Mots-Clés

modélisation moléculaire ARN simulations de dynamique moléculaire méthodes QM/MM données de réactivité chimique

Description

Context

The internship will be conducted in the STAV (Structure et traduction des ARN viraux) team of CiTCoM (UMR CNRS 8038, Université Paris Cité), a multidisciplinary unit with expertise in molecular modelling, biochemistry, organic chemistry, structural biology, and microbiology. 

The position is part of the four-year project MAGENTA (Modelling RNA structures usinG chEmical probiNg daTA) funded by ANR (Agence National de la Recherche) in the JCJC scheme. The objective of MAGENTA is twofold: first, to understand the chemical origin of SHAPE reactivity, and unveil the complex relationship between measured reactivities, local geometry of RNA, and its environment for free RNA molecules; secondly, to integrate this information into a newly developed theoretical and computational framework, to bias and predict RNA structures. The project is conducted in close collaboration with our experimental colleagues in the team who are expert in biochemical probing, like SHAPE.

Position and assignments

The M2 internship is related to the study of the relationship between the structure, flexibility, local geometry of RNA and the biochemical reactivity of nucleotides using molecular modelling. In particular, the research project aims to understand the impact of chemical probes on a set of RNA structures and determine their binding energy and chemical free energy using and developing innovative approaches. To do so, the chemical probes will be taken into account explicitly in the QM/MM simulations, as well the binding state and the approach of the probe to the RNA molecules. A set of suitable structural parameters describing the local geometry will be evaluated and put in relationship with SHAPE reactivity.

The M2 internship has to 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 softwares 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 2023/2024 M2 courses (January/February 2024). The intern will also have the possibility to apply to the doctoral school competition.