Postdoctoral position, Integrative Molecular Dynamics Simulations, University of Lyon, France (Deadline: 15.05.2025)

Job description

A postdoctoral position is available in the group “Biophysics of complex systems” (see http://olivier-walker.univ-lyon1.fr or http://olivier-walker.univ-lyon1.fr ) in Lyon (France) to work on integrative molecular dynamics simulations to elucidate the mechanism of protein folding upon metal binding in the context of bacterial resistance. Indeed, interaction with metal cations can shape the conformational landscapes of proteins in several ways. Metals can promote protein unfolding, misfolding or aggregation, which may lead to neurodegenerative disorders. Conversely, metals at an optimum concentration are essential for proteins and more than 30 % of proteins employ one or more metals to achieve their function. Metals can be involved at different stages of folding and can help maintain the 3D structure of proteins. Recent research by our group has showed that the bacterial intrinsically disordered protein SilE locally folds into α-helices upon binding of silver cations Ag+.
The goal of this post-doctoral project is to combine biophysical data with molecular dynamics simulations to describe the conformational ensemble of SilE and how it is shaped by silver, paying particular attention to the interplay between metal interaction and SilE folding. To address these, we propose to use enhanced sampling simulation methods such as well-tempered metadynamics in combination with integrative modelling methods to guide the simulations with the available experimental data. In parallel, QM/MM methods will be used to accurately describe the binding of silver ions to SilE.

Desired skills and experience

The successful candidate should hold a PhD in Physics, biophysics or physical chemistry and must have an expertise in biased molecular dynamics. Experience with NMR and SAXS data is also an advantage (skills in biophysics with knowledge in some scripting and/or programing languages e.g. bash, python, C, C++). Funding is available for one year. The contract must start no later than 1st of June 2025. Interested candidates should send a CV, a cover letter and the contact information of at least one reference to Olivier Walker (olivier.walker@univ-lyon1.fr).

About the employer

The Biosys group makes use of biochemistry, NMR, SAXS and computational methods to explore bimolecular interactions and flexibility/plasticity of multidomain proteins as well as metalloproteins. The “Institut des Sciences Analytiques” is a brand-new institute (opened in November 2012) which carry out cutting edge science with over 200 researchers. The successful candidate will benefit from several GPU based computers additional to national HPC infrastructures.

Location

Lyon is the 3rd most populated city of France https://traveltrade.lyon-france.com/en/discover-lyon. This charming city is located south east of France and has more than 2000 years of history. One can enjoy a huge number of cultural and entertaining events as well as gastronomy and fine dining. Lyon is located close to the Alps, making it the perfect spot to enjoy ski (1 hour from the first ski resorts), as well as the Mediterranean Sea (1.5 hours by train).

References

Babel, L., et al., Chem comm 2021, 57 (70), 8726-8729, https://dx.doi.org/10.1039/d1cc02597j
Arrault, C., et al., J Biol Chem 2023, 299 (8), https://doi.org/10.1016/j.jbc.2023.105004
Monneau, Y., et al., Phys Chem Chem Phys 2023, 25 (4), 3061-3071, https://dx.doi.org/10.1039/d2cp04206a