Postdoc positions in anti-bacteriophage defense system cryo-EM, cryo-ET and protein design

3 postdoctoral positions are available in the Taylor group (Structural Biology of Molecular Machines), at the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen. We aim to recruit scientists with extensive experience in one or more of the techniques of interest to help pioneer and establish this new research field. The positions are for 2 years in the first instance and can be renewed for up to 4 years in total, providing a unique long-term opportunity to work on an exciting project in a well-equipped and supportive environment.

Background
Bacteria are under constant attack by bacteriophages, and have evolved intricate systems to tackle this constant threat (Doron et al, Science, 2018). We have a special focus on bacteriophage defense at the bacterial cell envelope/membrane, for which we recently received a large Hallas Møller Ascending Investigator grant from the Novo Nordisk Foundation. We have been actively working on bacteriophage defense in the past years with our first preprint about to be submitted (Hu et al., in preparation).

We will investigate defense systems using three approaches: single particle cryo-EM, cryo-electron tomography, and protein bioinformatics/design. Together with expert collaborators in phage biology, engineering and light microscopy, we aim to unravel fundamentally novel mechanisms in bacteriophage defense and biology.

We are looking for three motivated postdocs with experience in one of the three approaches to help tackle this exciting challenge.

Position 1
The postdoc will be involved in the expression and purification of components of anti-bacteriophage defense systems interacting with the bacterial cell membrane. Using single particle cryo-electron microscopy, the postdoc will investigate the structure of these systems in different states.

Position 2
The postdoc will study anti-bacteriophage defense systems interacting with the bacterial cell membrane using cryo-electron tomography. They will investigate how the defense systems are able to ward of bacteriophage infections.

Position 3
The postdoc will investigate anti-bacteriophage defense systems as well as phage-encoded inhibitors for these defense systems from a computational point of view. In particular, they will use structure prediction to predict novel defense systems and protein design to design new defense systems.

If you have any questions about the positions, please contact: [email protected] .

Environment

Taylor group – Structural Biology of Molecular Machines

The Taylor group (https://www.cpr.ku.dk/research/protein-structure-function-program/taylor ) studies how molecular machines transport molecules across membranes. Using a combined structural and functional approach the group tries to understand how these machines function and how they can be inhibited, with the ultimate aim to contribute fundamental insight into this key biological mechanism as well as contribute to the development of better personal medical treatments. The group uses cryo-EM as its main method to achieve this goal (see e.g. Santiveri et al., Cell, 2020, Adaixo et al., Nat. Commun. 2022, Hu et al., Nat. Commun. 2023 and postdoctoral studies priorto CPR: Taylor et al., Nature, 2016; Taylor et al., Nature, 2017; Manolaridis et al., Nature, 2018; Jackson et al., Nat. Struct. Mol. Biol., 2018). We have now started to complement these studies using cryo-electron tomography as well as protein design.

Responsibilities and tasks 

Postdoc 1 will use protein purification, especially of membrane proteins, followed by single particle cryo-electron microscopy and other biophysical techniques to characterize the defense systems.

Postdoc 2 will use cryo-electron tomography and subtomogram averaging to unravel the in situ mechanism of the studied defense systems.

Postdoc 3 will use in silico protein structure prediction and design integrating sequence data as well as structural cryo-EM data to obtain better structural models and provide sequence-structure-function information on a variety of anti-defense and anti-anti-defense systems.

We have excellent access to a Titan Krios microscope, equipped with Falcon 4i direct electron detector and Volta phase plates, and a Glacios microscope with Falcon 3EC at the Core Facility for Integrated Microscopy as well as direct access to an internal GPU cluster.

The positions are available immediately, but the starting date will be agreed upon with the selected candidate.

Qualifications
Candidates for the postdoctoral positions must be expecting or holding a PhD degree (or equivalent). The successful candidates will have strong qualifications or experience within several of the following areas: 

Position 1

• Bacterial protein cloning and overexpression
• Protein purification
• Membrane proteins
• Cryo-electron microscopy
• Model building
• Nucleic acids
• Bacteriophages
• Anti-bacteriophage defense systems

Position 2

• Bacterial protein cloning and overexpression
• Cryo-electron tomography
• Subtomogram averaging
• Model building
• Nucleic acids
• Bacteriophages
• Anti-bacteriophage defense systems

Position 3

• Protein structure prediction (Rosetta, AlphaFold, …)
• Protein design
• Data science
• Deep learning
• Large-scale sequence analysis
• Nucleic acids
• Bacteriophages
• Anti-bacteriophage defense systems

As this is a large, collaborative project, strong team player skills are required for all positions.

Place of employment and work
The employment is at CPR (www.cpr.ku.dk ), University of Copenhagen, located in central Copenhagen. The research environment at CPR is ambitious and international, with approx. 30 different nationalities currently represented. The center comprises modern laboratories, supercomputer resources and state-of-the-art facilities within protein science. Seminars with high-profile international speakers and regular internal research seminars are organized at the center. The selected candidate should expect some travel activity. 

For more information on working and living in Denmark, visit www.ism.ku.dk  (International staff mobility) and www.workingconditions.ku.dk  

Terms of salary and employment 

The average weekly working hours are 37 hours per week.

The position is a fixed-term position limited to a period of 2 yearsThe starting date is 1 April 2024 or after agreement.

Salary, pension and other conditions of employment are set in accordance with the Agreement between the Ministry of Taxation and AC (Danish Confederation of Professional Associations) or other relevant organisation. Depending on qualifications, a supplement may be negotiated. The employer will pay an additional 17.1 % to your pension fund.

Foreign and Danish applicants may be eligible for tax reductions, if they hold a PhD degree and have not lived in Denmark the last 10 years.

The position is covered by the Job Structure for Academic Staff at Universities 2020.

Application procedure 
Your online application must be submitted in English by clicking ‘Apply now’ below. Furthermore, your application must include the following documents/attachments – all in PDF format:

Deadline for application: January 8 2024, 23.59pm CET

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process
After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor. Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.

You can read about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/

The applicant will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities.

The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background.

Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.