Research  >  Mesoscopic modelling of biopolymers

Mesoscopic modelling of biopolymers

Members: Jean Cognet.

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.

Figure 12D and 3D representations of a hairpin oligonucleotide from NMR data and/or from BCE constructions.

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Affinity labelling in situ of the bL12 protein on E. coli 70S ribosomes by means of a tRNA dialdehyde derivative - J. Biochem.
C. Hountondji , J.B. Crechet , J.P. Le Caër , V. Lancelot , J.A.H. Cognet , S. Baouz
  URL Full text PDF Bibtex doi:doi:10.1093/jb/mvx055
Classifications of ideal 3D elastica shapes at equilibrium - J. Maths Phys.
O. Ameline , S. Haliyo , X. Huang , J.A.H. Cognet
  URL Full text PDF Bibtex doi:


Solution structure of a truncated anti-MUC1 DNA aptamer determined by mesoscale modeling and NMR - The FEBS Journal
M. Baouendi, , J.A.H. Cognet , C.S. Ferrriera , S. Missailidis , J. Coutant , M. Piotto , E. Hantz, , C. Hervé du Penhoat,
  URL Full text PDF Bibtex doi:doi:10.1111/j.1742-4658.2011.08440.x