Modélisation Moléculaire

BF2I

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Atelier de Bioinformatique
Adresse

INSA Bâtiment Louis Pasteur
20 avenue Albert Einstein

69621 Villeurbanne cedex
France

Téléphone
+33 (0)4 72 43 83 56
Fax
+33 (0)4 72 43 85 34
Description (English)

Research at BF2I is focused on the comprehension of the functions managing the interaction of specific insect pests (aphids and weevils) with their direct biological partners (host plants and symbiotic microorganisms). Research approaches are multi-disciplinary thanks to the different expertise of the staff members.

The central theme of our research is to understand the relationships established between insects and their symbionts elucidating the molecular mechanisms that allow the establishment, maintenance and persistence of these complex interactions in multiple insect generations.

The final goal of research on these complex biological interactions, often involving multiple partners in interaction with the environment, is to identify tools and define new concepts for an integrated approach for plant protection against insect pests. Our research results are to be central for the development of agricultural practices that are sustainable, and respect both the environment and human health.

English keywords
symbiosis, insect pests, functional genomics, systems biology
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Membre de la SFBI

M3

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Modélisation Moléculaire Mésoscopique
Adresse

Laboratoire Jean Perrin
Université Paris 6 CNRS UMR 8237
4 place Jussieu T32-33 4e, Case Courrier 114

75252 PARIS Cedex 05, France
France

Téléphone
+33 (0)1 44 27 47 12
Fax
+33 (0)1 44 27 47 16
Description (English)
Mesoscopic modelling of biopolymersMembers: Jean CognetOlivier Ameline.

Our objective is to develop a tool of modelling and simulation of nucleic acids (NA). The proposed approach consists in describing the conformation as a flexible beam, represented by a ribbon, by means of the theory of non-linear elasticity of beams.

The determination of the conformation of NA (DNA or RNA) is a challenge as great as that put by the conformation of proteins. Indeed, the current knowledge of the detailed conformations of NA is very low (5-10 % of the Protein Data Bank, PDB, the bank of all the known conformations of biological macromolecules). Nevertheless since 2000, we admit that the conformation of NA could be as rich and varied as that of the proteins, and that the part of the genome transcribed in ARN is of an order of magnitude greater than that of the proteins. Therefore, the conformational wealth of NA and the low level of current knowledge make difficult the bioinformatic approach, which consists in deducing a conformation from those already known. That is why the physical modelling of biomolecules is very important for NA and one of the major objectives of research in molecular modelling is the treatment of the various scales, atomic and mesoscopic (residues, several nucléotides) in a coherent and physical way.

We developed an approach of molecular modelling called Biopolymer Chain Elasticity (BCE). It is based on the observation that the sugar-phosphate chain of NA behaves at mesoscopic scales as a flexible beam. We recently finalized a protocol for the resolution of the conformation of DNA hairpins [1] (cf. banner above), with which we solved the structure of an aptamer anti-MUC1 [2] (cf. figure 1). The results are remarkable because the conformations correspond at the same time to a minimum at different scales : global, intermediate, and local, i.e. an energy minimum on the scale of the loop of several nucleotides, of the individual nucleotides in the loop, and atomic bonds [1, 2]. Our objective is to generalize this methodology for the hierarchical modelling of NA chains by using the theory of the non-linear elasticity of beams. We approach the problem on two scales: (I) that of the skeleton treated as a geometrical and mechanical object, and (II) that of the side chains, considered as stiff objects articulated around their attachment point onto the skeleton. From then on, a tool of simulation containing real active ribbons for the resolution of macromolecules is possible.

 

English keywords
Mesoscopic modelling of biopolymers
SFBI
Membre de la SFBI

MOBI

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Modeling Biological macromolecules
Adresse

France

Description (English)

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.

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N'est pas membre de la SFBI

DMMP

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Dynamique des membranes et manteaux protéiques
Adresse

Institut de Pharmacologie Moléculaire et Cellulaire (IPMC)
660 Route des Lucioles
SOPHIA ANTIPOLIS

06560 VALBONNE
France

Téléphone
04 93 95 77 69
Fax
04 93 95 77 08
Description (English)

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...).

SFBI
Membre de la SFBI

MTi

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Molécules à vocation Thérapeutique par approches In silico
Adresse

INSERM UMR-S 973
35 rue H. Brion

75205 Paris Cedex 13
France

English keywords
Structural bioinformatics, chemoinformatics, in silico screening, molecular modeling, peptide and protein structure
SFBI
Membre de la SFBI

DSIMB

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Dynamique des Structures et Interactions des Macromolécules Biologiques
Adresse

DSIMB,  INSERM UMR-S 665,
Universite Paris Diderot - Paris 7,
INTS,
6, rue Alexandre Cabanel

75739 Paris Cedex 15, France
France

English keywords
Bioinformatics, Molecular Modeling, Molecular Dynamics, Functional Genomics, Nucleic Acid Structure, Protein Structure
SFBI
Membre de la SFBI