Postdoc of Computational Protein Biophysics
Department of Biology
Faculty of Science
University of Copenhagen
The Lindorff-Larsen group at the Linderstrm-Lang Centre for Protein Science Department of Biology Faculty of Science University of Copenhagen Denmark invites applicants for a postdoctoral position in computational protein biophysics. The position is part of the ERC Synergy project DynaPLIX (Dynamics of ProteinLigand Interactions) that aims to combine molecular dynamics simulations NMR spectroscopy and time-resolved crystallography to quantify the dynamical pathways of how ligands bind to proteins. The postdoc project involves the computational aspects of DynaPLIX. DynaPLIX is a collaboration with the groups of Mikael Akke (Lund Sweden; NMR) and Eike Schulz (Hamburg Germany; crystallography) and the postdoc is expected to interact with researchers in these groups also. The position is for two years with the possibility of extension.
The start date is expected to be 1 October or as soon as possible thereafter. Details about the project what we are looking for and how to apply can be found below.
The project
Our knowledge of protein function is primarily based on static structures which have provided great insights about structure-function relationships. Proteins are however not static molecules but undergo spontaneous transitions between alternative structural states some of which are rare transient conformations that are essentially invisible to traditional methods. These dynamical properties are known to be critically important for function but high-resolution studies of dynamics have so far been conducted merely as an add-on following structural studies.
In DynaPLIX we aim to establish integrative biomolecular dynamics by developing methods that integrate time-resolved X-ray crystallography nuclear magnetic resonance spectroscopy and molecular simulations to study the motions of proteins while they carry out their function. The postdoc will work with other researchers in the Lindorff-Larsen group on the computational aspects of DynaPLIX and will also work closely also with researchers performing experiments in the groups in Sweden and Germany.
The project is focused on the challenging problem of molecular recognition specifically of how proteins bind ligands by describing with atomic resolution the entire dynamic process to reach a consistent kinetic thermodynamic and structural view. From the computational side this involves performing molecular simulations of protein-ligand binding processes and constructing kinetic models of these. In addition to using molecular dynamics simulations ideally aided by machine learning methods a key aspect of the project is to develop and apply theory of how to integrate simulations and time-resolved and time-dependent experiments. For some background see for example our review (https://doi.org/10.1016/bs.pmbts.2019.12.006; also available as a preprint at https://doi.org/10.48550/arXiv.1909.06780).
Who are we looking for?
We are seeking motivated applicants with a PhD degree in molecular biophysics physics chemistry or biochemistry or similar fields. The candidate should ideally have prior research experience within one or more of these areas:
- Advanced molecular dynamics methods (i.e. beyond standard molecular simulations) including for example using and developing enhanced sampling methods
- Analysing molecular simulations using machine learning or Markov state models
- Integrating biophysical experiments and molecular simulations
Some of the projects in DynaPLIX involve substantial methods development and the ideal candidate for the project has a solid theoretical background and programming skills. Other projects are more applied and experience with using molecular simulations to study the biophysics of protein-ligand kinetics is also useful. Previous experience with integrating molecular simulations with NMR or X-ray crystallographic data will be very useful.
Our group and research- and what do we offer?
The positions are part of an interdisciplinary research effort called DynaPLIX (Dynamics of ProteinLigand Interactions) that aims to combine molecular simulations NMR spectroscopy and time-resolved crystallography to quantify the dynamical pathways of how ligands bind to proteins. The DynaPLIX project is funded by a six-year ERC synergy grant and is a collaboration with the groups of Mikael Akke (Lund Sweden; NMR) and Eike Schulz (Hamburg Germany; crystallography). The postdoc will interact with researchers in these groups also in addition to other researchers in the DynaPLIX project in the Lindorff-Larsen group.
The postdoc will work in the group of Kresten Lindorff-Larsen located at the Department of Biology in central Copenhagen. The group is also part of an interdisciplinary and collaborative research environment at the Linderstrm-Lang Centre for Protein Science and you will have the chance to work with scientists from a number of disciplines. The group is highly international and a good level of spoken and written English is required.
We offer creative working conditions in dynamic and international research environment. Current members of the research group come from a broad range of scientific and personal backgrounds and we value collaborations and interdisciplinary work. We are strong proponents of open science.
Inquiries about the position can be made to Professor Kresten Lindorff-Larsen Department of Biology E-mail: lindorff@bio.ku.dk.
The Universitywishesour staff toreflect the diversity ofsociety and thus welcomes applications from all qualified candidates regardless of personal background.
Terms of employment
The position is covered by the Memorandum on Job Structure for Academic Staff.
Terms of appointment and payment accord to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State.
Negotiation for salary supplement is possible.
The application in English must be submitted electronically by clicking APPLY NOW (SG STILLINGEN) below. Only applications submitted via this system will be evaluated and you should not submit applications directly via e-mail.
Please include
- A motivated letter of application (max. one page) explaining your background key skills and how they are relevant to the research in DynaPLIX
- Curriculum vitae (max. two pages) including information about your education experience language skills and other skills relevant for the position
- Publication list including manuscripts available on pre-print servers. Please do not enclose copies of the papers
- Diplomas (Master and PhD degree or equivalent)
- If you do not yet hold your PhD degree and would like to apply please submit a letter from your supervisor regarding your expected hand-in and graduation dates
The deadline for applications is 1 August 2023 23:59 GMT +2.
After the expiry of the deadline for applications the authorized recruitment manager selects applicants for assessment on the advice of the Interview Committee.
You can read about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/.
Interviews with selected candidates are expected initially to be held online followed by in-house interviews on dates agreed upon with the candidate.
