Université Pierre et Marie Curie - Paris 6

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

ARTbio

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Accessible, Reproducible & Transparent Bioinformatics
Adresse

75005 Paris
France

Téléphone
+33144277005
English keywords
Galaxy, RNA-seq, single cell RNAseq, small RNAs, virus metagenomics, continuous integration, cloud computing
SFBI
Membre de la SFBI

LPMA-PSB

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Laboratoire de Probabilités et Modèles Aléatoires - Equipe Probabilités, Statistiques et Biologie
Adresse

Université Pierre et Marie Curie
Case courrier 188
4 place Jussieu

75252 PARIS Cedex 05, FRANCE
France

Description (English)

PSB gathers probabilists and statisticians of LPMA interested in mathematical problems inspired by biology or/and applying mathematics to biological problems.

English keywords
Ecology, Evolution, Genomics, Neurosciences
SFBI
Membre de la SFBI

GENOPHY

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Genomique Evolutive et Environnementale du Phytoplancton
Adresse

France

SFBI
N'est pas membre de la SFBI

ABI

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

75005 Paris
France

Téléphone
01 40 79 48 09
English keywords
bioinformatics, structural bioinformatics, génomic analysis, population genetics
SFBI
Membre de la SFBI