Master 2
Practical construction of a multi-scale general description of biopolymers
Supervisor: Jean Cognet

Background: Our overall goal is to develop a new approach to interactive modeling and simulation of biopolymers (Proteins and Nucleic Acids, DNA and RNA).

A very effective approach is to describe their conformations as a flexible beam, represented by a ribbon, by means of the nonlinear elasticity theory [Santini et al. 2009, Baouendi et al. 2012]. We now have a robust interactive analytical system capable of generating all the solutions to the problem of folding flexible beams [Ameline et al. 2017, 2018].

Another approach is to describe their conformations as kinematic chain trajectories (set of articulated rigid bars). We have shown that these two infinite descriptions, continuous (beam), and discrete (biopolymer chain), have the same geometric characteristics, which gives a means of equivalence between them.

Objectives of the internship: After having finalized the correspondences between these two descriptions, they will be applied to describe the main constitutive elements of the proteins: the different sheets β, the different α-helices, the main loops relying on a data-bank of protein loops (established by J. Chomilier, IMPMC - SU), and other motifs such as those of collagen, and more generally those of structural protein alphabets. These new descriptions may better reflect some ribosome proteins that are considered unstructured [Hountondji et al. 2017]. They will be applied also to two very well resolved nucleic acid loops [Santini et al. 2009, Baouendi et al. 2012] to characterize them mechanically (see references downloadable on this web site).

These modeling approaches open up new perspectives and are relevant for describing biopolymers at different scales, for splicing, assembling, and manipulating them interactively through molecular virtualization with haptic feedback.

Techniques used: Computer modeling with Mathematica, and molecular modeling platforms (Chimera, VMD, ...).

 Qualifications of the candidate: Master student of Physics or Engineering, a student engineer, wishing to explore a subject at the interface of mechanics and biophysics.

Related publications

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:https://doi.org/10.1063/1.4983570
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
Nucleic acid folding determined by mesoscale modeling and NMR spectroscopy: solution structure of d(GCGAAAGC) - J. Phys. Chem. B
G.P. Santini , J.A.H. Cognet , K.K. Singarapu , C. Hervé du Penhoat
  URL Full text PDF Bibtex doi:doi: 10.1021/jp8100656
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
Analytical expression of elastic rods at equilibrium under 3D strong anchoring boundary conditions - Journal of Computational Physics
O. Ameline , S. Haliyo , X. Huang , J.A.H. Cognet
  URL Full text PDF Bibtex doi://doi.org/10.1016/j.jcp.2018.07.021

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