[ccp4bb] postdoc positions at the University of British Columbia (Vancouver, Canada)

2021-08-19 Thread Filip Van Petegem 
Dear colleagues,



Two postdoctoral positions are available at The University of British
Columbia in Vancouver, Canada:



*Position 1:*



 A postdoctoral position is available immediately to work on ion channel
structural biology in the lab of Filip Van Petegem, Department of
Biochemistry and Molecular Biology.



The project combines X-ray crystallography, cryo-EM, and electrophysiology.
Our lab has steady access to the in-house X-ray and cryo-EM facilities:



- Microscopes: 300kV Titan Krios with Falcon IV detector and Selectris
Energy filter.   A 200kV Glacios (Falcon III detector) is available for
prescreening grids.

- X-ray equipment in the lab includes Mosquito and Dragonfly robotics, and
we have regular access to an in-house X-ray diffractor (Rigaku Micromax-007
HF with Saturn 744+ CCD detector) and various synchrotron beamlines



Minimum requirement for applicants include a PhD in Biochemistry or a
related discipline with extensive experience in either X-ray
crystallography or cryo-EM, as well as protein expression and
purification.  Direct experience with membrane proteins is an additional
plus.



The lab values diversity and inclusivity, and applicants from all
backgrounds are encouraged to apply. This is an opportunity for people with
structural biology expertise to learn electrophysiological methods.



Recent work from the lab includes an investigation of how Ryanodine
Receptors are modulated by small molecules, disease mutations, and
post-translational modification, using cryo-EM, X-ray crystallography,
planar lipid bilayer electrophysiology, and enzyme kinetics.

Woll et al (2021) *Nature Comm.* 12:807

Ma et al (2020) *Nat Chem Biol*. 16,1246-1254

Haji-Ghassemi et al (2019) *Molecular Cell* 75,1-14



For more information on recent work, see http://crg.ubc.ca/VanPetegem/



The lab is housed within the Life Sciences Centre at UBC (lsi.ubc.ca),
located on the Point Grey campus in Vancouver.



Interested candidates should send a CV, along with names and contact
details for 3 references to *filip.vanpete...@gmail.com
*.









--

*Position 2:*


A postdoctoral position is available to work on a joint project between the
labs of Filip Van Petegem and Robert Molday, both in the Department of
Biochemistry and Molecular Biology at the University of British Columbia.



The project will involve Cryo-EM on neuronal membrane proteins and will
make use of the excellent cryo-EM facility within the Life Sciences
Institute.  Microscopes available include a 300kV Titan Krios with Falcon
IV detector and Selectris Energy filter.   A 200kV Glacios (Falcon III) is
available for prescreening grids. The structural biology will be
complemented with various functional assays.



The ideal candidate will have a PhD in Biochemistry or a related
discipline, as well as extensive experience with either X-ray
crystallography and/or Cryo-electron microscopy. Direct experience with
membrane protein expression and mammalian cell cultures is an additional
asset.



The Molday and Van Petegem labs are housed within the Life Sciences
Institute (https://lsi.ubc.ca/).



For more information on the labs, see

http://crg.ubc.ca/VanPetegem/

and

https://biochem.ubc.ca/person/robert-molday/



Interested candidates should send a CV, along with names and contact
details for 3 references to both  mol...@mail.ubc.ca and
filip.vanpete...@gmail.com.



-- 
Filip Van Petegem, PhD
Professor, Dept. of Biochemistry and Molecular Biology
The University of British Columbia
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3

phone: +1 604 827 4267
email: filip.vanpete...@gmail.com
http://crg.ubc.ca/VanPetegem/

Twitter: @FilipPetegem



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[ccp4bb] Senior Lecturer/Reader (Assistant Professor) Position at University of Essex

2021-08-19 Thread Prischi, Filippo 
Dear all,

We have a Senior Lecturer/Reader (Assistant Professor) position available in 
the School of Life Sciences at University of Essex. We encourage applicants 
with a skillset and research interest in structural biology, biochemistry, and 
structural bioinformatics.
For more info and details on how to apply, please follow this link 
https://hrorganiser.essex.ac.uk/tlive_webrecruitment/wrd/run/ETREC107GF.open?VACANCY_ID=622280OPvw&WVID=9918109NEm&LANG=USA

Kind Regards,
Filippo

~~
Dr Filippo Prischi
Senior Lecturer in Biochemistry
School of Life Sciences
University of Essex

T.  +44 (0)1206 873370
E.  fpris...@essex.ac.uk
► http://www.essex.ac.uk/bs/staff/profile.aspx?ID=4512
► http://filippoprischilab.org/




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Re: [ccp4bb] malonate and histidine interaction

2021-08-19 Thread Wim Burmeister 

  
  
Hello Ana,
it looks very much like a covalent bond with the His. You may get
  some hints from the chemistry of the reaction, which is normally
  catalysed. Are there possible side products involving malonate,
  alternative substrates present in the buffer etc ?
Occupancy refinements of the different atom groups may also yield
  some information.

This looks really interesting
Cheers
Wim

I 

Le 18/08/2021 à 13:13, Ana Ebrecht a
  écrit :


  
  Hello Jon, 
Thanks for the comments. Yes, the His is part of the active
  site, and the distances are very close, like a covalent bond.
  That's why I was wondering if the malonate can be bound to the
  His.


We tried to model the malonate in the different
  conformation, but that didn't work. But I'll check about the
  protease inhibitor. Thanks!


Kind regards
Ana
  
  
  
On Tue, 17 Aug 2021 at 14:48,
  Jon Cooper 
  wrote:

Hello,
  only other thought was that malonate might be binding in two
  conformations, i.e. dual occupancy, and did you use a protease
  inhibitor cocktail, since the constituents can react? The
  density looks a bit like citrate, but too close to the His. I
  couldn't read the distances to the His in your figure. Is it
  part of the active site and if so can you say what the enzyme
  is? Anomalous difference maps are popular here, too. Is the
  surrounding structure totally OK because odd features in the
  difference map can indicate problems nearby e.g. I did see a
  leucine which looked slightly strained on the left, but maybe
  I am wrong. Good luck. Cheers, Jon.C.
  
  
  Sent from ProtonMail mobile
  
  
  
   Original Message 
  On 17 Aug 2021, 12:11, Ana Ebrecht < anaebre...@gmail.com> wrote:
  
Hi Jon,
  Thanks for the reply. I don't think this is
acetylation, because I only see this density in the
crystals that grew with malonate. In other conditions
doesn't show anything like that. So I thought it'd be
the malonate. But I'll check on that. 
  Thanks for the suggestion.
  
  
  Kind regards
  Ana



  On Mon, 16 Aug 2021 at
16:56, Jon Cooper 
wrote:
  
  Hello, could the His
be partially acetylated? 

Best wishes Jon.C.


Sent from ProtonMail mobile



 Original Message 
On 16 Aug 2021, 14:52, Ana Ebrecht < anaebre...@gmail.com>
wrote:

  
Dear all, 

  
I am building
the structure of a protein that was
crystallized in 0.2 M sodium malonate pH 5.0,
20% w/v polyethylene glycol 3,350.
During
the refinement, we found what we think is a
malonate molecule in the active site, but it
seems like is bound
somehow to the histidine (this His is the
catalytic residue of the enzyme), almost like a
covalent interaction. Under other
  conditions of crystallization, the protein bound a
  sulfate and an acetate in the site but did not
  show this type of interaction with the histidine. 

  
We
couldn't find anything that explains a reaction
between the malonate and the histidine.

Does anyone have
experience with this reaction or have seen
something similar before? 


Thanks 
Kind regards
Ana











  
  
  
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