Mots-Clés
computational chemistry
bioinformatics
molecular modelling software
protein-RNA complex
RNA modifications
Description
Context
The internship will be conducted in the STAV (Structure and Translation of Viral RNAs) team of CiTCoM (UMR CNRS 8038, Université Paris Cité UPC), a multidisciplinary unit with expertise in molecular modelling, biochemistry, organic chemistry, structural biology, and microbiology. One of the team research axes is dedicated to RNA functional modifications from experimental to computational point of view. For this reason, for example we have been investigated several RNA methyltransferases (MTases) enzymes in the last years, including METTL3-14, METTL16, with the aim to develop new inhibitors. It is important to point out that RNA modifications are notably involved in cancer progression as well as viral infection but also are important in conceiving vaccines. From the computational point of view, we have tackled this complex problem by using a large variety of approaches including molecular dynamics simulations and quantum mechanics/molecular mechanics calculations. The project will be conducted in close collaboration with our experimental colleagues in the team who are expert in biochemistry and biology, as well as our collaborators at UPCité.
Position and assignments
The M2 internship is related to the study how RNA modifications impact the RNA structure and/or protein-RNA interactions and the enzyme activities. In this context, one of our strategies is to develop new specific small molecules to target the RNA MTases. To do so, docking calculations and standard and advanced all-atom MD simulations will be performed. To study the reactivity, preliminary QM/MM calculations will be conducted. Statistical and bioinformatics analyses will be performed by using standard tools and by developing new scripts.
The M2 internship should be considered as an initiation into theoretical and computational methods spanning from simple QM calculations to standard and advanced all-atom molecular dynamics simulations using a variety of molecular modelling software and visualisation tools. Moreover, the intern will have the opportunity to learn about bash script coding, python, Matlab, High Performance Computing and to perform bibliographic research.
The internship will start at the beginning of the second semester of 2025/2026 M2 courses (January/February 2026). The intern will also have the possibility to apply to the doctoral school competition.