NMR of biomolecules

Group leaders: Karine LOTH & Agnès DELMAS

The research activities of the NMR group focus on the determination of the 3D solution structures of biomolecules from NMR data. While a wide range of biological questions are addressed, the constant objective in all these studies is to establish relationships between the biomolecules NMR 3D structures and their biological functions.
Most of the time structural studies involve studying the interactions with other biological molecules (DNA-protein, protein-peptide or protein-ligand complexes), and the dynamics in the free or bound form.
Up to now, NMR has been the main technique used to develop our research projects, combined with molecular modelling and docking techniques.

I. Small cystein-rich defense proteins

Our biological research theme concentrates on small cystein-rich defense proteins. The aim is to advance our understanding of the mechanism of action at the atomic level. It will lead us to study complex systems by liquid NMR and to closely associate a series of complementary biophysical or biological techniques.

Two families of small cystein-rich defense proteins are studied: Antimicrobial proteins and entomotoxins, adopting different 3D folds and different disulfide bridges arrays. Many of these molecules are now obtained by chemical synthesis in close collaboration with A. Delmas’ group.

3 levels are explored:
- Studying new molecules with therapeutic/agronomic interest
- Exploring other biological functions
- Understanding the mechanism of action at the atomic level

II. methodological expertise: nmr, modelling and docking

In order to respond to the variety of questions addressed by our biologist collaborators, we carry on a series of more methodological NMR projects. The defense proteins projects and these methodological expertises are mutually supportive, and are inseparable.

Ex1 : The folding dynamics of the dimeric
protein HU involved in the cold response.

rmn_structure_3d_dimere_proteine_hu_1_pour_internet.gif
Structure 3D du dimère de la protéine HU de E. Coli (Le Meur et al. En prep)

Ex2 : MC1 is a small architectural protein
from Methanosarcina which curves and
compacts the DNA of these Archaea.

rmn_modele_complexe_mc1_adn_courbe_pour_internet.gif
Modèle du complexe entre MC1 et l’ADN courbé (Paquet et al . 2014)

III.Métabolomic

A very recent development of our research concerns the metabolomic approach of various pathologies (phenylketonuria, Huntington's disease, glioma). We seek to identify characteristic metabolites to better understand their pathways of biosynthesis and degradation and possibly develop new therapeutic strategies.

NMR spectrometers
Techniques in few words
Software

significant publications :

  • Paquet, F., Delalande, O., Goffinont, S., Culard, F., Loth, K., Asseline, U., Castaing, B., and Landon, C.Model of a DNA-protein Complex of the Architectural Monomeric Protein MC1 from Euryarchea.PlosOne (2014) 9, e88809
  • Hervé-Grepinet, V., Meudal, H., Labas, V., Réhault-Godbert, S., Gautron, J., Berges, M., Guyot, N., Delmas, A. F., Nys, Y., and Landon, C.3D NMR structure of hen egg gallin (chicken ovo-defensin) reveals a new variation of the beta-defensin fold.J. Biol. Chem. (2014) 289, 7211-20
  • Senille, V., Lelievre, D., Paquet, F., Garnier, N., Lamb, N., Legrand, A., Delmas, A. F., and Landon, C.The addressing fragment of mitogaligin : first insights into functional and structural properties.Chembiochem : a European journal of chemical biology (2013) 14, 711-720
  • Derache, C., Meudal, H., Aucagne, V., Kevin, M., Cadène, M., Delmas, A. F., Lalmanach, A.-C., and Landon, C.Initial insights into the structure-activity relationships of avian β-defensins.J. Biol. Chem. (2012) 287, 7746-7755
  • Tavel, L., Jacquillard, L., Karsisiotis, A.I., Saab, F., Jouvensal, L., Brans, A., Delmas, A., Schoentgen, F., Cadène, M., and Damblon, C.Ligand binding studies of human PEBP1/RKIP : interaction with nucleotides and Raf-1 peptides evidenced by NMR and mass spectrometry.PloS One (2012) 7, e36187
Publications