Mesoscopic modelling of biopolymers

The team of Mesoscopic Modeling of Biopolymers of the Jean Perrin Laboratory studies research topics related to structural modelling, bioinformatics or kinetics of molecules. We can classify in two types of activity:

Biology and modelling in collaboration

The first type of activity concerns biological subjects in collaboration with local or external teams for whom the molecules play a very important, but complex and poorly identified role. Here we present four very different examples that have given rise to publications:

The ribosome is not a ribozyme

The problematic of this subject under study is the assembly core of the peptide chain in the ribosome: in prokaryotes with bL12 (E. coli), and in eukaryotes with eL42 (Schizosaccharomyces pombe).

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The ribosome is an extraordinary complex assembly of RNA and proteins capable of translating a messenger RNA sequence into a protein chain. In 2009, the Nobel Prize in Chemistry rewarded the magnificent resolutions of the ribosome structure at the atomic scale. Catalysis of peptide chain formation must take place not far from the aminoacyl-tRNA and the peptide chain exit tunnel, i.e., in a region called Peptidyl Transferase Center (PTC). Since the closest proteins are 18 Å of the PTC, an important assumption was that the ribosome is a ribozyme, that is, an enzyme catalyzed by RNA and not by one or more proteins. However, this widespread hypothesis could not be verified experimentally. This is a very important problem because the ribosome is the target of more than 50% of known antibacterial drugs and is also an important target for cancer treatment.

Highlights

C. Hountondji used the dialdehyde derivative of tRNA (tRNAox) to transform the CCA arm of tRNA into a ribosomal protein affinity tag. It is an exceptional affinity marker for many reasons: (i) the conversion of the 2', 3'-cis diol group to the 2', 3'-aldehyde diol at the 3'-terminal ribose of tRNA represents a slight modification that does not affect the affinity of tRNA for its protein partners; (ii) the aldehyde groups quantitatively form a covalent bond with the amino groups of the side chains of lysyl or arginyl residues; (iii) the formation of a covalent protein-ARNtox complex is a zero-distance labeling reaction unlike the majority of reactive tRNA analogs; (iv) the crosslinking reaction at tRNA stoichiometry: protein (1: 1), (v) the pK of the reacting amino acid side chain can be measured by monitoring the covalent reaction as a function of pH. This remarkable affinity tag shows that yeast E. coli and eL42 ribosomal proteins L7L12 contribute to the catalytic activity of the ribosome at PTC. More generally, these proteins and the PTC have been examined with methods of genetics, sequence alignments, molecular biology, mass spectroscopy, data analysis, and different modellings.

Specific inhibitor of STAT3

Different specific properties of very similar DNA sequences are exploited to design STAT3 and not STAT1 inhibitors:

The aim was to design oligonucleotide sequences that could block STAT3 (Signal Transducer and Activator of Transcription 3) and thus induce cell death, and that do not interact with STAT1, which is essential, whereas their recognition sites are very similar. We have succeeded in designing these inhibitory oligonucleotides by taking advantage of the global and local properties of the DNA sequences to be recognized.

Photochimical properties of DNA sequences

UV irradiation at 254 nm of sequences with two adjacent thymines stacked in a double strand of DNA results in the formation of photoproducts responsible for cell death and skin cancer. The detailed examination of the molecular dynamics makes it possible to understand how different molecules can nevertheless have very similar photoproduct distributions, because, even if the geometries of these molecules are different, the stacking geometries remain similar.

Two strategies or RNA resistance

PCR analysis linked to RNA and DNA sequences:

The use of a SELEX method to look for resistant RNA sequences at high saline concentrations (2M NaCl) at the temperature of 80°C for 65 h has led to the demonstration of two very different families I and II. I is much more resistant to thermal degradation than II, while II is replicated much more efficiently. The detailed study of PCR shows that the behavior of RT-PCRs are very different for these two families of sequences, especially when extremely low concentrations of molecules are amplified.

The « rubAN » project : nucleic acids ribbon

The second type of activity concerns the project "rubAN" - Nucleic Acid ribbon -, which we have set up with Sinan HALIYO (ISIR-UMR 7222, Interaction team) in nanorobotics, and Sébastien NEUKIRCH (Modelling and Engineering of Solids and Structures - UMR 7190).

This project was started in 2014, and aims to robustly calculate real DNA or RNA ribbons for interactive molecular modelling at different scales. It represents a major reorientation of our previous research on biopolymers [Baouendi et al. 2012, and Santini et al. 2009] to mechanics and to the theory of elasticity of beams. It is at the origin of the thesis of Olivier Ameline (Grant "Interface For the Living" - IPV 2014-2017). Olivier Ameline has classified for the first time all the possible conformations of the solid forms of elastic beams in a half-dimensional space, and has highlighted 3 types of chirality. From this fundamental study, he was able to establish a protocol and write a computer program to solve the problem of calculating ribbons from embedding constraints [Ameline et al. 2017, 2018].

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We have developed a molecular modelling approach called Biopolymer Chain Elasticity (BCE): it is based on the observation that the sugar-phosphate chain of ANs behaves at mesoscopic scales like a flexible beam. We have developed a protocol for the resolution of DNA hairpin structure [cf. header of http://www.labos.upmc.fr/ljp/?article12], with which we have solved the structure of an anti-MUC1 aptamer [Baouendi et al. 2012]. The results are remarkable because the conformations correspond to a global, intermediate, and local minimum, i.e. a minimum at the loop level of several nucleotides, the nucleotide in the loop, and the atomic bond [Baouendi et al. 2012, Santini et al. 2009].

Project

Our general objective is to develop an innovative model for biopolymers, nucleic acids (NA) and proteins, where the macromolecular chain is represented by an elastic beam with large deformations. This model is inspired by the ribbons, commonly used in biology to identify the geometric structure of a macromolecule. By superimposing an elastic beam on these ribbons, and using the theory of the nonlinear elasticity of the beams, we wish to use them not only to visualize the molecule, but also to describe their geometric, physical and mechanical properties. We approach the problem on two scales: (I) that of the skeleton treated as a geometric and mechanical object, and (II) that of the side chains, considered as rigid objects articulated around their point of attachment to the skeleton. Therefore, a simulation tool including real active ribbons for the resolution of macromolecules is conceivable.

Members

Staff scientists

Publications liées

The ribosome is not a ribozyme

« Affinity labeling in situ of the bL12 protein on E. coli 70S ribosomes by means of a tRNA dialdehyde derivative. » C. Hountondji et al., J. Biochem. (2017) 163, 437-448.

« Ribosomal protein eL42 contributes to the catalytic activity of the yeast ribosome at the elongation step of translation. » C. Hountondji et al., Biochimie (2018)

STAT3

 « A STAT3-inhibitory hairpin decoy oligodeoxynucleotide discriminates between STAT1 and STAT3 and induces death in a human colon carcinoma cell line.» Souissi et al.Molecular Cancer (2012) 11:12

Photochimical properties of DNA sequences

« Dinucleotide TpT and its 2'-O-Me analogue possess different backbone conformations and flexibilities but similar stacked geometries. » Santini et al., J. Phys. Chem. B (2007) 1119400-9409.

Two strategies or RNA resistance

« In vitro selection of halo-thermophilic RNA reveals two families of resistant RNA. » Vergne et al.Gene (2006) 371, 182–193.

The « rubAN » project : nucleic acids ribbon

« Solution structure of a truncated anti-MUC1 DNA aptamer determined by mesoscale modeling and NMR », Baouendi et al., The FEBS Journal (2012) 279, 479-490,

Nucleic acid folding determined by mesoscale modeling and NMR spectroscopy: solution structure of d(GCGAAAGC), Santini et al., J. Phys. Chem. B (2009), 113, 6881-6893.

Classifications of ideal 3D elastica shapes at equilibrium, O. Ameline, S. Haliyo, X. Huang, J.A.H. Cognet, J. Maths Phys. (2017) 58, 062902, 1-27,11,5.

Analytical expression of elastic rods at equilibrium under 3D strong anchoring boundary conditions, O. Ameline, S. Haliyo, X. Huang, J.A.H. CognetJournal of Computational Physics (2018) 373, 736-749.