off topic: the effects of spontaneous oligomerization on crystallization

From: 杨贝 <joybeiyang
Date: 6 April 2012 16:41

Dear All,

 

I have a 100KD protein which elutes as a mixture of 90% monomer and 10% dimer on HPLC, if I pool the monomer fractions and  reload them onto the column, the elution profile is still 90% monomer plus 10% dimer, and the same is true if I do so to the dimer peak. Collectively, there seems to be a equilibrium between the monomer and the dimer. So far, I have not got crystals yet, since the purity of the protein is fairly high (99% pure), I am wondering if the lack of crystallization is caused by the heterogeneity introduced by the spontaneous oligomerization, and if so, what can I do to improve the homogeneity? Will a additive/detergent screen help (this is not a membrane protein)?  

 

Any comments will be greatly appreciated!

 

Best,

 

Joy

----------
From: Bosch, Juergen

If you have a DLS you can try playing with different [NaCl] or pH and see if you can push the equilibrium in one direction.

Jürgen

......................
Jürgen Bosch

arp_waters still available?

From: Bernhard Rupp (Hofkristallrat a.D.)
Date: 5 April 2012 04:23


Dear Developers,

in some older scripts I still call the ccp4 version of arp_waters, which
worked well for dummy atom picking.
It does not seem to be included in recent 64 bit CCP4 packages. Does anyone
perhaps have
a precompiled 64 bit version of arp_waters that might run on RHEL62?

Best regards, BR

----------
From: Victor Lamzin


Dear Bernard,

arp_waters is a very old code and it gets even older as we speak.

Try to use ARP/wARP version 7.2, where you can run the same task:
from the command line ($warpbin/auto_solvent.sh)
from the CCP4i GUI (ARP/wARP Solvent)
from ArpNavigator (Model Solvent)

There should be both 32 and 64-bit versions.

Best regards,
Victor

postdoctoral position in Warsaw

From: Marcin Nowotny
Date: 22 May 2012 17:00

The group of Dr. Marcin Nowotny at the International Institute of Molecular and Cell Biology (IIMCB) in Warsaw, Poland is seeking candidates for postdoctoral fellows. The fellows will work on protein complexes involved in DNA and RNA metabolism using protein crystallography and protein biochemistry (for examples of our previous work please see: Jaciuk M. et al. Nat. Struct. Mol. Biol. 18(2):191-7 and Rychlik M.P., et al. Mol. Cell  40(4):658-70). Further information about IIMCB can be found at: http://www.iimcb.gov.pl. The Institute has state-of-the-art equipment and facilities, including crystallization robots, an automated crystallization station and a microfocus home X-ray source.

 

The candidates should hold a Ph. D. degree, must be motivated, well-organized and able to work independently as well as a part of the team. Experience with protein expression, purification and biochemical characterization is required. Knowledge and experience in protein crystallography will be an advantage.

 

The candidates should send their detailed CV to mnowotnyATiimcb.gov.pl with reference contact information.

 

X-ray Crystallography Research Associate Position at Novartis in Cambridge, MA

Date: 21 May 2012 13:54
Subject: [ccp4bb] X-ray Crystallography Research Associate Position at Novartis in Cambridge, MA
To: CCP4BB@jiscmail.ac.uk

Research Associate – X-ray crystallography

 

Job Description 

The candidate will join a state-of-the art unit that provides structural biology information to expedite drug discovery projects undertaken at the NIBR Cambridge campus. The candidate will be part of the biomolecular structure group responsible for expression, purification, crystallization and structure determination of proteins and protein-ligand complexes. The candidate will be expected to be able to participate in experimental design and to independently conduct experiments in a priority-driven environment.

 

Minimum Requirements

B.S/M.S. in biochemistry or a related discipline with at least 2 years of research laboratory experience. Experience in protein chemistry (e.g. expression, purification and characterization) is required. Experience with crystallization, x-ray data collection, structure solution and/or biophysical characterization of proteins would be a decided asset.  The candidate must possess good oral and written communication skills and work well in a team.

 

For immediate consideration, please apply on-line at http://www.novartis.com/careers using Job Code 97236BR.  Novartis is committed to embracing and leveraging diverse backgrounds, cultures, and talents to achieve competitive advantage.  Novartis is an equal opportunity employer.  M/F/D/V

Postdoctoral Position at UCSF - Structure of Receptor Tyrosine Kinases

From: Jura, Natalia
Date: 16 May 2012 19:35


UNIVERSITY OF CALIFORNIA SAN FRANCISCO (UCSF)
POSTDOCTORAL POSITION, JURA LAB
Crystallographic studies of receptor tyrosine kinases

A postdoctoral position in Receptor Tyrosine Kinase Structural Biology is available immediately for highly motivated individuals with a strong interest in crystallographic studies of tyrosine kinase signaling in the lab of Prof. Natalia Jura at the University of California, San Francisco (UCSF).  The Jura Lab merges structural, biochemical, imaging and cell biology approaches to dissect the mechanism of multi-protein assemblies involved in receptor tyrosine kinase signaling at the plasma membrane. More information is available at the lab website: http://www.cvri.ucsf.edu/~jura

The position offers ideal opportunities for experienced crystallographers interested in continuing structural studies, but who would like to complement his or her expertise with other, diverse tools for understanding the molecular basis for regulation of growth signaling at the plasma membrane and general kinase activation mechanisms. The fellow will benefit from both the multidisciplinary environment in the lab and the highly collaborative UCSF community. The lab has extensive crystallographic resources, including (as part of the UCSF crystallography group) two R-axis IV systems and regular access to synchrotron beamline 8.3.1 at the nearby Advanced Light Source (ALS) in Berkeley.

Candidates should have (or expect) a Ph.D. or M.D. and should have experience in protein purification, crystallization, and structure determination.

Interested individuals should send a current CV to Prof. Natalia Jura at natalia.juraATucsf.edu<mailto:daniel.minorATucsf.edu>


_
--

Natalia Jura, Ph.D.
Assistant Professor
Lab Website: http://www.cvri.ucsf.edu/~jura





----------
From: Jura, Natalia


Date: May 16, 2012 11:35:34 AM PDT

UNIVERSITY OF CALIFORNIA SAN FRANCISCO (UCSF)
POSTDOCTORAL POSITION, JURA LAB
Crystallographic studies of receptor tyrosine kinases

A postdoctoral position in Receptor Tyrosine Kinase Structural Biology is available immediately for highly motivated individuals with a strong interest in crystallographic studies of tyrosine kinase signaling in the lab of Prof. Natalia Jura at the University of California, San Francisco (UCSF).  The Jura Lab merges structural, biochemical, imaging and cell biology approaches to dissect the mechanism of multi-protein assemblies involved in receptor tyrosine kinase signaling at the plasma membrane. More information is available at the lab website: http://www.cvri.ucsf.edu/~jura

The position offers ideal opportunities for experienced crystallographers interested in continuing structural studies, but who would like to complement his or her expertise with other, diverse tools for understanding the molecular basis for regulation of growth signaling at the plasma membrane and general kinase activation mechanisms. The fellow will benefit from both the multidisciplinary environment in the lab and the highly collaborative UCSF community. The lab has extensive crystallographic resources, including (as part of the UCSF crystallography group) two R-axis IV systems and regular access to synchrotron beamline 8.3.1 at the nearby Advanced Light Source (ALS) in Berkeley.

Candidates should have (or expect) a Ph.D. or M.D. and should have experience in protein purification, crystallization, and structure determination.

1 postdoctoral position available @cnio

From: Daniel Lietha
Date: 20 May 2012 22:48

Dear All,

I would like to inform you that an opening for a postdoctoral position is available in the Structural Bases of Genome Integrity Group at the Spanish National Cancer Research Centre in Madrid (CNIO, Madrid)

We seek for candidates with a PhD in structural biology, biochemistry or a related field and proven experience in molecular biology, protein expression and purification. Additional experience in macromolecular X-ray crystallography and/or single-particle electron microscopy is highly desirable. Experience with protein expression in eukaryotic systems is an advantage. Fluency in English is required.

The research focuses on structural and functional aspects of genome integrity, with particular emphasis on employing X-ray crystallography and single-particle electron microscopy to elucidate the structures and understand the function of large macromolecular complexes involved in DNA recombination and repair.

The candidate will be part of a team of highly motivated structural biologists and biochemists and will have the opportunity to collaborate with cell biology and computational groups at the CNIO. The Structural Bases of Genome Integrity Group is led by Santiago Ramon-Maiques.

Applications can be sent at any time. Applicants should submit a CV, a statement of research interests, and the names and contact information of two references to Santiago Ramon-Maiques (sramonATcnio.es). All enquiries and applications will be treated confidentially.   


Regards,

Santiago Ramón-Maiques

Postdoc position at the Noble Foundation, USA

From: Wang, Xiaoqiang
Date: 10 May 2012 15:01

Postdoc position at the Noble Foundation, USA

 

A Postdoctoral position is available in the Structural Biology Laboratory in the Plant Biology Division at the Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA, to study structures of proteins including membrane transport proteins involved in natural product biosynthesis, nutrient uptake, and gene regulation. The lab is well equipped with state-of-the-art equipment for molecular biology, protein biochemistry, and crystallography, including AKTAPurifers, VP-ITC, Phoenix crystallization robot and an X-ray imaging plate system. Applicants should have a Ph.D. with experience in crystallography and protein expression and purification. Starting salaries begin at $41,200 with excellent benefits. Informal inquiries can be made to Dr. Xiaoqiang Wang (Email: xwangATnoble.org).

 

Application Instructions: Applicants are requested to apply online by completing the application and submitting a resume, contact information for three references, and a cover letter explaining interest in the position and career goals. Applications will be accepted until a candidate is hired. Interested applicants should apply at http://www.noble.org/recruiting/ (Position ID PB-S065-56).

Xiaoqiang Wang, Ph.D

Associate Professor

http://www.noble.org/PlantBio/Wang/lab.html

 

Membrane Protein Crystallography Postdoctoral Fellow, Caffrey Lab, Trinity College Dublin, Ireland

From: Martin Caffrey
Date: 17 May 2012 16:11

Postdoctoral Research Fellow – Macromolecular Crystallography

Membrane Structural and Functional Biology – Caffrey Lab

Trinity College Dublin, Ireland

Trinity College Dublin is inviting applications for the post of Postdoctoral Research Fellow in the Caffrey Membrane Structural and Functional Biology Research Group.  The major theme within the Group is structure and function of membrane proteins by crystallographic means.  Systems under investigation include human GPCRs, transducers, transporters, lipid metabolizing enzymes, respiratory complexes, and quorum sensing-related and biofilm forming membrane proteins of Pseudomonas aeruginosa.  Purified protein and in meso-grown crystals of several targets are already in hand. 

Person Specification

 

- A Ph.D. in macromolecular X-ray crystallography

- Experience and demonstrated success with macromolecular crystallization

- Experience and demonstrated mastery of all of the computational aspects of crystal structure determination to include MR, MAD, SAD, MIR, and S/MIRAS

- Experience with low-resolution structure determination

- Experience and demonstrated mastery of the latest crystallographic software on UNIX-based operating systems to include the CCP4 suite, CNS, Phenix, Phaser, Sharp and other relevant packages

- Recent experience and demonstrated mastery of on-site data collection at a synchrotron X-ray source

- Availability and willingness to travel to synchrotrons and collaborators worldwide

- A commitment to quality and innovative research

The candidate should be a self-motivated individual who enjoys working as part of a collaborative, multidisciplinary team.  Strong leadership, communication and teaching skills are decided assets. 

Salary: based on experience

The closing date for receipt of applications is Tuesday, 19^th June 2012.

Further information for applicants and application material are available online from: www.tcd.ie/vacancies

 

Post-doc position available

From: Stewart Turley
Date: 17 May 2012 22:09

A  position is available now in the laboratory of Wim Hol, as described below.  Please respond to the address at the end of the advertisement.

Postdoctoral Position Available

Laboratory of Wim Hol

Department of Biochemistry, School of Medicine

 University of Washington, Seattle, USA

 

Structural Biology of the type II secretion system

from pathogenic bacteria

 

            The projects in Wim Hol's protein crystallography group at the University of Washington are all focused on providing a basis for development of new therapeutics for tropical diseases. This particular available postdoctoral position is part of a major effort to unravel the architecture, mechanism of action and biogenesis of the "type II secretion system" (T2SS). 

 

The sophisticated T2SS occurs in many pathogenic bacteria.  This machinery is responsible for translocating a wide variety of proteins in a folded state from the periplasm across the outer membrane into the extracellular milieu. One of these proteins is cholera toxin which has been studied intensively in the Hol lab. The large T2SS consists of  multiple copies of  ~14 different proteins that span the inner and the outer membrane, and is associated with  a secretion ATPase in the cytoplasm which provides the energy for the secretion process. Another remarkable feature of the T2SS is a helical sub-assembly in the periplasm which is likely serving as a piston pushing cholera toxin and other exoproteins through a pore in the outer membrane.

 

            The successful candidate will have the opportunity to:

(i) carry out protein expression and protein chemistry studies to obtain insight into protein-protein interactions involving the T2SS from pathogenic bacteria like Vibrio cholera, enterotoxigenic E. coli, and other bacteria;

(ii) purify and characterize multi-protein and multi-membrane protein complexes;

(iii) determine high resolution crystal structures of these complexes;

(iv) analyze these structures and combine this with other biochemical data;

(v) interact with several collaborating groups which are using other methods to obtain structural and functional insight into the mechanism of this sophisticated secretion system.

 

For more information regarding the laboratory of Wim Hol see the following website:

http://www.bmsc.washington.edu/WimHol/

 

For more information regarding the type II secretion system see our recent review:

Korotkov, K. V., Sandkvist, M. and Hol, W. G. J.

The type II secretion system: biogenesis, molecular architecture and mechanism.  Nature Reviews Microbiology 10, 336-351 (2012) 

 

 

START DATE:         Immediately

 

INSTITUTION:        Department of Biochemistry

                                    Biomolecular Structure Center

                                    School of Medicine

                                    Box 357742

                                    University of Washington

                                    Seattle, WA, 98195  USA

 

 

Requirements

Experience with membrane protein preparation, including molecular biology techniques, membrane protein characterization and protein crystallography.

 

Application

If you are interested, please send your CV, including a description of your experience and technical know-how, a list of publications and presentations, and names and email addresses of three references able to assess your scientific experience and capabilities to: wghol@u.washington.edu

COSMX Course Announcement on complementary optical spectroscopic methods in macromolecular crystallography - ESRF 19 -21 September 2012

Date: 18 May 2012 12:13

COURSE ANNOUCEMENT

Introduction to complementary optical spectroscopic methods in
macromolecular crystallography
ESRF-EMBL-IBS, Grenoble, France, 19 - 21 September 2012


The COSMX training event will be hosted by the ESRF in Grenoble,
France, from 19 to 21 of September 2012. The course addresses young
scientists and students who intend to apply in crystallo optical
spectroscopy techniques to macromolecular crystallography.


The course will train selected participants through a series of
lectures, practicals, on both on-line and off-line ESRF facilities,
and tutorials, that will include, UV-vis absorption, Raman
spectroscopy and Fluorescence. Relevance of these technique for
radiation damage studies will also be discussed.

Confirmed tutors include:
Philippe Carpentier (ESRF Grenoble, France)
Daniele de Sanctis (ESRF Grenoble, France)
Florian Dworkowski (SLS - PSI Villigen, Switzerland)
Martin Fuchs (SLS - PSI Villigen, Switzerland)
Mike Hough (University of Liverpool, UK)
Max Nanao (EMBL Grenoble Outstation, France)
Robin Owen (DLS Didcot, UK)
Arwen Pearson (University of Leeds, UK)
Alexander Popov (ESRF Grenoble, France)
Antoine Royant (IBS/ESRF, Grenoble, France)
David von Stetten (ESRF Grenoble, France)
Martin Weik (IBS/ESRF, Grenoble, France)


The number of participants is limited to 15 and the deadline for
application is July 20th, 2012.
Additional information, course programme and instructions to apply to
the course can be found in the course webpages:
http://www.esrf.eu/events/conferences/COSMX_training_course

This course is funded by BioStruct-X (WP10) and by ESRF

With best regards

Daniele de Sanctis

ἀρετή

Workshop: Practical Course in Crystallization of Membrane and Large Complexes of Macromolecules

Date: 18 May 2012 15:07

========================================================================================================

Crystallography Workbench

 

June 11-13, 2012

 

Three day practical course in crystallization of membrane and large complexes of macromolecules

 

Location:
National Synchrotron Light Source, Brookhaven National Laboratory

========================================================================================================

 

Purpose & Scope of Workshop:
 The purpose of this course is to provide participants with hands-on experience of a variety of crystal growth methods for obtaining high quality crystals. The course will address both conventional and non-conventional methods in membrane protein crystal growth and large complexes. Introductory lectures will precede the three practical sessions planned for the course. Time for discussions and informal meetings with the tutors is scheduled. A special session on cryogenic protection and crystal quality assessment will be conducted at the X6A and X4C beam lines on the last day.

 

Intended Audience: Graduate students, post-doctoral fellows and research scientists interested in learning about different approaches to crystallization. Participation is limited on a first come basis. All participants are required to have a valid BNL guest appointment at the beginning of the workshop. If you do not have a valid appointment with BNL, you will need to register in the BNL Guest Information System (GIS).

 

Samples: Participants can bring samples to try during the workshop. Samples are required to be non-hazardous. If you have any questions, please contact one of the organizers.

 

For more information and in order to register see

 

http://workshops.ps.bnl.gov/default.aspx?w=crystalJun2012

 

BioSAXS and other postdoc positions open at CHESS

From: Richard Gillilan
Date: 10 May 2012 15:59

Note: CHESS has multiple postdoc positions open in various areas of x-ray science. I am posting the BioSAXS ad here, but applicants will automatically be considered for all the positions. 

--------------------------------------------------------------------------------

Job opening: Postdoctoral Associate

Biological Small-Angle Solution Scattering (BioSAXS)

MacCHESS, Cornell High-Energy Synchrotron Source  

The Macromolecular Diffraction Facility of the Cornell High-Energy Synchrotron Source (MacCHESS) has an opening for a Postdoctoral Associate.  Applicants should have a Ph.D. degree in a field relevant to structural biology.  Preference will be given to those with experience in x-ray solution scattering on biological systems (SAXS and WAXS).  Activities will include automating BioSAXS data processing at the beamline, developing novel microfluidic lab-on-a-chip methods, applying state-of-the art algorithms to BioSAXS data (especially as related to handling mixtures of oligomers), developing CryoSAXS technology, and modeling macromolecular complexes.  Experience in developing hardware and software for automation is desirable.  Software development will be done primarily in Python.  While MacCHESS postdocs are not required to do general beamline user support, they will be expected to help with the biannual BioSAXS Essentials training course.  The successful postdoc will take full advantage of the rich variety of high-profile groups visiting MacCHESS by co-authoring publications and collaborating on research.  MacCHESS is a heavily team-oriented environment.  Good clear communication skills are a must, including fluency in the English language.  This position is a 1-year appointment, renewable for up to 3 years total, contingent upon availability of funds and employee performance.  The starting date is negotiable. 

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

Applications should be submitted at http://academicjobsonline.org/ (posting #1522) and should include a cover letter, a CV, a list of publications, and a detailed summary of research experience and interests.  Applicants must arrange to have at least three letters of recommendation uploaded, as per instructions on the academicjobsonline website.  For information about the position, contact Dr. Marian Szebenyi 

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