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[ccp4bb] PostDoc program in Integrated Structural Biology @Umeå University

Postdoctoral Program in Integrated Structural Biology at Umeå University


Two postdoctoral fellowships are open for the 2019 call at the Integrated Structural Biology (ISB) environment at Umeå University.  Umeå University offers a vibrant and international atmosphere for structural biology research. There are 19 research groups and close to 100 persons affiliated with ISB. The ISB environment has regular seminars and candidates will be broadly exposed to different structural biology techniques. The university has state of the art infrastructure for cryoEM, NMR spectroscopy, supercomputing and x-ray crystallography (please visit www.biostruct.umu.se for details on equipment).


The openings will be filled using a procedure adapted from EMBL and the two top candidates that has applied to one of the six available projects will be selected. The projects are interdisciplinary and will ensure that the candidate will receive competitive training.


The program is open to all nationalities with relevant doctoral level education and work experiences and the openings will include the following to be considered by potential candidates: 

·           Two years funding (incl. running costs) for research within a multidisciplinary structural biology environment 

·           Access to ISB affiliated core facilities and technical platforms 

·           Integration with postdocs at ISB and also MIMS (Molecular Infection Medicine Sweden)  for carrier development and joint activities



Candidates should (in addition to submitting their CV, publications, certificates, etc.) write a “MOTIVATION LETTER” (1-2 pages) specifying: i) why you are interested in performing postdoc research studies within ISB and ii) why in particular you wish to do this with the PI:s and project idea selected from our list The applicants must also write a one-page research plan for the project. We encourage the applicants to contact the PIs for discussion of the project before submission. Please email your application to ISB@umu.se no later than October 15. For inquires please contact the indicated lead-PI or co-PI’s from the list of projects. Further info about the ISB Postdoctoral program can be found here: https://www.biostruct.umu.se/isb-postdoctoral-program/



Below please find a list of the available projects together with contact information to PI’s.


Mechanistic origin of ATP-dependent ion transport

Computational methods can be used to reveal connections between subtle trigger events and large-scale conformational changes in proteins. In this project, computer simulations and time-resolved X-ray solution scattering experiments (TR-WAXS) will be used to identify such connections in ATP-dependent membrane protein transport. Specifically, classical MD and QM/MM simulations will characterize effects of phosphorylation, protonation/deprotonation, and ion binding in P-type ATPase ion transport. Existing high-resolution protein structures as well as low-resolution models of transient states in solution (obtained from time-resolved X-ray scattering experiments) will serve as the basis for the simulations. The project aims to determine structural dynamics and corresponding free energy levels to provide a structural/thermodynamic basis for understanding ATP-driven ion transport across biological membranes. The project will be lead by Dr. Andersson (classical MD/X-ray scattering) and Dr. Nam (QM/MM). Part of the project will take place at University of Texas, Arlington, USA.

Lead PI: Magnus Andersson: magnus.p.andersson@umu.se

Co-PI:   Kwangho Nam: kwangho.nam@umu.se


Mechanistic study of the autophagic protein ATG8/LC3 in membrane morphogenesis

Autophagy is a highly conserved and sophisticated “self-eating” process in eukaryotes and plays a key role in human health and disease. Formation of double-membrane autophagosomes is the key process in autophagy and the LC3 protein family is required for autophagosomal membrane expansion and closure. However, the molecular mechanisms of these processes remain unclear. In this project we will focus on the membrane interactions of the LC3-PE protein. Wu’s lab have prepared LC3-PE by semisynthetic approaches and showed that LC3-PE promotes membrane fusion in vitro . The protein will here be studied using structural biology tools, primarily NMR spectrosocpy, together with Mäler’s group. The proposed project provides an excellent opportunity for combining Wu’s expertise concerning protein chemistry with biophysical and structural biology (NMR) studies of the interaction between one key component in autophagy and lipids in Mäler’s group.

Lead PI: Lena Mäler: lena.maler@umu.se  

Co-PI:  Yaowen Wu:  yaowen.wu@umu.se


Functional and structural analyses of the dynamic conformational changes of Opsins upon photo responsiveness

Opsins, including Opn3 and Opn5, are G-coupled receptors that detect light by transforming the energy of a photon into a cellular response. The specific roles of Opn3 and Opn5 are unresolved, and their wide _expression_ patterns in the brain and other organs make them attractive for structure/function studies. By using biophysical techniques coupled to structural and molecular biology, this project aims to examine the structure and conformational changes of Opn3 and Opn5 upon light activation. The suitable postdoc candidate will purify protein complexes that will be studied with Cryo-EM, and time-resolved wide angle x.-ray scattering (TR-WAXS). Three PI:s with complementary set of expertise are connected to this project: Linda Sandblad has extended knowledge of Cryo-EM to study protein structure and membrane proteins in cellular environments. Magnus Andersson has previous experience with analyzing conformational changes in light sensitive membrane proteins using TR-WAXS. Lena Gunhaga has an expertise in sensory neural development using a range of molecular biology methods.

Lead PI: Linda Sandblad: linda.sandblad@umu.se

Co-PI:  Magnus Andersson: magnus.p.andersson@umu.se

Co-PI:   Lena Gunhaga: lena.gunhaga@umu.se


The structural basis of promiscuity in toxin-antitoxin networks

Bacterial toxin-antitoxin (TA) systems have diverse functions, including defence against phages and maintenance of genetic elements. The lab of Gemma C. Atkinson has discovered a large network of promiscuous toxin-antitoxin domain pairs that swap partners across vast evolutionary distances. These novel TAs are being characterised microbiologically and biochemically in collaboration with the lab of Vasili Hauryliuk. This post-doctoral project aims to discover the structural and molecular evolutionary basis of toxicity, neutralisation by antitoxins, and partner swapping. TA complexes will be analysed structurally by X-ray crystallography in the lab of Karina Persson (lead PI), and the dynamics of complex formation will be investigated with NMR, working with the lab of Gerhard Gröbner. The successful post-doc will receive training in these two structural biology methods, as well as the interpretation of structures in the light of evolution and molecular function.

Lead PI: Karina Persson: karina.persson@umu.se

Co-PI:  Gerhard Gröbner: gerhard.grobner@umu.se

Co-PI:  Gemma C. Atkinson: gemma.atkinson@umu.se


Understanding assembly and function of the bacterial cell wall

Bacteria are protected from environmental insults by a peptidoglycan (PG) cell wall. Hence, the enzymes involved in the production and turnover of PG are preferred targets for many of our most successful antibiotics. Our team has discovered a novel PG synthetic protein in Vibrio cholerae (i.e. PBP1V), the causative agent of Cholera. PBP1V is conserved in a number of Gram negative pathogens and appears to support cell wall integrity under challenging conditions. Understanding the nature and function of PBP1V will help to address fascinating questions regarding peptidoglycan homeostasis and plasticity and might provide a new target against bacterial infections. The recruited postdoc will work on the structural and biochemical characterization of PBP1V. The team composed by Elisabeth Sauer-Eriksson, Felipe Cava and Magnus Andersson will provide a stimulating environment and the right interdisciplinary cross training for the postdoc. 

Lead PI: Elisabeth Sauer-Eriksson:  elisabeth.sauer-eriksson@umu.se

Co-PI:   Felipe Cava: felipe.cava@umu.se

Co-PI:   Magnus Andersson:  magnus.p.andersson@umu.se


A molecular basis of factors involved in honeybee hive collapse

During the last decade, studies have identified factors that cause a dramatic decline in honeybee hives. Habitat loss, intensified agriculture, pollution and climate change weakens wild and managed honey bee cultures causing their disappearance. Similarly, an alarming prediction suggests the extinction of more than 40 % of the world’s insect species in the next decades with implications for the pollination of many essential plants.This interdisciplinary project involves the analysis of affected environmental samples using microscopy, microbiology and molecular biology to confirm existing and identify novel elements involved in honeybee hive collapse. This will be followed by a targeted biochemical and structural characterization of critical molecular factors using cryo-EM and X-ray crystallography. The candidate will have the opportunity to participate in research that explores a significant environmental problem with a multi-angle approach to relate observations made in nature with the underlying atomic basis.

Lead PI: Jonas Barandun: jonas.barandun@umu.se

Co-PI:  Uwe. H. Sauer:  uwe.sauer@umu.se

Co-PI:   Natuschka Lee: natuschka.lee@umu.se





From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Sonja Lorenz
Sent: den 3 september 2019 11:47
Subject: [ccp4bb] PhD position to explore the structural mechanisms of ubiquitin ligases in infection; Sonja Lorenz' lab, Würzburg, Germany


Dear colleagues,

we are looking for a PhD student to study the structural basis of ubiquitin signaling in an exciting infection model system. 

I would be grateful if you would make the ad below available to suitable candidates at your institutions.

Thank you very much and best wishes,

Sonja Lorenz




The ubiquitin signaling research group headed by Sonja Lorenz at Rudolf Virchow Center for Experimental Biomedicine, Würzburg, Germany

is recruiting a PhD student

The Lorenz lab explores the fundamental mechanisms of how posttranslational modifications encode specificity in cellular signaling with a particular focus on the ubiquitin system in tumorigenesis and infection. Our lab combines cryo-EM and X-ray crystallography with biophysical, biochemical, and cell biological analyses.

 We are supported by the EMBO Young Investigator Program, the Emmy Noether Program of the German Research Foundation, the Mildred Scheel Cancer Center, research unit FOR2314 (“Therapeutic windows”), and the graduate training group GRK2243 (“Understanding ubiquitylation”). The successful candidate will have the opportunity to be affiliated with GRK2243 and investigate the structural mechanisms of an exciting class of enzymes essential for infectious disease.

The Rudolf Virchow Center is a highly competitive international research institute with an outstanding infrastructure. The Lorenz lab has in-house access to state-of-the-art instrumentation in cryo-EM (Titan Krios), X-ray crystallography, and an extensive range of modern biophysical and cell biological equipment. We are integrated into a stimulating environment that includes the Helmholtz Institute for RNA-based Infection Research, the Max Planck Research Group in Systems Immunology, the Biocenter, the Institute for Molecular Infection Biology, and the University Hospital in Würzburg.

Würzburg is located in the beautiful, wine-growing area of Franconia, in proximity of Frankfurt (1 hour by train) and Munich (2 hours).

Applicants should have an MSc or equivalent degree in the life sciences or a related discipline and a passion for structural biology and protein biochemistry. Good English language skills are necessary; knowledge of German is not required.

The position can begin immediately or upon mutual agreement. Salary will be according to the German TVL scale. In case of equivalent qualifications, disabled applicants will be preferentially considered.

Applications and inquiries should be sent to Sonja Lorenz by email and include a letter of motivation stating research interests and expertise, a CV, and the contact information of at least two references. 
Application deadline: 30 September 2019. Review of applications will begin immediately until the position is filled.

twitter @ SLorenzLab

Sonja Lorenz, PhD
Rudolf Virchow Center for Experimental Biomedicine
University of Würzburg, 97080 Würzburg, Germany
E-mail: sonja.lorenz@virchow.uni-wuerzburg.de


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