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Sugars such as glucose, fructose, mannose or galactose exist in different forms and are particularly difficult to discriminate. The high selectivity of a specific foldamer towards fructose thus seems to be a promising solution regarding such an issue. Designed from modular artificial strands and able to fold into well-defined conformations, foldamers may form cavities complementary to small molecules such as monosaccharides. The highly predictable structure of these artificial molecules is a clear advantage in creating new receptors.

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Chandramouli, N., Ferrand, Y., Lautrette, G., Kauffmann, B., Mackereth, C.D., Laguerre, M., Dubreuil, D., Huc, I. 2015. Iterative design of a helically folded aromatic oligoamide sequence for the selective encapsulation of fructose. Nat. Chem., dor:10.1038/nchem.219512.

A short commentary on the atomic complexity that forms the basis of functional interactions between proteins. In this case, the highlight is on the interaction between the splicing factors SUP-12 and ASD-1, and our data from the 2014  article in Nature Communcations.
Mackereth, C.D. 2014. Splicing factor SUP-12 and the molecular complexity of apparent cooperativity. Worm. 3:e991240
(open access)
Worm Worm

In collaboration with the team of Denis Dupuy we have looked into the atomic details of RNA-binding for the alternative splicing SUP-12. This protein helps to regulte muscle-specific alternative splicing in the worm Caenorhabditis elegans, and we have determined the structure of the RNA-binding domain bound to a high affinity ligand G-G-U-G-U-G-C, by using NMR spectroscopy.The atomic details were used to make mutations in fluorescent mini-gene reporters, in order to translate the in vitro findings to observations in live worms. We have also investigated the interaction of SUP-12 with another alternative splciing factor, ASD-1. We found that ASD-1 directly contacts SUP-12 on the RNA but does not increase its affinity for RNA.
Amrane, S., Rebora, K., Zniber, I., Dupuy, D., Mackereth, C.D. 2014. Backbone-independent nucleic acid binding by splicing factor SUP-12 reveals key aspects of molecular recognition. Nat. Commun. 5:4595. NatureCommunications

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Shape-shifting mechanism in the regulation of human genes

In order to create proteins, the protein-coding gene must be transcribed into RNA and in the so-called splicing process interrupting segments are removed to form the correct protein-building instructions. Along with scientists at the Helmholtz Zentrum München and the Technical University of Munich (TUM), the European Molecular Biology Laboratory (EMBL) in Heidelberg and the Centre for Genomic Regulation in Barcelona, we have now discovered how the human U2AF protein enables this process. The results have been published in the July 21 issue of Nature.

The genes in the human genome have a specific structure. Sections with relevant exons alternate with areas known as introns, which contain irrelevant information. In order for a protein to be created, the pre-messenger RNA (pre-mRNA) first has to be copied from the DNA. The copy is then spliced and the introns are removed, leaving only the mRNA; which consists solely of exons. For this purpose, the introns must be recognized and accurately excised. This process is also known as the central dogma of molecular biology: genetic information only flows in one direction: from the DNA to RNA to proteins.

Splicing requires the cooperation of different proteins, or splicing factors. One such splicing factor, U2AF, was examined in collaboration with German and Spanish scientists. It consists of two structural units and binds to the RNA close to the intron-exon interface. The spatial structure of the U2AF protein alternates between a closed and an open conformation. A matching RNA sequence in the intron causes the U2AF to favour an open conformation, which activates splicing and leads to the elimination of the intron. The intron’s RNA sequence determines how effectively this conformational change can be stabilized. This shift of balance between the closed and the open form of the U2AF protein occurs through a process of natural selection. we presume that similar shape-shifting mechanisms – balanced between a closed, inactive and an open, active conformation – play an important role in the regulation of many other signal pathways in the cell.

conformational selection

Mackereth, C.D., Madl, T., Bonnal, S., Simon, B., Zanier, K., Gasch, A., Rybin, V., Valcarcel, J., Sattler, M. 2011. Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF. Nature 475: 408-411. PubMed PDB PDB

Also reported in :
Le Quotidien du médecin

Structure_Cover_April_2011 We have recently investigated a tight heterodimer formed between two proteins from a yeast Saccharomyces cerevisiae complex involved in the 3' processing of pre-mRNA. The cleavage/polyadenylation factor IA (CF IA) complex is composed of four proteins (Clp1p, Pcf11p, Rna14p, Rna15p) that recognize RNA sequences adjacent to the cleavage site and recruit additional processing factors. We have solved the solution structure of the tether complex composed of the interacting regions between Rna14p and Rna15p. The C-terminal monkeytail domain from Rna14p and the hinge region from Rna15p display a coupled binding and folding mechanism, where both peptides are initially disordered. We have used the structure to understand the molecular basis of temperature-sensitive mutations and find that the main consequence is the loss of Rna15p (and its important RNA-binding domain) from CF IA. This tight association complex is not just important for yeast: conservation of interdomain residues reveals that the structural tethering is preserved in the homologous mammalian cleavage stimulation factor (CstF)-77 and CstF-64 proteins of the CstF complex.

Moreno-Morcillo, M., Minvielle-Sébastia, L., Fribourg, S., Mackereth, C.D. 2011. Locked tether formation by cooperative folding of Rna14p monkeytail and Rna15p hinge domains in the yeast CF IA complex. Structure. 19: 534-545. PubMed PDB

Joining the efforts of IECB colleague Sébastien Fribourg and his laboratory, we have helped to reveal the structure and dimerization of the N-terminal domain of Drosophila CstF-50. This small domain, composed of three alpha-helices, forms a homodimer both in the crystal structure and in solution. The protein is a component of the Cleavage Stimulation Factor (CstF), a complex that is a critical part of the pre-mRNA 3' processing machinery, and is required for accurate production of the mature mRNA poly(A) tail. CstF consists of the three subunits CstF-50, CstF-64 and CstF-77. Along with the dimerization of CstF-77, the dimer function of the domain strengthens an overall stoichiometry of two copies of each subunit in the complex, creating a hexameric CstF assembly.

Moreno-Morcillo, M., Minvielle-Sébastia, L., Mackereth, C., Fribourg, S. 2011. Hexameric architecture of CstF supported by CstF-50 homodimerization. RNA. 17: 412-418. [Open Access] PubMed PDB