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Integrative Biological NMR

Andrew Atkinson & Olivier Saurel

Group Leaders

Our research focuses on the development of NMR and MD methods and their applications in structural biology and to the biophysics of membranes. We characterize pathogen-derived lipids and study their effects on pathogen or host membranes, and analyze intermolecular processes involving membrane proteins (ligand-receptor, metal transport), with a particular focus on mycobacterial infection.

The Integrative Biological NMR group applies its expertise and state-of-the-art equipment to pursue ambitious projects in structural biology with important implications in pharmacology. The structure, dynamics and interactions of biomolecules are the three pillars for elucidating biochemical processes at atomic resolution. NMR combined with MD simulations is ideally suited to the study of such processes. We continuously explore new avenues, such as the structure and function of complex membrane assemblies, and the influence of macromolecular dynamics on interactions, in the context of bacterial infection.

 

Structure, dynamics, and interactions of macromolecules, with a focus on membrane proteins.
In recent years, we have characterized the internal dynamics of OmpA from Klebsiella pneumoniae in liposomes using fast-MAS solid state NMR (2017, JACS). In the high impact field of G protein-coupled receptors (GPCRs), we determined the structures and characterized the dynamics of dynorphin and ghrelin agonists bound to KOR and GHSR receptors, respectively (2015, 2019, PNAS).

Our current research focuses on understanding key molecular processes involved in Mycobacterium tuberculosis (Mtb) infection and the defence mechanisms developed by Mtb in macrophages. Host membrane proteins include receptors for which ligand binding at the cell surface leads to activation of intracellular signaling pathways. We are currently studying the human C-lectin Mincle to understand its interactions with glycolipids from Mtb that contribute to mycobacterial virulence and stimulate the host immune system.

The transmembrane signaling mechanisms are poorly understood but are thought to involve interactions with the FcRgamma receptor. We are seeking to characterize these interactions experimentally and using MD simulations.
Human macrophages respond to Mtb infection by raising the concentration of zinc ions to levels that are toxic to the mycobacterium. To counteract this response, mycobacterial metallochaperones coupled to metal efflux pumps of the P-type ATPase superfamily of membrane-bound proteins act to reduce the metal ion concentration. We are studying the molecular mechanisms involved in the interaction of the metallochaperone Zmc with the P-type ATPase CtpC (collaboration with O. Neyrolles, IPBS).


Biophysics of membranes, with a focus on the Mtb envelope.

Mycobacterial lipids constitute the building blocks of the extremely thick mycobacterial envelope which constitutes a diffusion barrier to drugs, thus contributing to Mtb persistence. In addition to binding to host receptors such as Mincle, they also serve as virulence factors acting on the host membrane, causing damage and modulating the immune response. We are investigating the structure and dynamic of these lipids (e.g. DIM, 2019 PNAS) by solid-state NMR and MD simulations to decipher their role in Mtb infection.

 

 

Macromolecular interactions by NMR : Solution structure of the THAP zinc finger of THAP1 in complex with its DNA target (PDB entry 2KO0).

© Olivier Saurel
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Main Publications

Ferré et al. (2019) Structure and dynamics of G protein-coupled receptor-bound ghrelin reveal the critical role of the octanoyl chain. Proc Natl Acad Sci USA

 

Augenstreich et al. (2019) The conical shape of DIM lipids promotes Mycobacterium tuberculosis infection of macrophages. Proc Natl Acad Sci USA

 

Gervais et al. (2018) Small molecule-based targeting of TTD-A dimerization to control TFIIH transcriptional activity represents a potential strategy for anticancer therapy. J Biol Chem

 

Saurel et al. (2017) Local and global dynamics in Klebsiella pneumoniae Outer membrane protein A in lipid bilayers probed at atomic resolution. J Am Chem Soc

 

Carrel et al. (2017) Identification of specific posttranslational O-mycoloylations mediating protein targeting to the mycomembrane. Proc Natl Acad Sci USA

 

Cukier et al. (2017) NMR secondary structure and interactions of recombinant human MOZART1 protein, a component of the gamma-tubulin complex. Protein Sci

 

Menchon et al. (2016) Structure-based virtual ligand screening on the XRCC4/DNA ligase IV interface. Sci Rep

 

O’Connor et al. (2015) NMR structure and dynamics of the agonist dynorphin peptide bound to the human kappa opioid receptor. Proc Natl Acad Sci USA

 

Scientists

Andrew Atkinson

CNRS Senior Research Associate

Alain Milon

Professor - University of Toulouse

Georges Czaplicki

Professor - University of Toulouse

Pascal Demange

CNRS Research director

Matthieu Chavent

CNRS Research associate

Evert Haanappel

CNRS Research associate

Isabelle Muller

Associate Professor - University of Toulouse

Valerie Réat

CNRS Research associate

Olivier Saurel

CNRS Engineer

Research Assistants

Nathalie Doncescu

CNRS Engineer

Pascal Ramos

University of Toulouse Engineer

Olivier Saurel

CNRS Engineer

PhD students

Guillaume Ferre

2018

  • Drozdz, W., Walczak, A., Bessin, Y., Gervais, V., Cao, X. Y., Lehn, J. M., Ulrich, S., and Stefankiewicz, A. R. (2018) Multivalent metallosupramolecular assemblies as effective DNA binding agents, Chemistry.
  • Drozdz, W., Bessin, Y., Gervais, V., Cao, X. Y., Lehn, J. M., Stefankiewicz, A. R., and Ulrich, S. (2018) Switching Multivalent DNA Complexation using Metal-Controlled Cationic Supramolecular Self-Assemblies, Chemistry 24, 1518-1521.

2017

  • Duncan, A. L., Reddy, T., Koldso, H., Helie, J., Fowler, P. W., Chavent, M., and Sansom, M. S. P. (2017) Protein crowding and lipid complexity influence the nanoscale dynamic organization of ion channels in cell membranes, Sci Rep-Uk 7.
  • Cukier, C. D., Tourdes, A., El-Mazouni, D., Guillet, V., Nomme, J., Mourey, L., Milon, A., Merdes, A., and Gervais, V. (2017) NMR secondary structure and interactions of recombinant human MOZART1 protein, a component of the gamma-tubulin complex, Protein Sci 26, 2240-2248.
  • Carel, C., Marcoux, J., Reat, V., Parra, J., Latge, G., Laval, F., Demange, P., Burlet-Schiltz, O., Milon, A., Daffe, M., Tropis, M. G., and Renault, M. A. M. (2017) Identification of specific posttranslational O-mycoloylations mediating protein targeting to the mycomembrane, Proc. Natl. Acad. Sci. USA 114, 4231-4236.
  • Saurel, O., Iordanov, I., Nars, G., Demange, P., Le Marchand, T., Andreas, L. B., Pintacuda, G., and Milon, A., Local and Global Dynamics in Klebsiella pneumoniae Outer Membrane Protein a in Lipid Bilayers Probed at Atomic Resolution, J.A.C.S. 139, 1590-1597 (2017).

2016

  • Menchon, G., Bombarde, O., Trivedi, M., Negrel, A., Inard, C., Giudetti, B., Baltas, M., Milon, A., Modesti, M., Czaplicki, G., and Calsou, P. (2016) Structure-Based Virtual Ligand Screening on the XRCC4/DNA Ligase IV Interface, Sci. Rep. 6, 22878 (2016).
  • Hemmann, J. L., Saurel, O., Ochsner, A. M., Stodden, B. K., Kiefer, P., Milon, A., and Vorholt, J. A., The One-carbon Carrier Methylofuran from Methylobacterium extorquens AM1 Contains a Large Number of alpha- and gamma-Linked Glutamic Acid Residues, J. Biol. Chem. 291, 9042-9051 (2016).
  • Cukier, C. D., Maveyraud, L., Saurel, O., Guillet, V., Milon, A., and Gervais, V., The C-terminal region of the transcriptional regulator THAP11 forms a parallel coiled-coil domain involved in protein dimerization, J. Struct. Biol. 194, 337-346 (2016).
  • Brison, Y., Malbert, Y., Czaplicki, G., Mourey, L., Remaud-Simeon, M., and Tranier, S., Structural Insights into the Carbohydrate Binding Ability of an alpha-(1→2) Branching Sucrase from Glycoside Hydrolase Family 70, ‎J. Biol. Chem. 291, 7527-7540 (2016).

2015

  • Sinnige, T., K. Houben, I. Pritisanac, M. Renault, R. Boelens, and M. Baldus. Insight into the conformational stability of membrane-embedded BamA using a combined solution and solid-state NMR approach. J. biomol. NMR 61, 321-332 (2015)
  • O’Connor, C., K. L. White, N. Doncescu, T. Didenko, B. L. Roth, G. Czaplicki, R. C. Stevens, K. Wuthrich, and A. Milon. NMR structure and dynamics of the agonist dynorphin peptide bound to the human kappa opioid receptor. PNAS 112, 11852-11857 (2015).
  • Berthoumieu, O., P. H. Nguyen, M. P. Castillo-Frias, S. Ferre, B. Tarus, J. Nasica-Labouze, S. Noel, O. Saurel, C. Rampon, A. J. Doig, P. Derreumaux, and P. Faller. Combined experimental and simulation studies suggest a revised mode of action of the anti-Alzheimer disease drug NQ-Trp. Chemistry 21, 12657-12666 (2015).
  • Bartolami, E., Y. Bessin, V. Gervais, P. Dumy, and S. Ulrich. Dynamic Expression of DNA Complexation with Self-assembled Biomolecular Clusters. Angew. Chemie 54, 10183-10187 (2015).

2014

  • Sinnige, T., M. Weingarth, M. Renault, L. Baker, J. Tommassen, and M. Baldus. Solid-state NMR studies of full-length BamA in lipid bilayers suggest limited overall POTRA mobility. J. Mol. Biol. 426, 2009-2021 (2014).
  • Planchard, N., E. Point, T. Dahmane, F. Giusti, M. Renault, C. Le Bon, G. Durand, A. Milon, E. Guittet, M. Zoonens, J. L. Popot, and L. J. Catoire. The use of amphipols for solution NMR studies of membrane proteins: advantages and constraints as compared to other solubilizing media. J. Membr. Biol. 247, 827-842 (2014).
  • Nars, G., O. Saurel, F. Bordes, I. Saves, M. Remaud-Simeon, I. Andre, A. Milon, and A. Marty. Production of stable isotope labelled lipase Lip2 from Yarrowia lipolytica for NMR: investigation of several expression systems. Protein Expr. Purif. 101, 14-20 (2014).
  • Nakatani, Y., N. Ribeiro, S. Streiff, M. Gotoh, G. Pozzi, L. Desaubry, and A. Milon. Search for the Most ’primitive’ Membranes and Their Reinforcers: A Review of the Polyprenyl Phosphates Theory. Orig Life Evol Biosph 44, 197-208 (2014).
  • Gater, D. L., O. Saurel, I. Iordanov, W. Liu, V. Cherezov, and A. Milon. Two classes of cholesterol binding sites for the beta2AR revealed by thermostability and NMR. Biophys. J. 107, 2305-2312 (2014).
  • Bissaro, B., O. Saurel, F. Arab-Jaziri, L. Saulnier, A. Milon, M. Tenkanen, P. Monsan, M. J. O’Donohue, and R. Faure. Mutation of a pH-modulating residue in a GH51 alpha-l-arabinofuranosidase leads to a severe reduction of the secondary hydrolysis of transfuranosylation products. Biochim Biophys Acta. 1840, 626-636 (2014).
  • Abot, A., C. Fontaine, M. Buscato, R. Solinhac, G. Flouriot, A. Fabre, A. Drougard, S. Rajan, M. Laine, A. Milon, I. Muller, D. Henrion, M. Adlanmerini, M. C. Valera, A. Gompel, C. Gerard, C. Pequeux, M. Mestdagt, I. Raymond-Letron, C. Knauf, F. Ferriere, P. Valet, P. Gourdy, B. S. Katzenellenbogen, J. A. Katzenellenbogen, F. Lenfant, G. L. Greene, J. M. Foidart, and J. F. Arnal. The uterine and vascular actions of estetrol delineate a distinctive profile of estrogen receptor alpha modulation, uncoupling nuclear and membrane activation. EMBO Mol Med 6, 1328-1346 (2014).

2013

  • Renault, M., L. Shintu, M. Piotto, and S. Caldarelli. Slow-spinning low-sideband HR-MAS NMR spectroscopy: delicate analysis of biological samples. Scientific reports 3, 3349 (2013).
  • Renault, M., J. Garcia, T. N. Cordeiro, M. Baldus, and M. Pons. Protein oligomers studied by solid-state NMR—the case of the full-length nucleoid-associated protein histone-like nucleoid structuring protein. FEBS J. 280, 2916-2928 (2013).
  • Gater, D. L., V. Reat, G. Czaplicki, O. Saurel, A. Milon, F. Jolibois, and V. Cherezov. Hydrogen bonding of cholesterol in the lipidic cubic phase. Langmuir : the ACS journal of surfaces and colloids 29, 8031-8038 (2013).
  • Rath, P., Saurel, O., Czaplicki, G., Tropis, M., Daffe, M., Ghazi, A., Demange, P. et Milon, A. Cord factor (trehalose 6,6’-dimycolate) forms fully stable and non-permeable lipid bilayers required for a functional outer membrane, BBA - Biomembranes 1828, 2173-2181 (2013).
  • Gervais, V., Campagne, S., Durand, J., Muller, I. et Milon, A. NMR studies of a new family of DNA binding proteins: the THAP proteins, J. Biomol. NMR 56, 3-15 (2013).
  • Cala, O., Remy, M. H., Guillet, V., Merdes, A., Mourey, L., Milon, A., and Czaplicki, G. Virtual and biophysical screening targeting the gamma-tubulin complex—a new target for the inhibition of microtubule nucleation, PLoS One 8, e63908 (2013).
  • Arab-Jaziri, F., Bissaro, B., Dion, M., Saurel, O., Harrison, D., Ferreira, F., Milon, A., Tellier, C., Faure, R., and O’Donohue, M. J. Engineering transglycosidase activity into a GH51 alpha-l-arabinofuranosidase, N. Biotechnol. 30, 536-544 (2013).
  • Gater, D. L., Reat, V., Czaplicki, G., Saurel, O., Jolibois, F., Cherezov, V. et Milon, A. Hydrogen bonding of cholesterol in the lipidic cubic phase. Langmuir 29, 8031-8038 (2013).
  • Rath, P., Saurel, O., Tropis, M., Daffe, M., Demange, P., and Milon, A. NMR localization of the O-mycoloylation on PorH, a channel forming peptide from Corynebacterium glutamicum, FEBS Lett. 587, 3687-3691 (2013).
  • Halberg F., Powell D., Otsuka K., Watanabe Y., Beaty L.A., Rosch P., Czaplicki J., Hillman D., Schwartzkopff O. and Cornelissen G. Diagnosing vascular variability anomalies, not only MESOR-hypertension, Am J Physiol Heart Circ Physiol. 305, 279-94 (2013).

2012

  • Iordanov, I., Renault, M., Reat, V., Bosshart, P. D., Engel, A., Saurel, O., and Milon, A. Dynamics of Klebsiella pneumoniae OmpA transmembrane domain: The four extracellular loops display restricted motion behavior in micelles and in lipid bilayers, Biochim Biophys Acta 1818, 2344-2353 (2012).
  • Bosshart, P. D., Iordanov, I., Garzon-Coral, C., Demange, P., Engel, A., Milon, A., and Muller, D. J. The Transmembrane Protein KpOmpA Anchoring the Outer Membrane of Klebsiella pneumoniae Unfolds and Refolds in Response to Tensile Load, Structure 20, 121-127 (2012).
  • Campagne, S., Muller, I., Milon, A., and Gervais, V. Towards the classification of DYT6 dystonia mutants in the DNA-binding domain of THAP1, Nucleic Acids Res 40, 9927-9940 (2012).
  • Arab-Jaziri, F., Bissaro, B., Barbe, S., Saurel, O., Debat, H., Dumon, C., Gervais, V., Milon, A., Andre, I., Faure, R., and O’Donohue, M. J. Functional roles of H98 and W99 and beta2alpha2 loop dynamics in the alpha-l-arabinofuranosidase from Thermobacillus xylanilyticus, FEBS J 279, 3598-3611 (2012).
  • Mazarguil, H., Mollereau, C., Czaplicki, G., and Zajac, J. M. Study of the N-terminal part of peptidic selective NPFF2 agonists, Peptides 37, 157-160 (2012).
  • Renault, M., Pawsey, S., Bos, M. P., Koers, E. J., Nand, D., Tommassen-van Boxtel, R., Rosay, M., Tommassen, J., Maas, W. E., and Baldus, M. Solid-State NMR Spectroscopy on Cellular Preparations Enhanced by Dynamic Nuclear Polarization, Angew Chem Int Edit 51, 2998-3001 (2012).
  • Renault, M., Tommassen-van Boxtel, R., Bos, M. P., Post, J. A., Tommassen, J., and Baldus, M. Cellular solid-state nuclear magnetic resonance spectroscopy, Proc Natl Acad Sci USA 109, 4863-4868 (2012).

2011

  • Rath, P., Demange, P., Saurel, O., Tropis, M., Daffe, M., Dotsch, V., Ghazi, A., Bernhard, F., and Milon, A. Functional expression of the PorAH channel from Corynebacterium glutamicum in cell-free expression systems: implications for the role of the naturally occurring mycolic acid modification, J Biol Chem 286, 32525-32532 (2011).
  • Irague, R., Massou, S., Moulis, C., Saurel, O., Milon, A., Monsan, P., Remaud-Simeon, M., Portais, J. C., and Potocki-Veronese, G. NMR-based structural glycomics for high-throughput screening of carbohydrate-active enzyme specificity, Anal Chem 83, 1202-1206 (2011).
  • Demange, P., Réat, V., Weinandy, S., Ospital, R., Chopinet-Mayeux, L., Henri, P., Milon, A., and Teissié, J. Targeted Macromolecules Delivery by Large Lipidic Nanovesicles Electrofusion with Mammalian Cells, J. Biomater. Nanobiotech. 2, 527-532 (2011).
  • Campagne, S., Gervais, V., and Milon, A. Nuclear magnetic resonance analysis of protein-DNA interactions,J R Soc Interface 8, 1065-1078 (2011).
  • Renault, M., Bos, M. P., Tommassen, J., and Baldus, M. Solid-State NMR on a Large Multidomain Integral Membrane Protein: The Outer Membrane Protein Assembly Factor BamA, J Am Chem Soc 133, 4175-4177 (2011).

Download the complete list of publications from 2016 to 2002

Collaborations inside France

  • L. Mourey, M. Daffé, M. Tropis, P. Calsou, O. Cuvillier, IPBS, University of Toulouse – CNRS
  • M. Remaud-Siméon, A. Marty, I. André, R. Fauré, M. J. O’Donohue, LISBP, University of Toulouse – INRA - CNRS
  • J. F. Arnal, I2MC, University of Toulouse – INSERM
  • J.L. Banères, IBMM, Montpellier
  • S. Granier, IGF, Montpellier
  • G. Pintacuda, CRMN, Lyon

 

International Collaborations

  • M. Baldus, Utrecht University, The Netherlands
  • L. Eggeling, IBG-1, Jülich, Germany
  • V. Cherezov and R. Stevens, USC, Los Angeles, USA
  • K. Wüthrich, The Scripps Research Institute, La Jolla, USA
  • J.A. Bengoechea, Queen’s University, Belfast, UK