 52 74
jean.cavare...@unistra.fr
Structural Biology of Epigenetic Targets
Integrated Structural Biology Department
IGBMC. UMR7104 CNRS-UDS, INSERM U964.
F - 67404 Illkirch

[ccp4bb] ReNaFoBiS. Oleron 2018. Registration is now open

2018-01-18 Thread VIE 

ReNaFoBiS. Oleron 2018. Registration is now open

We are pleased to announce the 5th RéNaFoBiS Oléron workshop, dedicated to 
Integrative Structural Biology, that will take place on the Oléron island 
(France), from June the 1st until June the 8th, 2018. The main objective of 
this workshop is to offer a theoretical and practical training in the different 
techniques used in integrative structural biology (X-ray diffraction, small 
angle X-ray scattering, NMR, cryo-electron microscopy, sample preparation for 
structural biology,  biophysical methods to study and characterize 
macromolecular interactions). The goals are to explain and illustrate, to an 
audience mainly composed of doctoral students and young researchers, the 
contributions and limitations of each method with a strong emphasis on their 
complementarity and future developments.
The official language of the workshop is French but presentations may be given 
in English, depending on the overall profile of the students. For practicals, 
English and French speaking groups may be organised.

Registration is open on the web site:
https://ecolebios2018.sciencesconf.org/

Deadline for registration: April 9, 2018 (maximum number of participants: 25)
Applications will be evaluated upon deposition.

More information on the French Initiative ReNaFoBiS : http://www.renafobis.fr/

Best  regards
Jean Cavarelli
National ReNaFoBiS Coordinator
Professor of Structural Biology
"Structural biology of epigenetic targets"
Department of Integrated structural biology
UMR7104 CNRS-UNISTRA, INSERM U964.
e-mail : c...@igbmc.fr
phone : +33 (0)3 69 48 52 74
 

[ccp4bb] ReNaFoBiS. First Announcement Oleron 2018.

2017-12-19 Thread VIE 

ReNaFoBiS. First Announcement Oleron 2018.

We are pleased to announce the 5th RéNaFoBiS Oléron workshop, dedicated to 
Integrative Structural Biology, that will take place on the Oléron island 
(France), from June the 1st until June the 8th, 2018. The main objective of 
this workshop is to offer a theoretical and practical training in the different 
techniques used in integrative structural biology (X-ray diffraction, small 
angle X-ray scattering, NMR, cryo-electron microscopy, sample preparation for 
structural biology,  biophysical methods to study and characterize 
macromolecular interactions). The goals are to explain and illustrate, to an 
audience mainly composed of doctoral students and young researchers, the 
contributions and limitations of each method with a strong emphasis on their 
complementarity and future developments.
The official language of the workshop is French but presentations may be given 
in English, depending on the overall profile of the students. For practicals, 
English and French speaking groups may be organised.

Registration is will open in January 2018 on the web site: 
https://ecolebios2018.sciencesconf.org/
Deadline for registration: April 9, 2018 (maximum number of participants: 25)
Applications will be evaluated upon deposition.
More information on the French Initiative ReNaFoBiS : http://www.renafobis.fr/

Best  regards
Jean Cavarelli
National ReNaFoBiS Coordinator

--

Jean Cavarelli
Professor of Structural Biology
Tél : +33 (0)3 69 48 52 74
jean.cavare...@unistra.fr
Structural Biology of Epigenetic Targets
Integrated Structural Biology Department
IGBMC. UMR7104 CNRS-UDS, INSERM U964.
F - 67404 Illkirch

Re: [ccp4bb] peroxy-glutamate?

2017-05-04 Thread VIE 

Le Jeudi 4 Mai 2017 12:25 CEST, Andrew Leslie  a 
écrit:

Dear Andrew,
We looked in details to this problem of diffusion at ca. 100 K with bromine in 
"Ennifar et al., Acta D58(2002)1262" and we concluded

"It was attempted to derive a value for the diffusion coefficient of the free 
bromine species (most likely Br-) in amorphous ice at 100±110 K. This failed 
because the diffusion was much too rapid compared with both the radiolysis and 
datacollection timescales to permit such a determination."

Best regards
Philippe Dumas

> Dear Ed,
>
>   I find your electron density quite interesting, because 
> generally (I think, I would be happy to be corrected on this) when 
> de-carboxylation of Asp/Glu occurs due to radiation damage, there is no 
> evidence of what happens to the resulting CO2 group. One interpretation of 
> this is that it diffuses away from the side chain and is effectively totally 
> disordered, so no electron density is seen, but I was surprised that this 
> would always be the case, especially as I would have thought that diffusion 
> would be quite limited at 100K (maybe I’m wrong about that too, but that is 
> supposed to be one reason why radiation damage is less at 100K).
>
> If the residual density is due to partial de-carboxylation, then I would have 
> expected density for the CG-CD bond, which is not present (at your chosen 
> contour level).
>
> Do many of your Glu side chains have the residual density?
>
> Best wishes,
>
> Andrew
>
>
> > On 3 May 2017, at 22:19, Edward A. Berry  wrote:
> >
> >
> >
> > On 05/03/2017 02:46 PM, Gerard Bricogne wrote:
> >> Dear Ed,
> >>
> >>  Have you considered the possibility that it could be a water

> >> stepping in to fill the void created by partial decarboxylation of the
> >> glutamate? That could be easily modelled, refined, and tested for its
> >> ability to flatten the difference map.
> >>
> >>  Gerard.
> >>
> > Actually some of them do appear decarboxylated. Is that something that can 
> > happen? In the crystal, or as radiation damage?
> > However when there is density for the carboxylate (figure), it appears 
> > continuous and linear, doesn't break up into spheres at H-bonding distance 
> > - almost like the CO2 is still sitting there- but I guess it would get 
> > hydrated to bicarbonate. I could use azide. Or maybe waters with some 
> > disorder.
> > Thanks,
> > eab
> >
> > Figure- 2mFo-DFc at 1.3 sigma, mFo-DFc at 3 sigma, green CO2 is shown for 
> > comparison, not part of the model.
> >
> >

[ccp4bb] 4th ReNaFoBiS Integrated Structural Biology School. Oléron, June 16-23

2017-04-10 Thread VIE 

 
4th ReNaFoBiS Integrated Structural Biology School. Oléron, June 16-23There are 
still some limited places available for this school that will take place on the 
Oléron island (France), from June 16 to June 23, 2017. The main objective of 
this workshop is to offer a theoretical and practical training in the different 
techniques used in integrative structural biology (X-ray diffraction, Small 
angle X-ray scattering, NMR, cryo-electron microscopy, biophysical methods and 
macromolecular interactions.) The goals are to explain and illustrate, to an 
audience mainly composed of doctoral students and young researchers, the 
contributions and limitations of each method with a strong emphasis on their 
complementarity and future developments. The school include theoretical 
sessions in the morning and practical training in the afternoon.The official 
language of the workshop is French but presentations may be given in English, 
depending on the overall profile of the students. For practical’s, English and 
French speaking groups may be organized.

Deadline for registration: April 17, 2017 (maximum number of participants: 25)
https://ecolebios2017.sciencesconf.org/
More information on the French Initiative ReNaFoBiS : http://www.renafobis.fr/

 
4ème École de Biologie Structurale Intégrative
Oléron – du 16 au 23 juin 2017
Il reste quelques places pour la 4ème École de Biologie Structurale 
Intégrative. Cette quatrième école propose une formation théorique et appliquée 
aux différentes approches utilisées en biologie structurale (diffraction et 
diffusion des rayons X, RMN, cryo-microscopie, méthodes d'études et de 
caractérisations des interactions macromoléculaires).
Elle mettra l’accent sur l’intégration de plusieurs de ces méthodes pour 
répondre aux grandes questions de la biologie fonctionnelle à l’échelle 
cellulaire.Pour un public de doctorants ou de jeunes chercheurs, cette 
formation montrera les apports et les limites de chaque méthode et leur 
complémentarité. Elle inclura des sessions théoriques le matin et des travaux 
pratiques en groupes l’après-midi. Les conférences seront données 
principalement en français. Les supports des présentations seront en anglais, 
afin de permettre aux participants non-francophones de suivre plus facilement. 
Lors des sessions pratiques (TP), des groupes anglophones pourront être 
proposés si besoin.

Date limite pour les inscriptions : 17 avril 2017
https://ecolebios2017.sciencesconf.org/
Plus d’information sur le réseaun RéNaFoBiS
http://www.renafobis.fr/
 
 
 



Jean Cavarelli
Professor of Structural Biology
Tél : +33 (0)3 69 48 52 74
jean.cavare...@unistra.fr
Structural Biology of Epigenetic Targets
Integrated Structural Biology Department
IGBMC. UMR7104 CNRS-UDS, INSERM U964.
F - 67404 Illkirch

Re: [ccp4bb] ITC question

2017-03-17 Thread VIE 

Le Vendredi 17 Mars 2017 16:07 CET, Nicholas Larsen 
 a écrit:

Do you mean that the affinity from ITC is 100-fold weaker ? Which would mean 
that the Kd values from ITC are 100-fold larger (in the range 0.1-1 µM) ?
If this is the case, it makes me think to a problem that we have observed by 
comparing Kd values obtained by ITC and by Mass Spec. The Kd values by mass 
spec were very well determined and smaller (higher affinity) than those 
obtained by ITC after a classical processing. It turns out that processing the 
ITC data with two competing modes of binding revealed the correct higher 
affinity binding mode observed by Mass Spec (80 %) mixed with the 
lower-affinity binding mode (20 %). The a priori very strange thing, which we 
finally explained, is that the initial processing of the ITC data with only one 
binding mode had mixed wrongly the Kd for the low-affinity binding mode, but 
the DeltaH for the  high-affinity binding mode.

I suggest that you have a look to our paper: Wolff et al., J Am Soc Mass 
Spectrom. 2017; 28(2): 347–357 (Open access).
I hope it will help.
Philippe Dumas

> Dear colleagues,
> We have a target where people have measured Kd's for ligands using
> radioligand binding assays.  Several publications report Kd's of single
> digit nanomolar and we are able to reproduce that data using this assay
> format.  When we try to do the same measurement using ITC, we generate
> beautiful data, but the Kd's from ITC are at least 100-fold weaker.  Does
> anyone have a suggestion how to reconcile this huge difference?
>
> SPR studies show the ligands have a very long residence time, so one thing
> I wondered is if ITC can underestimate a Kd if the off-rate is on the order
> of minutes-hours.  Is this a reasonable explanation?
>
> Please, any other ideas are welcome.
> Best,
> Nick
>
> --
> [This e-mail message may contain privileged, confidential and/or
> proprietary information of H3 Biomedicine. If you believe that it has been
> sent to you in error, please contact the sender immediately and delete the
> message including any attachments, without copying, using, or distributing
> any of the information contained therein. This e-mail message should not be
> interpreted to include a digital or electronic signature that can be used
> to authenticate an agreement, contract or other legal document, nor to
> reflect an intention to be bound to any legally-binding agreement or 
> contract.]

Re: [ccp4bb] Slightly OT: crystallization teaching resources for kids

2017-01-05 Thread VIE 

Le Jeudi 5 Janvier 2017 08:56 CET, Tim Gruene  a écrit:

I did not follow all the previous details of this discussion, but I think one 
may say that the statement "The entropy of molecules arranged in a crystal must 
be greatly larger than in solution" is incorrect.
Of course, there is an increase of entropy (DeltaS = S(solution) - S(crystal) > 
0)  from the ordered crystalline state to the disordered solution state, hence 
S(crystal) < S(solution).
Te nice thing is that, without knowing anything about the crystallization 
process, one can also say that DeltaS (per mole) = DeltaH/T, where T is the 
absolute temperature anf DeltaH > 0 is the heat absorbed by one mole of 
molecules going from the crystal state to the solution state during the melting 
of the crystal. Hence, the crystallization process, as with ice formation, 
produces heat (releases heat in the solution). Would one measure (in a 
calorimeter) the heat -DeltaH produced during crystallization,  and the number 
of molecules having formed the crystal, then one would obtain immediately the 
DeltaS of crystallization.
To be accurate: all of that is correct as far as T is the equilibrium 
temperature where the two phases coexist and can exchange reversiby (i.e. 
DeltaG = DeltaH - T DeltaS = 0). For ice melting at atmospheric pressure this 
would be of course 273.15 K.
Philippe Dumas

> Dear Nicolas,
>
> are you sure this concept is correct?
>
> The entropy of molecules arranged in a crystal must be greatly larger than in
> solution. Hence the driving force for crystallisation is actually a drop in
> energy, and I am not sure there is actually a barrier.
>
> I would take the kids to the play ground and let them run around randomly.
> When I blow a wistle they should line up in an orderly manner.
>
> I am sure it will take some time before some sort of order is achieved, for
> the kids could face in various directions, or line up in blocks, or other
> shapes. Once a seed is there, i.e. once e.g. 4-5 kids have created a regular
> block, it will be much easier for the rest to line up (this is consistent with
> Patrick's explanation).
>
> Cheers,
> Tim
>
> On Wednesday 04 January 2017 05:45:50 PM Nicolas FOOS wrote:
> > Dear Evette,
> >
> > If I was is your situation (explaining nucleation and other concept). I
> > will discuss in terms of energy.
> >
> > I mean obtaining the initial nuclei is the "costly" step in terms of
> > energy. To represent that, out the classical curve of energy, I will use
> > a metaphoric representation such as jump over a barrier and run after.
> >
> > With this analogy, it's possible to explain that the first step is

> > difficult and the second more accessible. If the barrier is to high,
> > it's impossible to continue and run. If you don't have any barrier it's
> > easy to run and if you only have a small barrier is not to difficult to
> > jump over and run. But It also allow you to explain that if you
> > facilitate the apparition of the first "surface" thanks to appropriate
> > method (seeding, dust...) you can help the first step (to continue with
> > the barrier story, it like you have ladder to help, or the ability to> 
> > decrease the size of the barrier.
> >
> > For why the crystal and how, I will maybe use the example of orange
> > pyramid in the food store. Orange are stable together because they have
> > enough contact, because they have relatively homogeneous shape. If you
> > mixed orange with water melon it's difficult to obtain nice pyramid.
> >
> > For crystallization experiment which work, I have no Idea out of the one
> > you already mentioned.
> >
> >
> > Hope this help.
> >
> > Nicolas
> >
> > Nicolas Foos
> > PhD
> > Structural Biology Group
> > European Synchrotron Radiation Facility (E.S.R.F)
> > 71, avenue des Martyrs
> > CS 40220
> > 38043 GRENOBLE Cedex 9
> > +33 (0)6 76 88 14 87
> > +33 (0)4 76 88 45 19
> >
> > On 30/12/2016 11:06, Radisky, Evette S., Ph.D. wrote:
> > > Can anyone point to some especially useful resources to help explain
> > > to kids (pre-chemistry, ~age 10-12) how and why molecules crystallize?
> > > Maybe a good online movie or animation?  I am especially needing help
> > > with the concept of nucleation, and why nucleation is slower and then
> > > crystal growth faster once nuclei have formed.  I have been
> > > supervising some experiments growing sucrose crystals from
> > > supersaturated solutions, which have worked really well, but I am
> > > having more difficulty in explaining the underlying fundamental
> > > concepts in a way that is understandable to the kids.
> > >
> > > Thanks!
> > > Evette
> > >
> > > Evette Radisky, PhD
> > >
> > > Associate Professor of Cancer Biology
> > >
> > > Mayo Clinic Cancer Center
> > >
> > > Griffin Cancer Research Building
> > >
> > > 4500 San Pablo Road 
> > >
> > > Jacksonville, FL 32224 
> > >
> > > tel: 904-953-6372 
> > >
> > > fax: 904-953-0277 
> --
> --
> Paul Scherrer Institut
> Dr. Tim Gruene
> -

Re: [ccp4bb] just out of totally idle curiosity ...

2016-11-09 Thread VIE 

Le Mercredi 9 Novembre 2016 08:46 CET, David Briggs  
a écrit:

Calais University (Jungle campus) has just announced that its bureau of 
immigration will remain open until the wall is finished.
Philippe D

 will rem
> In the UK we have an authoritarian nationalist government seemingly hell
> bent on the destruction of our economy, so maybe give it a few years.
>
> Maybe try Germany? Actually - wait until after their election in 2017?
> Ditto for France.
>
> On Wed, Nov 9, 2016, 06:33 Ricardo Padua  wrote:
>
> > Science in Brazil will struggle with the "new" government as well, so I
> > wouldn't count on that.
> >
> > On Wed, Nov 9, 2016 at 12:56 AM, kaiser  wrote:
> >
> > Yeah, given Europe and Canada are obvious, I think Brazil and Japan are
> > actually viable alternatives if the first choices are getting too crowded.
> > They do have synchrotrons and "internets".
> >
> >
> >
> > Sent from my T-Mobile 4G LTE Device
> >
> >
> >  Original message 
> > From: "William G. Scott" 
> > Date: 11/8/16 21:37 (GMT-08:00)
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] just out of totally idle curiosity ...
> >
> > What’s the job situation in Europe looking like for refugee scientists
> > these days?
> >
> >
> >
> > William G. Scott
> > Director, Program in Biochemistry and Molecular Biology
> > Professor, Department of Chemistry and Biochemistry
> > and The Center for the Molecular Biology of RNA
> > University of California at Santa Cruz
> > Santa Cruz, California 95064
> > USA
> >
> > http://scottlab.ucsc.edu
> >
> >
> >
> >
> > --
> > Ricardo Padua
> > Postdoctoral fellow HHMI
> > Kern Lab
> > Brandeis University
> > Waltham, MA
> >
> > --
>
>
> [image: --]
>
> David Briggs PhD
> [image: https://]about.me/david_briggs
>

Re: [ccp4bb] DNA RNA annealing problem

2015-07-07 Thread DUMAS Philippe (VIE) 

Le Mardi 7 Juillet 2015 14:03 CEST, Almudena Ponce Salvatierra 
maps.fa...@gmail.com a écrit:

Hello
Do you have full complementarity of DNA and RNA  ?
Does the difference in lenght (17 nt/19 nt) mean that you have a bulge on the 
DNA when the duplex is formed ?
In short, what is the Tm of this duplex at these strand and salt concentrations?
If the Tm is 35 °C, then room temperature may be a bit hot depending on where 
you are in this month of July.
Also, what was the temperature of the gel during migration ?

Do you have access to ITC ?
If yes, we have found that this is a perfect technique (1) to check that you 
have formation of the duplex (basepair formation generates a lot of heat), (2) 
that you are using 100 % of each strand (or may be less...), (3) that you can 
stop injecting the second strand when the stoichiomertic ratio is 1/1 (no 
strand in excess: perfect for crystallization) and, finally, (4) that you can 
retrieve the sample from the cell, concentrate it and make crystallization 
drops.

See: Da Veiga C., Mezher J., Dumas P., and Eric Ennifar (2015).Isothermal 
Titration Calorimetry: Assisted Crystallization of RNA-Ligand Complexes. In 
Nucleic Acid Crystallography : Methods and Protocols. (Ennifar E., ed..) in 
press. Humana Press. NY. Abstract

I hope this can be useful.

Philippe Dumas



 2015-07-03 17:14 GMT+02:00 ChenWeiFei weife...@outlook.com:

  Dear all,
  I want to get a complex of DNA-RNA-protein. But I have a big problem of
  annealing DNA-RNA.
  The length of DNA is 19nt and RNA is 17nt.
  Annealing protocol:
  2uM DNA
  2uM RNA
  10mM Tris-Hcl
  100mMNaCl
  1mMEDTA
 
  Heated to 95 for 5min, cooling down slowly for nearly 2h to room
  temperature.
 
  I can just get a result of two single strand DNA/RNA. PAGE analysis.
 
  No double helix was founded.
 
  Does anyone have the same problem or know how to fix it.
 
  Thank you for your answering.
 
  Best regards,
  Weifei




 --
 Almudena Ponce-Salvatierra
 Macromolecular crystallography and Nucleic acid chemistry
 Max Planck Institute for Biophysical Chemistry
 Am Fassberg 11 37077 Göttingen
 Germany

[ccp4bb] In search of an article

2014-11-03 Thread DUMAS Philippe (VIE) 
I am looking for the reference of this little paper (in J. Appl. Cryst ?) 
describing how to make a loop and fish crystals...
You know, this kind of humble method used by all crystallographers (apart FEL 
users).
Thank you in advance

Philippe Dumas

Re: [ccp4bb] In search of an article

2014-11-03 Thread DUMAS Philippe (VIE) 

Le Lundi 3 Novembre 2014 19:06 CET, Frances C. Bernstein 
f...@bernstein-plus-sons.com a écrit:

Thank you all ! I got it.
Philippe D


 How appropriate that someone whose name is Picot would be
 the first one to have the answer.

 If you don't get it, put define:picot in a google search box.

Frances

 =
 Bernstein + Sons
 *   *   Information Systems Consultants
 5 Brewster Lane, Bellport, NY 11713-2803
 *   * ***
  *Frances C. Bernstein
*   ***  f...@bernstein-plus-sons.com
   *** *
*   *** 1-631-286-1339FAX: 1-631-286-1999
 =

 On Mon, 3 Nov 2014, Daniel Picot wrote:

  Hi Phhilippe,
 
  T. Y. Teng, J. Appl. Crystallogr.
  23,
  J. Appl. Crystallography 23:387?391 (1990)
  Mounting of crystals for macromolecular crystallography in a free-standing 
  thin film
 
  A method for mounting single crystals in macromolecular crystallographic 
  studies is described
  in which the crystal is suspended in a thin film. The film is formed from a 
  mixture of the
  crystallization buffer and a hydrophilic viscous material, confined within 
  a thin-wire loop by
  surface tension. Compared with conventional crystal mounting methods, this 
  method greatly
  simplifies and speeds the mounting procedure, is well suited to shock 
  freezing and to optical
  monitoring of the crystals, deforms fragile crystals less and gives a lower 
  and more uniform
  background in the X-ray diffraction patterns.
 
  I do not have a copy, but if I remember well it was done with a copper 
  wire, hair and nylon
  loops came later.
  Daniel
 
 
 
  Le 03/11/2014 18:23, DUMAS Philippe (VIE) a ?crit :
 
  I am looking for the reference of this little paper (in J. Appl. Cryst ?) 
  describing how to mak
  e a loop and fish crystals...
  You know, this kind of humble method used by all crystallographers (apart 
  FEL users).
  Thank you in advance
 
  Philippe Dumas

Re: [ccp4bb] ITC with unfolded proteins

2014-03-14 Thread DUMAS Philippe (VIE) 

Le Vendredi 14 Mars 2014 13:37 CET, Anita P crystals...@gmail.com a écrit:

Anita,

If one of the partners  is indeed more or less unfolded before interaction, 
then you should see a negative DeltaS upon complex formation.
Practically, I would try first putting the unfolded protein in the cell and the 
folded one in the syringe in view of possible solubility problems with an 
incorrectly folded protein.
Alanine scanning ? Yes on the paper, but may be less feasible in practice due 
to the amount of material to prepare.

Good luck
Philippe Dumas


 Hello everyone,

 I have a query for the scientists working on protein-protein interaction.
 It is known that some proteins exist in unfolded or molten globule state
 and attain structure on interaction with other folded proteins.
 Many a times, it is difficult to obtain the structure of these complexes.

 Is it possible to quantitatively determine the thermodynamics of
 interaction between an unfolded protein and a folded protein using ITC?
 Later may be perform an alascan to determine the residues of the unfolded
 partner involved in the interaction.

 Please share your ideas

 cheers
 Anita

[ccp4bb] Information on enzymes involved in TPP biosynthesis

2013-12-06 Thread DUMAS Philippe (VIE) 
Dear all,

By some extraordinary chance, could someone provide me information about the 
temperature dependence of  two E. coli enzymes:
(1) Hydroxyethythiazole kinase: EC 2.7.1.50  (encoded by the gene thiM)
(2) Enzyme participating in the synthesis of 4-amino-5-hydroxymethyl pyrimidine 
phosphate from 5-aminoimidazole ribotide (encoded by the gene thiC)

Something like  kCat(T), Km(T) would be magnificent.

And if I am very, very lucky: more generally, any information/reference on the 
temperature dependence of other enzyme(s) involved in thimamine pyrophosphate 
biosynthesis would be much welcome.

Many thanks in advance.

Philippe Dumas
Biophysics  Structural biology team
IBMC-CNRS, 15 rue René Descartes
Strasbourg, France
+33 (0)388 41 70 02