Sujet de stage / Master 2 Internship

Our objective is to develop a new methodology based on the combination of neutron and X-ray small-angle scattering (SANS/SAXS) experiments and ab initio modeling (coarse grain/all atom) allowing (i) to obtain low-resolution structural information of membrane proteins of unknown structure or of known structure but misfolded; (ii) to describe the structure of the amphiphiles associated with these proteins (belts of detergents and/or lipids).

Determining the structure of membrane proteins at the atomic scale is a challenge in structural biology because of the need to use amphiphiles to solubilize and manipulate them in vitro. Only 3% of entries in the “Protein Data Bank” (PDB) relate to membrane proteins, even though they represent 30% of proteins and constitute almost 60% of therapeutic targets.
Our objective is to develop a new methodology based on the combination of neutron and X-ray small-angle scattering (SANS/SAXS) experiments and ab initio modeling (coarse grain/all atom) allowing (i) to obtain low-resolution structural information of membrane proteins of unknown structure or of known structure but misfolded; (ii) to describe the structure of the amphiphiles associated with these proteins (belts of detergents and/or lipids).
We study the mouse protein TSPO (for TranSlocator PrOtein) (mTSPO), a transmembrane protein of major pharmacological interest: TSPO is a target for the diagnosis and therapy of several inflammatory and cancerous pathologies and a marker of neurodegenerative diseases.
SANS measurements make it possible to specifically characterize the structure of the mTSPO protein by making the signal of the belt "invisible", thanks to isotopic substitutions. A first objective of this M2 training is to obtain from these measurements the low resolution structure of mTSPO with ab initio Monte Carlo reconstruction methods. A second objective is to make the “PDB” file (structural data) of the envelope obtained by SANS readable by the MEMPROT software. This software, which makes it possible to determine the shape of the belt associated with a membrane protein, currently only works from a PDB file originating from X-ray crystallography measurements. This step will require modifying the code of the MEMPROT software and envelope files obtained by SANS.

A third objective is to use the same approach in the case of a partially unfolded membrane protein. In this case, the DADIMODO software, initially planned for SAXS and allowing large displacements of parts of a protein, will also be adapted to modify the structure of the protein from the adjustment of a SANS curve. Depending on the progress of the training, molecular dynamics simulations (classic or interactive) may complete this study, using the envelopes of SANS/SAXS as spatial constraints.

Profiles: student in bioinformatics knowing how to code in Python and strongly interested in the structural biology of proteins. Good level of English required.

This training will be based at LLB (Univ. Paris-Saclay) and will be co-supervised by S. Combet (LLB) for the scattering part and A. Koutsioumpas (neutron source, Munich, Germany) for the modeling part. It will be produced in close collaboration with F. Bonneté (IBPC, Paris), JJ. Lacapère (LBM, Paris), and S. Finet (IMPMC, Paris) experts in surfactants and the TSPO protein, as well as with J. Pérez and A. Thureau (SOLEIL synchrotron, St-Aubin) who developed the MEMPROT and DADIMODO softwares.

Contact : Sophie COMBET (CNRS Research Director) 01 69 08 67 20
sophie.combet@cea.fr