75724 Paris cedex 15
75724 Paris cedex 15
75724 Paris cedex 15
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.
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.
34396 MONTPELLIER cedex 5 FRANCE
IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org, is the global reference in immunogenetics and immunoinformatics, created in 1989 by Marie-Paule Lefranc (Université Montpellier 2 and CNRS). IMGT® is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MH superfamily (MhSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates. IMGT® provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT® works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT® consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools.
Institut de Pharmacologie Moléculaire et Cellulaire (IPMC)
660 Route des Lucioles
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.
- 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...).
Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT)
Chemin de Borde Rouge
31326 CASTANET-TOLOSAN cedex
The team develops mathematical, statistical and computational methods to address life science research problems. These methods are usually directly made available to biologists through dedicated software.
Bioinformatics problems addressed
The topics addressed in the team concern the localization and identification of functional elements in bacterial, plant and animal genomes. Three investigation levels are considered.
To go beyond the localization of isolated functional elements, we are are now increasingly interested in approaches aiming at the inference of gene regulatory networks. We are currently studying the simultaneous analysis of expression data and polymorphism data (such as SNP) on a collection of individuals. This allows to observe different perturbated modes of operation of the network to better infer gene network structures.
UMR CNRS 6214 - INSERM 1083
3 rue Roger Amsler
INSERM UMR-S 973
35 rue H. Brion
75205 Paris Cedex 13