Post-doctoral Position in Structural Biology and Membrane Trafficking: CIC bioGUNE, Bilbao, Spain

The position is available in the laboratory of Aitor Hierro to work in the area of structural
biology and membrane trafficking.

We study the interactions, in molecular mechanistic detail, that underlie the selectivity of
cargo transport vesicles for recognizing the correct target membrane. We do this using a
combination of structural, biochemical and biophysical approaches. The focus of the project
is on a series of soluble and membrane associated proteins (and their complexes), which
coordinate tethering and fusion of transport vesicles from endosomes to the Golgi apparatus
(for references, see PMDIs: 20615984; 21183348 and 17891154).

The position requires PhD. degree with a strong background in molecular biology for
heterologous recombinant protein expression in different hosts such Escherichia coli, insect
cell-baculovirus and mammalian cells. Previous experience in X-ray crystallography and the
use of biophysical or biochemical techniques for the characterization of protein complexes
would be an advantage.

Local resources at the institute include shared state-of-the-art facilities for high throughput
crystallization, and in-house X-ray data collection. We also have regular synchrotron
beamtime. Other biophysical instrumentation such DLS, ITC, DSC, CD, SEC-MALLS
and fluorescence spectrometers are also available. For testing our structural and in vitro
analyses we have complementary collaborations with leading laboratories in the cell biology
field. The institute is well-situated with numerous groups working in X-ray crystallography,
NMR and EM that form a critical mass in the area of structural biology. This position offers an
excellent opportunity for an experienced protein biochemist/biophysicist or cell biologist to
complement his or her expertise in X-ray crystallography working at the juncture between
structural biology and cell biology.

The position is available beginning December 2011 and funded for 3+2 years. Applications
will be accepted until the position is filled.

Interested candidates please email a cover letter, your CV, and names (including email
address) of at least two referees to rrhh@cicbiogune.es with ref. 3131 in the subject.

Employment Res Assoc/ Postdocs KU-Pharm and Tox

We are seeking highly motivated individuals to fill in Research Associate and Postdoctoral positions to study the structure and function of proteins involved in lipid metabolism or lipid signaling by means of X-ray crystallography in the laboratory of Dr. Alex Moise at the Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas http://midwestlipids.com. The positions are funded by NIH. The laboratory is well equipped to analyze lipid metabolism and study lipid signaling, cell and animal models with altered lipid signaling and to conduct protein expression and purification. Our funding and project oversight is from the KU COBRE Center in Protein Structure and Function http://psf.cobre.ku.edu/ which provides core services in protein purification, reagents and setup for crystallization screening, diffraction and structure determination by X-ray and NMR and use of equipment including a Rigaku RU-H3RHB X-ray generator with an R-axis IV++ imaging plate system, a Bruker Avance 800 MHz NMR instrument fitted with a TCI cryoprobe and a Bruker Avance III 600 MHz with a variety of probes, Biacore for label free studies. KU campus also hosts a High Throughput Screening Laboratory, a Center for Bioinfomatics and a Mass Spectrometry facility.  In addition, through our collaborators Scott Lovell and Kevin Battaile, we have regular access to synchrotron radiation beamlines at Argonne National Labs IMCA-CAT 17. The environment is excellent and there is a lot of good work to be done.

Successful candidates must have a Ph.D. in biochemistry or a related field with a strong background in purification of proteins, protein-ligand complexes and the use of structural methods to investigate enzyme mechanism and to develop modulators. A background in membrane protein purification or purification of lipid processing enzymes is preferred. For more information email alexmoise@ku.edu. Review of applications will begin shortly and will continue until the positions are filled. Salary will be commensurate with experience. If a candidate has more than five years post PhD than the candidate will be automatically considered for a Research Position as per HR. University of Kansas is an EO/AA Employer.

In 2011, KU School of Pharmacy ranked fourth in the nation among Schools of Pharmacy in the amount of National Institutes of Health funding; 2011 is the 10th consecutive year the school has been ranked in the top five receiving more than $18,400,000 in NIH research funding in fiscal year 2010. The KU School of Pharmacy is situated in Lawrence Kansas, which was named one of the top 10 US college towns along with Austin TX, Boulder CO, Madison WI, and Berkeley CA  by Parents &Colleges and also made the list of top college towns by the American Institute for Economic Research, MSN and MSNBC. Lawrence boasts a vibrant downtown, youthful attitude - nearly 50% of residents are younger than 24 years of age - and a multitude of outdoor activities at Clinton Lake, the Kansas River and the city's 50 parks. Kansas City, a 41 miles east of Lawrence is a major US city with a variety of renowned museums, athletic venues, dining and cultural institutions.

Staff scientist opening at MacCHESS

The Macromolecular Diffraction Facility of the Cornell High-Energy Synchrotron Source (MacCHESS) has an opening for a Staff Scientist (Research Associate) to pursue the development of novel techniques in x-ray scattering as applied to structural biology, and to support users at MacCHESS.  There will also be opportunities to pursue projects in structural biology, using current crystallographic and SAXS methods.  Research areas of particular interest include structure solution from multiple crystals, developing a pipeline approach for microcrystals, phasing methods, and use of Laue diffraction.  A Ph.D. in structural biology, biophysics, or a related field, and at least 5 years of experience beyond the degree in a relevant field is required.  A solid publication record is essential, and experience as a staff member at a synchrotron facility is highly desirable.  Excellent communication skills are a must, including fluency in the English language.  Appointments are nominally for three years with the possibility for renewal, subject to mutual satisfaction and the availability of funds.

Located on an Ivy League university campus in picturesque upstate New York, the Cornell High-Energy Synchrotron Source (CHESS) serves a world-wide user base of structural biologists, chemists, physicists, and engineers.  MacCHESS is an NIH-supported National Resource providing support for structural biology at CHESS.  MacCHESS is a heavily team-oriented environment.

Please provide an application and have at least three letters of reference sent to:

Dr. Marian  Szebenyi, Chair
MacCHESS Staff Scientist Search Committee
c/o Peggy Steenrod
Newman Laboratory
Cornell University
Ithaca, NY  14853  USA

Applications should include a cover letter, curriculum vita, a publication list, and a detailed summary of research experience and interests.  Electronic submissions and inquiries may be addressed to search-CLASSE@cornell.edu. Complete applications will be considered immediately.  The starting date is negotiable.

Cornell is an equal opportunity, affirmative action educator and employer.

Lectureship in Structural Biology at the University of Adelaide, Australia

Applications are invited from scientists in the fields of X-ray crystallography or Structural Biology. You will have a strong commitment to excellence in research and teaching, be expected to develop an active, externally funded research group and contribute to the undergraduate teaching responsibilities of the School of Molecular and Biomedical Science at the University of Adelaide, Australia.

Further information about the position can be viewed at  http://www.adelaide.edu.au/jobs/current/16987/

or from the Head of School, Professor David Adelson, telephone +61 8 83135328 or email head.mbs at adelaide.edu.au

Applications close: 26 October 2011

best wishes
Grant Booker

Space Group Table

From: James Stroud
Date: 14 September 2011 18:16


Hello All,

Is Table 6 of http://cci.lbl.gov/sginfo/hall_symbols.html the authoritative mapping of space group numbers to Hermann-Mauguin symbols (i.e., can we count on major software packages to honor this mapping if present in a PDB file)? I notice that this web page was authored by a couple of prominent developers.

Thank you,

James

----------
From: Ethan Merritt


I'm not sure that's the right question.  I think you need to start with
the question "Is this the list used by PDB files?".
And I'm pretty sure the answer is no, if only because the table you
link to does not list rhombohedral/hexagonal settings as starting with "H"
or "R".

See the note on the definition of the PDB field contents:
 http://www.wwpdb.org/documentation/format33/sect8.html

See also many threads over the past several years about inconsistent
handling of H3/R3.

       Ethan

--
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

Refinement with Low resolution data

From: Md Shaik
Date: 14 September 2011 15:34

Dear ccp4,

I am refining one structure at low resolution (3.5 A). I solved the structure in space group P622 by molecular replacement. The Rw/Rf after some cycle of rigid body refinement in Refmac5 is 34/37. But when I am trying to refine with Restrain refinement in Refmac the Rw is going down but the Rf is going up. This same happens with the phenix refinement. The protein is quite big 520 residues and one molecule is present in the crystal asymmetric unit. The maps are also not so bad except some region.

Please give me suggestion, what should I have to care during low resolution refinement? or is there any other tricks for this types of data?

Thanks in advance.

Md. Munan Shaik
PhD Student
Department of Biotehnology
School of Bioscience and Biotechnology
via G. Colombo 03
Padova 35131, Italy

----------
From: Pavel Afonine


Hi,

did you use refinement strategy suitable for low (3.5A) resolution (secondary structure restraints, Ramachandran plot restraints, proper ADP parameterization, SA, etc.... etc...)?

If you send me the data and model files off-list I will have a look.

Pavel

----------
From: Phil Evans


Are you sure of the space group? P622 is much rarer than P6(x)22 where x > 0
Phil

----------
From: Tim Gruene

Dear Md. Munan Shaik,
a couple of aspects you might check:
- - first build the model AS MUCH AS POSSIBLE before running the first
 refinement cycle
- - switch off automatic weight determination in refmac and use a low
 weight (e.g. 0.005) and many cycles of refinement
- - check that the geometry does not distort (rmsd angles and bond
 lengths reported in the refmac log-file must not go too high). if it
 does, lower the weight even further.

if your model stems from higher resolution data and is actually in good
agreement with the model you are going at, refinement might ruin the
good model if you use inappropriate settings, causing Rfree to go up.

Cheers, Tim

- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

neutron diffraction 'difference' map?

From: Francis E Reyes
Date: 13 September 2011 20:01


Hi all

Suppose you have a high resolution xtal structure (from usual x-ray diffraction) and you wanted to verify the location of a ligand. You can purchase a heavy atom isotope version of the ligand.

[1] Is it possible to do a neutron diffraction difference map (where you simply calculated Fobs(heavy) - Fobs(light) to verify the location of the ligand?

[1b] Suppose you couldn't measure the diffraction of the light version of the ligand. Can the x-ray data be combined with the neutron diffraction of the heavy atom isotope to unambiguously assign the ligand site?

[2] What would be the minimum resolution required from the neutron diffraction? (This is particularly important as you may be unable to grow high diffracting crystals or large crystals)


Note that you don't necessarily want to solve the structure of the structure from neutron diffraction from scratch, but rather you want to use it as a tool to verify the location of a ligand binding site.


Thanks!

F



---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

----------
From: Sean Seaver


Dear Francis,
It is possible, but would recommend exhausting all possibilities with X-ray crystallography.  The reason is that neutron crystallography as you mentioned has its own challenges/considerations such as possibly having to determine a new crystallization condition, crystal size, unit cell volume, symmetry, level of deuteration, data collection and processing (this table may serve as a good reference: http://1.usa.gov/qc5JoA ).  Of course, these can be overcome, but in the case of determining whether a ligand is present would stick with X-rays.  As a side note, I assume you've checked your possible isotope scatters neutrons well.
~2.2 Angstroms - this paper ( http://bit.ly/qgwHvI ) maybe handy see Table 3 on pg. 384, it compares the resolution of X-ray and neutron data collections.

Take Care,

Sean Seaver

P212121
http://store.p212121.com/

----------
From: Tim Gruene
Dear Francis,

ad [1]: if you are going for neutron diffraction, you probably want the
ligand to have its hydrogens replaced with deuteria, rather than a
'heavy atom derivative' of your ligand. The scattering power for
neutrons does not correlate with the weight of the nucleus und deuterium
scatters as strongly as O,C, ... (see ITCr, Vol. C, Chapter 4.4) In that
case you also do not need a difference map against the X-ray data
because the scattering of X-rays by hydrogens can be neglected.
ad [1b]: see [1]; remark: since we are doing science as opposed to math
or philosophy, there is no 'unambiguity'. There is only a model for the
experimental data which - depending on your means of validation - fits
the data more or less well.
ad [2]: That probably depends on whether your ligand site is fully
occupied and whether the ligand is disordered or not.

Cheers,
Tim

- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

COOT on CentOS 6 (x86_64)

From: Yuri Pompeu
Date: 12 September 2011 00:05


Hello everyone,
Could anyone tell me (or point me to) how to get COOT running on CentOS6 64-bit?
It doesnt launch due to failed dependencies, it requires packages that CentOS6 has replaced...
At least that is what it looks like to me...
Cheers,

----------
From: Paul Emsley


I would try the centos5 binaries - if that didn't work, I'd try to compile it myself (build-it-gtk2-simple).  You can try to fiddle it by linking the new library so files with the old names in coot's lib directory - but that doesn't seem like the best solution to me.

Paul.

----------
From: Yuri Pompeu


Hi Paul,
I am running the centos5 build. After a couple of yum installs it seems to be happy...

Except I cannot maximize the window for some reason.
Thanks for the reply.

Yuri

Pointless problems

From: Emmanuel Saridakis
Date: 14 September 2011 19:06

Dear All,

I am having problems when trying to run Pointless with input from
Denzo/Scalepack.

(1) Pointless refuses to work from the .sca file. The error message is:

CCP4 library signal mtz:File not identified as MTZ (Error)
CCP4MTZfile: open_read - File missing or corrupted: rn7e222test.sca

or

The program run with command: /programs/CCP4/ccp4-6.1.1/bin/pointless
has failed with error message
child process exited abnormally

(when run from ccp4i)

(2) Scalepack2mtz refuses to convert a Scalepack file produced using the
command: "NO MERGE original index" (i.e. as instructed by the Pointless
instructions). It fails with the rather tactless message:

*  Resolution Range :
   0.00202    0.00485     (     22.256 -     14.357 A )
 * Sort Order :
     0     0     0     0     0
 * Space group = 'P 2 2 2' (number     16)

 SCALEPACK2MTZ:  Check your data!

And, no my resolution range is not 22.2-14.3 A!!

(3) Pointless refuses to work with an .mtz file produced by Scalepack2mtz
from a .sca file obtained with the simple "NO MERGE" instruction (remember
the "NO MERGE original index" instruction is a no-go for Scalepack2mtz).
The error message in this case is quite simply:

HKLIN is merged and no HKLREF file is defined, SPACEGROUP or REINDEX.

I know the orthodox ccp4 reply would be "stop whining and use Mosflm!",
but is there an alternative if I really want to use Denzo/Scalepack? If
not, is there another way to check my point group/spacegroup starting from
Denzo/Scalepack?

Thanks a lot!

Emmanuel

----------
From: Ed Pozharski
If you are trying to choose the screw axes, you can always look at the
systematic absences. This script may be useful in extracting the (h00),
(0k0),(00l) and such (assuming you used P222 and thus scalepack kept
everything):
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Get_systematic_absences_from_.sca_file


Cheers,

Ed.

--
"Hurry up before we all come back to our senses!"
                          Julian, King of Lemurs

----------
From: Phil Evans
Pointless will read scalepack files. From ccp4i you need to select the "Scalepack file" option and give unit cell, see attached screen shot

Failing this you can do it from the command line

pointless << eof
scain file.sca
cel a b c alpha beta gamma
eof

Phil

Experimental Postdoctoral Position in High Throughput Small Molecule Ligand Screening

Experimental Postdoctoral Position in High Throughput Small Molecule Ligand Screening


Outstanding postdoctoral applicants to work jointly with Drs. Julia Kubakek, Mark Hay and Jeffrey Skolnick at the Georgia Institute of Technology are sought with the following qualifications:

* Extensive experience in enzyme kinetics studies, enzyme purification or other aspects of protein biology and enzyme activity. Experience in handling multiple protein systems would be a plus.
* A background in high throughput small molecule ligand screening is strongly preferred.
* Experience with or a desire to learn computational biology and molecular modeling of protein-ligand interactions.
* The ideal candidate is someone who gets satisfaction out of methods development and working through large data sets to see broad-scale patterns.


To apply, please email your CV to : skolnick at gatech.edu

Research Assistant Position in Molecular Biology at OPPF-UK

Research Assistant in Molecular Biology (Vacancy ID: 101125)
Wellcome Trust Centre for Human Genetics, Division of Structural Biology
Located at the Oxford Protein Production Facility - UK, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0FA
Grade 6: Salary £25,854 - £30,870 with a discretionary range to £33,734 p.a.

Applications are invited for a Research Assistant in Molecular Biology to join the Oxford Protein Production Facility- UK (OPPF-UK) team.

You will be responsible for carrying out cloning and expression screening of recombinant proteins as part of the services offered by the OPPF-UK to other academic groups (http://www.oppf.ox.ac.uk/). You will be involved in the development and automation of high throughput approaches to molecular biology and have the opportunity to undertake original research leading to academic publications as part of our own research projects.

You will have a BSc degree in biology, biochemistry or molecular biology and research experience in using recombinant DNA methods, including PCR, vector construction and transformation of E. coli. or experience of analysing protein expression by SDS-PAGE, Western blotting.

The position is funded by the Medical Research Council and is fixed term until 30th June 2013 in the first instance.

To apply for this role and for further details, including a job description and a person specification, please click on the link below:

https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=101125

Only applications received before 12.00 midday on 24th October 2011 will be considered.

Please quote reference 101125 on all correspondence. You will be required to upload a CV and supporting statement as part of your online application.

refmac and DNA (and now RNA)

From: Francis E Reyes
Date: 12 September 2011 19:23
Is ' U ' now the standard vs '  U' ? I'm used to right justified letters for RNA residues in the residue field.

This is with a recent refinement with refmac 5.6.0117 .

And of course this switch in naming convention breaks compatibility with molprobity (which requires right justified letters in the residue field)

F


On Sep 8, 2011, at 7:35 AM, Ed Pozharski wrote:

> After switching (finally) to 6.2.0 and therefore to Refmac 5.6.0117 I
> have found a problem working with DNA that I have not seen with
> 6.1.13/5.5.0109.  Namely,
>
> - if I use the pdb file produced by Coot (0.7.pre-1.3470) that seems to
> output DNA as Ad/Td/Gd/Cd no matter what the input names were, refmac
> fails with the warning that it found a new monomer.  It appears that it
> stumbles upon the very first thymidine, but in a strange twist it
> reports the problematic residue having the name "DY"!
>
> - if I use the pdb file previously produced by refmac, which has the
> A/T/G/C as residue names, it fails too but now complains about the "new"
> monomer named "T".
>
> - the workaround I found is to rename all the thymidines to "DT".  It is
> a bit annoying since coot keeps renaming them (well, not refmac/ccp4
> problem per se) and I have to rename back (easily scripted task, of
> course).  What is peculiar is that Ad/Gd/Cd don't need to be renamed
> (does this have anything to do with thymidine being the only one that
> changes residue name in RNA?).
>
> Has anyone else seen this or it's something specific to my setup?
>
> Cheers,
>
> Ed.
>
> --
> After much deep and profound brain things inside my head,
> I have decided to thank you for bringing peace to our home.
>                                    Julian, King of Lemurs



---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

----------
From: Phoebe Rice
Is there finally, at long last, one convention for nucleic acids?  I wonder how many cumulative person-years of exasperation this @#$% issue has caused?

And please note, even Mother Nature herself, let alone synthetic chemists, occassionally attaches U to deoxyribose or T to plain ribose.

=====================================
Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
http://www.rsc.org/shop/books/2008/9780854042722.asp

----------
From: Garib N Murshudov

Yes, new version of the dictionary uses U. Refmac will read right or left justified residue names, however pdb may use only one of them.

There are some backward compatibility code/dictionary elements. For example Ad/Ar are also accepted. However it is encouraged to use new pdb v2.3 residue/atom names. It will make sure that all software use same naming convention and moving between them is smooth. 

Hopefully we all will have one naming conventions.

regards

Garib

Garib N Murshudov
Structural Studies Division

MRC Laboratory of Molecular Biology

Hills Road 

Cambridge 

CB2 0QH UK
Web http://www.mrc-lmb.cam.ac.uk

----------
From: Francis E Reyes
Hi Garib

Thanks for the quick reply!

Refmac  however is writing my pdb's as with the residue letter in the centered position.

Is the newest pdb requiring centered residue letters for RNA?

F

----------
From: Garib N Murshudov

Hi Francis

Is that newer version of refmac?

regards

Garib