NMR, Structural Chemistry and Biology

The organization of the cell involves a very number of molecules (proteins, nucleic acids, small molecules). They represent a network of interactions that controls the development and the regulation of many biological processes. It is then of high interest to understand how these molecular components work independently and in presence of their natural partners. Il est donc particulièrement important de comprendre comment ces composants moléculaires fonctionnent de façon isolée et au contact de leurs partenaires naturels.

NMR (Nuclear Magnetic Resonance) has emerged as an essential tool to determine the tridimensional structure of these macromolecules at high resolution, together as X-Ray cristallography. In addition, NMR provides a wealth of information about the internal motions in terms of time scales, amplitudes and spatial localization. Furthermore, this technique is able to provide the structural characterization of intermolecular interactions between molecules from different families.

More generally, understanding the properties of molecular complexes of high and weak affinities opens the route to the development of biologically active molecules.

NMR has already proven to be highly efficient in this field. However, the development of new NMR methods can still extend the range of applications of NMR in biology.

NMR is also an essential tool in analytical chemistry, particularly for the analysis of complex mixtures, with applications in metabolomics, natural product research or reaction monitoring. Methodological developments, especially for multidimensional techniques, extend the scope and potential of NMR spectroscopy.

Organisation

The NMR team is divided in three different axis:

  • Research in Structural Biology and Development of new NMR Methods

The research is mainly centered on the analysis of structure, interactions and dynamics of biological macromolecules in solution by NMR. Most of our projects are selected for their biological relevance and their potential applications. Depending on the projects, we also use different methods such as X-Ray crystallography, ITC, … A number of our projects are at the edge of NMR possibilities (size of the systems, solubility, high flexibility, and require the use of state of the art NMR techniques. We are thus also highly interested in methodological developments for structural biology but also for fast multidimensional NMR and on varions forms of hyperpolarisation. A number of projects are developped in collaboration with groups of biologists or chemists at the national level (CEA, INSERM, INRA, Pasteur Institute, universities of PARIS XI, Nantes, Marseille, …) and international level (Southampton University, EPFL Lausanne, …)
When necessary, we also use the best suitable technique, which leads to the use of X-ray crystallography, microcalorimetry, biological functional tests, cell biology, biochemistry as well as molecular modeling.

The “olfaction” theme is also developed and focuses on understanding the complexity of odor perception at the molecular level. Using computer tools, biochemistry, chemistry, evolution, and sensory analysis, the aim is to elucidate our body’s strategy for perceiving its volatile environment. This includes establishing the link between the chemical structure of an odorant molecule, the biological processes involved, and the sensation it causes. We are particularly interested in studying the molecular role of evolutionarily conserved amino acid motifs in odorant receptors and how this defines their identity and structure within the GPCR family.

  • NMR Service

We continue our long tradition of applying NMR to chemistry. The chemists of ICSN have access to several NMR spectrometers (a two 300MHz, two 500MHz and a 600MHz) on a self-service basis for simple experiments. A computarized reservation system allows the users to book their time via the network and to check at any time for an available measurement time.
For difficult cases, they benefit from the assistance of the engineers of the team who realize the needed experiments, possibly at higher fields. These engineers also realize a number of more demanding NMR studies in the fields of chemical synthesis or natural products structure determination for chemists either from the institute or from external laboratories.

  • IR-RMN/Infranalytics (950 MHz)

Installed in december 2008, the 950 MHz spectrometer operates as a national facility. IR-RMN has since then merged with the Renard (EPR) and FT-ICR infrastructures within the infrastructure Infranalytics. For more information, visit the facility webpage.

Keywords

NMR, Proteins, Nucleic Acids, Structure, Dynamics, Interactions, G Protein Coupled Receptor, Olfaction

Skills

Molecular biology, Production and purification of proteins, Isotope labeling of proteins in prokaryotic and eukaryotic cells, NMR of proteins and small molecules, X-ray crystallography, SAXS, Molecular modelling, Structures elucidation, Enzymology, Molecular interactions, cell biology

Equipment

For Chemistry and Structural biology ( RMNHC@UPSay plateform) :

  • 5 NMR spectrometers : 2 * 600 MHz liquid cryoprobe TCI and QCI-19F or TBI, 700 MHz liquid cryo TXO, 800 MHz liquid cryoprobe TCI, and 950 MHz liquid cryoprobe TCI, Samplejet, RMN high pressure, and equipment for molecular biology and purification.

For routine structure determination at the NMR service (http://icsn.cnrs.fr/plateformes/rmn):

  • two 300 MHz, two 500 MHz, and one 600 MHz

Senior staff

Since 2012, Nadine Assrir is a scientist in Eric Guittet’s team. She received a master of toxicology (Paris Descartes) and completed a PhD in biochemistry, molecular and cellular biology (Paris-Sud University) at the Institut Gustave Roussy. Her research projects focus on the relationship between structure and protein function including the impact of this relationship on the biological processes after post-translational modifications or molecular interactions. Currently, she is studying the impact of interactions of three proteins involved in cell proliferation, tumor reversion or cell motility, namely ErbB2, TCTP and iASPP. Her duties also include the co-management of the FRISBI platform (production of labelled proteins in eukaryotic cells). Nadine Assrir is also in charge of lessons in biochemistry, since many years, in the Bachelor and Master programs of the Versailles–St Quentin University.

François Bontems is a CNRS senior scientist (DR2). After his PhD on the structural organization of scorpion toxins in the Centre d’étude nucléaire de Saclay, he joined the NMR team led by Jean-Yves Lallemand at the Ecole polytechnique. He mainly worked on a system coupling RNA translation and inactivation during E. coli infection by the T4 phage (« S1-RegB » system). Then, he integrated the NMR group at ICSN and currently shares his time between this team and the Structural virology unit at Pasteur Institut. His present interests mainly concern the structural properties of the E and NS1 proteins of flaviviruses (yellow fever, dengue and Zika), which are the main targets of the immune system after an infection. In this aim, he developed and implemented at ICSN some tools allowing the labeling with stable isotopes of these proteins that can not be produced in E. coli and are generally expressed in insect or mammalian cells. In addition, he also organises colloquia devoted to science and society relationships and is responsible of a Pasteur course on the same topic. He is also member of the steering committee in charge of a Livre Blanc « society, higher education and research ».

Claire de March is a CNRS Assistant professor (CRCN). She trained in flavor science and industry at the ISIPCA in Versailles and had an industry experience as a sensory analyst in the Bel group. She received her Ph.D. at Université Nice Côte d’Azur in 2015 where she investigated the molecular mechanisms involved in odorant receptor recognition of odorant molecules. From 2016 to 2022, she joined the Hiroaki Matsunami lab at Duke University (NC, USA) to continue studying how odorant receptors are used to trigger an odor percept but on the bench side. Since 2022, she joined ICSN as a CNRs assistant professor. She uses the synergy of in silico and in vitro approaches to establish the link between the chemical structure of an odorant molecule, the biological processes involved, and the sensation it causes. She is particularly interested in role of evolutionarily conserved amino acid patterns in odorant receptors and how that defines their identity and structure within the GPCR family. Outside of the lab, she practices many types of crafts and Thai boxing and enjoys relaxing time with her friends and family.

Jean-François Gallard is an NMR engineer.

Diego Gauto had received his M.Sc. in chemistry (2009) and Ph.D. in computational biology (2013) from the school of sciences at Buenos Aires University, Argentina. Immediately after his PhD, he took a postdoctoral position in solution NMR at the Institute of Molecular and Cell Biology of Rosario (IBR), Argentina and then move to France to start a postdoctoral positions at IBS (Institut de Biologie Structurale) with Dr. Paul Schanda to study protein structure and protein dynamic by solid state NMR and developing methods for structural elucidation combining NMR and CryoEM. Then, he continues his postdoctoral training with Drs. Sabine Hediger and Gaël De Paëpe at CEA, Grenoble in order to perform NMR under cryogenic temperatures and DNP conditions. From 2020 to nowadays, he is a CNRS research assistant scientist at the Institut de Chimie des Substances Naturelles (ICSN), Gif-sur-Yvette where he is interesting in understand the structural basis of protein cages and their application in the chemistry and health.

François Giraud is engineer.

Eric Jacquet is CNRS research associate.

Ewen Lescop is a CNRS senior scientist. He received his Ph.D. at the ICSN in the group of Eric Guittet, with a work on a honeybee odorant-binding protein. He then performed postdoctoral research at Beijing University (2004-2006, C. Jin, China) and the Institute of Structural Biology (2006-2007, B. Brutscher). In 2007 he returned to the ICSN to develop NMR methods for proteins and study a variety of biological systems with structural-biology approaches. Outside the lab, Ewen is a keen and active player of traditional folk music, especially breton music, and he always likes a good meal and a drink.

Nelly Morellet works as a research engineer at the ICSN (CNRS-IRHC). She obtained a doctorate under the supervision of Jean-Claude Beloeil in 1989 at the ICSN. From 1990 to 2010 she studied several viral proteins by NMR (HIV-1, SIV, Birnavirus, Rotavirus, etc.) in the unit of B.P Roques then D.Scherman at the Faculty of Pharmaceutical and Biological Sciences, Paris. In 2010 she joined the Chemistry and Structural Biology team at the ICSN. She is involved in several projects: antibiotic resistance (NDM-1 protein and RNaseY), domesticated transposases and transposases (PiggyBac and PiggyMac proteins), and overexpressed proteins and receptors in breast cancer (ErB2).

Annie Moretto is a CNRS technician.

Naïma Nhiri is CNRS research engineer.

Christina Sizun completed a PhD in Chemical Physics in 2000 at the Louis Pasteur University in Strasbourg, where she was trained in NMR spectroscopy of catalytic systems. She then joined the group of Burkhard Bechinger at the Max Planck Institute for Biochemistry in Martinsried as a post-doc to work on solid state-state NMR of membrane peptides. After a second post-doc in the team of Erick Dufourc at the Institut Européen de Chimie et Biologie in Bordeaux, she was recruited as a researcher in 2003 at the ICSN, where she developed her interest for structural biology by NMR. Her main focus is on the structure-function relationship of viral proteins (respiratory syncytial virus) as a member of a collaborative network including INRA and Institut Pasteur. She also participates to one of the projects dedicated to therapeutic targets in the frame of the LERMIT LabEx (modulators of the CXCL12/CXCR4 signaling axis). She is involved in teaching of biological NMR and biophysics in several university programs.

Carine van Heijenoort is a CNRS senior scientist. After studies in chemistry, she received her Ph.D. in 1994 in the group of Eric Guittet at the ICSN, with work on the characterization of internal flexibility of proteins by NMR. In 1999-2000, she went to Utrecht University as an invited scientist in the group of Rob Kaptein and Rolf Boelens where she explored her dutch roots and protein-protein interactions. Her research interests are focused on the characterization of multiple states of proteins and their link to function, with a particular interest on intrinsically disordered proteins and their interactions. She is currently coordinator of the department of Analytical and Structural Biology and Chemistry of ICSN. Outside the lab, Carine has three wonderful daughters, she actively practices horse riding, is fond of dogs, cats, music, reading and discussions with friends.

Non-permanent members

Jiawei Dong is a doctoral student at Paris Saclay University under the supervision of Christina Sizun. His Ph.D. focuses on the structural characterization of the respiratory syncytial virus protein NS1, involved in the escape of the host immune response, and on its interaction with subunit 25 of the Mediator complex. Jiawei followed the specialty Engineering and Chemistry of Biomolecules from the Master of Health Biology at the University of Paris Saclay, after obtaining a bachelor's degree in Life and Earth Sciences from the University of Strasbourg and a DUT in Biological Engineering from the University of Lorraine.

Luce Dreno graduated from the Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM) in 2019 with a degree in chemical engineering, specializing in Chemistry-Biology-Health. She focused her studies on the interface between chemistry and biology thanks to her specialty but also by completing a double degree, master's degree in Health Biology specializing in Translational Medicinal Chemistry, in the last year of engineering school. Interested in research in biology in the field of health, she began a doctorate at the end of 2019 within the UMR981 (Molecular predictors and new targets in oncology) at Gustave Roussy under the supervision of Anne CHAUCHEREAU (CRHC-HDR) and in co-direction with Ewen LESCOP (DR2-HDR) within the ICSN (Structural and Analytical Chemistry and Biology department). Her thesis work focuses on the study of the FKBP7 protein, a new potential therapeutic target in chemoresistant prostate cancer. Her work combines cellular and molecular biology approaches at Gustave Roussy, as well as structural biology at the ICSN in order to better understand the activity of this protein in resistance to taxane-based chemotherapies (docetaxel, cabazitaxel) used in advanced stages of prostate cancer.

Clarisse Fourel obtained a degree in chemical engineering, specializing in physical chemistry, from ENSCBP (National School of Chemistry, Biology, and Physics) in Bordeaux in 2023. In her final year, she completed the module 'Chemistry and Bioengineering' offered by ENSTBB (National School of Biomolecule Technology) in Bordeaux. She is currently pursuing a Ph.D. at ICSN under the supervision of Ewen Lescop and also works under the guidance of Laurent Catoire at IBPC (Institut de Biologie Physico-Chimique) in Paris. Her topic is as follows: 'Probing the dynamic coupling between lipids and membrane proteins by NMR under hydrostatic pressure.

Former members (since 2014)

  • Jean-Nicolas Dumez CNRS Research Associate (CRCN) at ICSN (2014-2018). Jean-Nicolas moved to CEISAM, Nantes in 2018.
  • Arthur Besle (CDD IT)
  • Hans Lafaille (CDD IT)
  • Prishila Ponien (CDD IT)
  • Oriane Frances (PhD thesis 2011-2015) : Sanofi (France).
  • Safa Lassoued (PhD thesis 2012-2015)
  • Adrien Le Guennec (PhD thesis 2012-2015): Post-doc at University of Georgia (U.S.A.).
  • Marion André (PhD thesis 2012-2015) : Cortecnet (France).
  • Stefano Caldarelli (Professeur 2012-2015)
  • Fataneh Fatemi (PhD thesis 2010-2013): Beheshti University of Tehran (Iran)
  • Séverine Moriau (PhD thesis 2013-2016)
  • Nelson Pereira (PhD thesis 2013-2016)
  • Célia Deville (PhD thesis 2012-2015): Post-doc at Birkbeck University (U.K.).
  • Ludmilla Guduff (PhD thesis 2015-2018)
  • Florian Malard (PhD thesis 2016-2019)
  • Louise Pinet (PhD thesis 2016-2019)
  • Maria Grazia Concilio (Postdoc 2017-2018).
  • Corentin Jacquemoz (PhD thesis 2017-): he continues his PhD thesis at CEISAM in Nantes.
  • Camille Doyen (PhD thesis 2017-2020)
  • Ghanem Hamdoun (Postdoc ).
  • Christophe Cardone (Thèse 2016-2019)
  • Claire-Marie Caseau (Thèse 2017-2021)
  • Djabir Larkem (Thèse 2018-2021)
  • Silva Khodjoyan (Thèse 2020-2023)