Dynamique Moléculaire

We study the structure, dynamics, and interactions of biological macromolecules using a range of molecular modeling tools, including structural bioinformatics and molecular simulations. We also develop our own  tools, both in the area of bioinformatics and in molecular simulations. Our ultimate goal is to better understand of the links between structure, interactions and, ultimately, biological functions at the molecular level. Our main activities focus on:

Biomembranes: structure, dynamics, and interactions

Biological membranes envelop and compartmentalize all living cells. Biomembranes are extremely dynamic entities at all levels – in fact the vast majority of them is liquid, in physiologically relevant states, which makes it very challenging to obtain structural information at high resolution with experimental techniques. We use molecular simulations at multiple levels, from quantum mechanics to all-atom and coarse-grained molecular dynamics simulations, to gain insight into membrane structure, dynamics, interactions, and transformations.

Protein-protein interactions

The main focus is on the prediction of protein-protein interactions (PPI), at the molecular level (assessment of docking methods) and at the cellular level (development of bioinformatics methods to predict PPI networks). The latter uses sequence similarity between a set of interacting proteins (reference PPI) and the proteins of the organism under scrutiny to infer interaction between its proteins.

Various proteins remodel the membranes of organelles involved in intracellular transport. Protein coats deform membranes to promote the budding of vesicles. Golgins, sort of molecular strings, tether vesicles to restrict their diffusion. Lipid transporters adjust the membrane composition. Although very different, most of these mechanisms are controlled by small G proteins of the Arf family and by the physical chemistry of membranes.

We study these mechanisms through molecular, cellular and in silico approaches. With original assays based on fluorescence and light scattering, we follow elementary reactions such as the assembly cycle of protein coats, the tethering of liposomes by a golgin or the transfer of lipids. With fluorescence light microscopy and electron microscopy, we visualize these events in cells and in reconstituted systems. With molecular dynamics, we describe at the atomic level how specific protein motifs sense the chemistry and curvature of lipid membranes.

Recent Findings:

- Intracellular transport of cholesterol through the counter exchange of a phosphoinositide and its hydrolysis.
- Phospholipids with omega 3 acyl chains boost membrane deformation and fission
- Atomic description of the packing of lipids in membranes of various curvature and composition

HELIQUEST: a bioinformatics tools to analyze amphipathic helices with specific properties and search for sequences with similar properties (amino-acid composition, hydrophobic moment...).