Île-de-France

BiGR

Acronyme ou nom de la structure: 
Nom complet (en toutes lettres): 
Bioinformatics platform, Gustave Roussy
Adresse: 
Plateforme de bioinformatique BiGR UMS AMMICA INSERM US23 / CNRS UMS3655 PF de l'Institut Français de Bioinformatique (IFB) Bâtiment B2M - étage 1 - pièce 136 114, rue Édouard-Vaillant 94805 Villejuif Cedex - France
Téléphone: 
0142114112
SFBI: 
0

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
Téléphone: 
+33 (0)1 44 27 47 12
Fax: 
+33 (0)1 44 27 47 16
Description (English): 

Mesoscopic modelling of biopolymers

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
Plate-forme: 
0
SFBI: 
Membre de la SFBI
Adhésion morale: 
0

BIS

Acronyme ou nom de la structure: 
Nom complet (en toutes lettres): 
Unité de Bioinformatique Structurale
Adresse: 
Unité de Bioinformatique Structurale 25-28 Rue du Docteur Roux 75724 Paris cedex 15
SFBI: 
Membre de la SFBI

SMILE

Acronyme ou nom de la structure: 
Nom complet (en toutes lettres): 
Stochastic Models for the Inference of Life Evolution
Adresse: 
Stochastic Models for the Inference of Life Evolution CIRB - Collège de France 11 place Marcelin Berthelot 75005 Paris France
Téléphone: 
+33144271391
Plate-forme: 
0
SFBI: 
0
Adhésion morale: 
0

iSSB-MEGA

Acronyme ou nom de la structure: 
Nom complet (en toutes lettres): 
Modelling and Engineering Genome Architecture
Adresse: 
institute of Systems and Synthetic Biology University of Evry-Val-d'Essonne 5 rue Henri Desbruères Genopole Campus 1, Bât. 6 F-91030 ÉVRY CEDEX, FRANCE
English keywords: 
biological regulatory networks
SFBI: 
0
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