Institut de Biologie StructuraleGrenoble / France

Contact person(s) related to this article / FAVIER Adrien / laguri cédric / SCHANDA Paul / Simorre Jean-Pierre

Presentation of the Biomolecular NMR Spectroscopy group

Welcome to the Biomolecular NMR Spectroscopy group.

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Nuclear magnetic resonance (NMR) has become an important technique for the determination of the three-dimensional structure of biological macromolecules. The ability to characterize structure and dynamics as well as interactions with physiological partners have made NMR an essential tool for understanding biological processes. The study of molecular complexes, even in the case of weak affinity, opens up powerful opportunities for the development of pharmacologically active molecules.

We are using and actively developing solution- and solid-state NMR approaches to tackle a number of challenging biological questions. In four different teams, we focus on different biomolecular applications, and different aspects of NMR methods development. Further information can be obtained by clicking on the images below, that lead to the pages of the four teams.

For any information concerning our research, you may also contact
either Jérôme Boisbouvier, head of the NMR group, or the team leaders
B. Brutscher, J. Boisbouvier, P. Schanda, J.-P. Simorre


 

Please click on the images to get more information about the research of the NMR teams:
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NMR of large Biomolecular Assemblies
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Bacterial Cell Wall
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Protein & RNA folding and methods development
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Solid State NMR and Dynamics

LATEST NEWS

Research Internship "Protein purification"
We are searching a candidate ("niveau Bac+2") for an internship. Find details in the attached document:

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PhD and Post-Doctoral Positions in the biomolecular NMR group available

We currently have several openings to work on different topics of the group:
• Development of innovative solution/solid-state NMR methods and isotopic labeling approaches for the study of challenging biological systems.
• Solid–state and solution-state NMR studies of biomolecular dynamics and interactions, in a number of challenging systems in which motion is an inherent feature for function.
• Protein and RNA folding, and chaperone activity studied by combination of NMR and EM approaches.
• Antibiotic resistance: Structural and functional studies of proteins involved in the synthesis of the bacterial cell wall using liquid and solid state NMR.

Please find more details in the document below:

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Direct insight into overall rocking motion of a protein a crystals

We recently directly observed, for the first time, how protein molecules "rock" inside protein crystals. By a unique combination of solid-state NMR spectroscopy, molecular dynamics simulations and x-ray diffraction we provided evidence that this motion is a key determinant for resolution in X-ray experiments, and also solid-state NMR.
See paper in Nature communications link

NMR pulse sequence tools for Bruker spectrometers

The IBS pulse sequence library consists of a combination of python setup scripts and Bruker pulse sequence programs that allow for easy use and sharing of protein NMR experiments.
Currently, the IBS library contains most of the fast NMR experiments (SOFAST-HMQC, HET-SOFAST, BEST-HSQC, BEST-TROSY, HADAMAC, ...) developed during recent years at IBS. In addition, it also contains a few basic experiments (1H-13C and 1H-15N HSQC, 15N T1, T2 and HETNOE, ...), as well as tools for pulse calibration, setup of composite pulse decoupling, and advanced data processing.

The IBS library can be downloaded here

Atomistic views of interactions in an intact bacterial cell wall

The bacterial cell wall is the primary target of antibiotic strategies. Understanding how the peptidoglycan - the major polymer forming the cell wall - is built, is therefore of crucial importance. Ironically, we know very little about the the interactions of proteins which are responsible for building the cell wall on an Spectroscopyatomic level. This relates to the fact that most structural biology techniques fail at seeing the cell wall at atomic resolution: the cell wall is large, heterogeneous and of course non-crystalline.
We have very recently used solid-state NMR spectroscopy to overcome these challenges, and have obtained the first 3D structure of a cell-wall/protein complex at atomic detail. Our approach, based on solid-state NMR and modeling, provides interesting clues about how the cell wall is built, and may pave new avenues for designing inhibitors of cell-wall synthesis.

The original research paper can be found here, and a press release is available here


PLATFORMS MANAGED BY THE NMR GROUP

Our group is in charge of several platforms for high-field NMR spectroscopy and preparation of biological samples. Please visit the links below for more information.

HIGH FIELD NMR SPECTROSCOPY

Credit photo CEA/D.Morel

Our group uses state-of-the-art NMR equipment for solution- and solid-state NMR.
With 6 spectrometers from 600 MHz to 950 MHz field strength, the NMR platform at IBS is among the best-equipped sites in Europe.

The NMR platform at IBS, in partnership with the NMR platform at CRMN Lyon, is part of national and European large-scale facilities, that grant access to our high-field NMR spectrometers to external users.
IR-RMN (French large-scale NMR facility):
European NMR facility
RALF-NMR (Rhone-Alpes Large-Scale NMR facility)

We also offer a service for protein quality control (purity, oligomerization state, degree of structure). For more details, see
1D quality control platform


PROTEIN PRODUCTION & WET LAB EQUIPMENT

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The production of functional protein samples with suitable isotopic labeling patterns, either by bacterial expression or cell-free synthesis, is a crucial requirement for NMR spectroscopic studies. In our dedicated wetlab facilities, we develop innovative isotope labeling schemes for solution- and solid-state NMR samples.
The expertise is also available to external users via our isotope labeling and the cell-free expression platforms.


The group


Recent publications

Observing the overall rocking motion of a protein in a crystal.
Peixiang Ma, Yi Xue, Nicolas Coquelle, Jens D Haller, Tairan Yuwen, Isabel Ayala, Oleg Mikhailovskii, Dieter Willbold, Jacques-Philippe Colletier, Nikolai R Skrynnikov, and Paul Schanda
Nature Communications 2015, 6: 8361-66 link

Probing Transient Conformational States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy
Ma P, Haller JD, Zajakala J, Macek P, Sivertsen AC, Willbold D, Boisbouvier J, Schanda P
Angewandte Chemie 2014, 53, 4312. link
Ranked as "Very Important Paper" by the journal

The RNA-binding region of human TRBP interacts with microRNA precursors through two independent domains.
Benoit MP, Imbert L, Palencia A, Pérard J, Ebel C, Boisbouvier J, Plevin MJ.
Nucleic Acids Res. 2013 ;41(7):4241-52. link

Interaction of non-structural protein 5A of hepatitis C virus with SH3 domains using non-canonical binding sites.
Schwarten M, Solyom Z, Feuerstein SE, Aladag A, Hoffmann S, Willbold D, Brutscher B.
Biochemistry. 2013 Aug 15. [Epub ahead of print] link

Structure of Enterococcus faeciuml,d-Transpeptidase Acylated by Ertapenem Provides Insight into the Inactivation Mechanism.
Lecoq L, Dubée V, Triboulet S, Bougault C, Hugonnet JE, Arthur M, Simorre JP.
ACS Chem Biol. 2013 Apr 12. [Epub ahead of print] link

Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate.
Rennella E, Cutuil T, Schanda P, Ayala I, Forge V, Brutscher B.
J Am Chem Soc. 2012 May 16;134(19):8066-9. link.

Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy.
Tollinger M, Sivertsen AC, Meier BH, Ernst M, Schanda P.
J Am Chem Soc. 2012 Sep 12;134(36):14800-7. link.

Plevin, M. J., D. L. Bryce, and J. Boisbouvier.
Direct detection of ch/pi interactions in proteins.
Nature Chemistry (2010) 2, no. 6: 466-471. link.

Second double-stranded RNA binding domain of dicer-like ribonuclease 1: structural and biochemical characterization.
Burdisso P, Suarez IP, Bologna NG, Palatnik JF, Bersch B, Rasia RM.
Biochemistry. 2012 Dec 21;51(51):10159-66. link.

Dynamics induced by β-lactam antibiotics in the active site of Bacillus subtilis L,D-transpeptidase.
Lecoq L, Bougault C, Hugonnet JE, Veckerlé C, Pessey O, Arthur M, Simorre JP.
Structure. 2012 May 9;20(5):850-61. link.

Stereospecific isotopic labeling of methyl groups for nmr spectroscopic studies of high-molecular-weight proteins.
Gans, P., O. Hamelin, R. Sounier, I. Ayala, M. A. Dura, C. D. Amero, M. Noirclerc-Savoye, B. Franzetti, M. J. Plevin, and J. Boisbouvier.
Angewandte Chemie (2010) Edition 49, no. 11: 1958-1962.

The full list of publications can be found here