Structure, dynamique et fonction des biomolécules par RMN

Présentation

Group Leaders: Christian Roumestand et André Padilla

 

EQUIPE RMN
                 Karine DeGuillen     André Padilla      Philippe Barthe   Christian Roumestand    Hélène Déméné   Yinshan Yang
                 (IE INSERM)                 (CR CNRS)                  (IR UM)                     (Professeur UM)                 (CR CNRS)               (IR CNRS)

 

The aim of the team is to take advantage of a broad spectrum of complementary skills to study complex biological systems from an interdisciplinary perspective. The ability to use several structural biology techniques will ensure the proper development of the scientific challenges. In addition, all the team members are also involved in platform activities.

 

 SLIDE LOGOS

 

 

• High Pressure NMR and Protein Folding •

Coordinator: Christian Roumestand

The phenomenon of spontaneous protein folding underlies all key biological processes. Despite decades of intense research and significant progress in both experimental and theoretical approaches, the mechanisms and determinants of folding remain incompletely understood.

A protein is a hetero-polymer, the basic motif for which is one of the 20 natural amino acids. The chaining of these motives constitutes the sequence of the protein. Individual protein sequences have evolved in order to adopt a tridimensional (3D) structure that confers the level of stability and conformational dynamics required for their optimal function under the conditions in which the organism must survive. However, we have yet to reveal the subtle rules by which sequence determines these properties. Protein folding energy landscapes remain to be experimentally mapped. A general description of folding transition states and routes cannot be predicted for arbitrary amino acid sequences. Likewise, a protein's propensity to aggregate cannot be deduced from its sequence. Finally, we do not know how sequence encodes the conformational fluctuations and heterogeneity required for function in specific contexts.

Importantly, numerous "conformational" diseases (Alzheimer, Parkinson, Prion diseases) are associated with a deregulation of the folding/unfolding equilibrium for a specific protein, which justifies the efforts dedicated to the study of this phenomenon. Nevertheless such a high level of understanding will be required for further progress in the modulation and de-novo conception of proteins, enzymes and small molecules for hard bioscience, therapeutic or biotechnological applications.

NMR staff : Philippe Barthe

 

• Plant Pathogens and Infectious Diseases •

Coordinator: André Padilla

Agropolis International in Montpellier has a large range of expertise in the area of agriculture, food, environmental biology and biodiversity. The CBS teams have engaged since years collaborations with many Agropolis Teams.

- Recognition of avirulence (AVR) proteins by plant immune Receptors.

Plant resistance to microbial pathogens is a complex process relying on two major levels of resistance triggered by distinct types of plant receptors. Beside the first line of immunity, in which microbial molecules, such as bacterial flagellin or cell wall components of the pathogen are perceived, leading to plant resistance, the second layer of plant immunity relies on the recognition of certain pathogen-derived effectors by so-called plant resistance proteins (R) encoded by R genes. Effectors that are specifically recognized are called Avirulence proteins (Avr) and induce a plant Effector-Triggered Immunity. We use the rice blast model system to investigate R protein function and AVR protein recognition. Rice blast caused by the ascomycete fungus Magnaporthe oryzae is the most important rice disease wide worldwide and as such is a serious economic problem and a major threat for food security and health care linked to pesticides usage. Our collaboration (INRA Montpellier) resulted in the generation of NMR structures for the M. oryzae effectors AVR1-CO39 and AVR-Pia and the project aims at identifying the structure of R rice immune receptors.

 topology

 

The molecular details of R binding are elucidated In vitro and In vivo to validate structural models of Avr recognition and to investigate structure-function relations. Plant diseases are among the most important problems in agriculture and the use of disease resistance (R) genes is a key strategy for sustainable crop protection.

chami

NMR Staff : Karine deGuillen

Coll.: Thomas Kroj (INRA)

 

 

• Structure and Activation of G-Protein Coupled Receptors •

Coordinator: Hélène Déméné

This work is issued from a close collaboration between the CBS partners and the IGF partners.

G-Protein Coupled Receptors represent the largest class of membrane surface cell receptors involved in signal transduction in eukaryotes. They sense molecules outside the cell and activate signal transduction pathways inside the cell and, ultimately, cellular responses, by coupling with G-proteins. Our research themes focus on the receptors of the vasopressin (V1R and V2R) and on the µ-opioid receptor (µOR).

In the past, we have deciphered the structural features of isolated intracellular loops of V1aR and V2R. We have shown how they fold by themselves, independently from the rest of the receptors, and are also able to recruit intracellular effectors by themselves. We have proposed a method to produce them under a recombinant form mimicking the natural anchoring in the receptor.

We now investigate on the structure-activity of whole GPCRs, taking advantage of the sensitivity of methyl-based NMR. In particular, we have shown that the ligand- and G-protein binding interfaces are weakly coupled in µOR, extending the concept observed before for the ß2 adrenergic receptor by the Kobilka's team. Based on the NMR spectral parameter changes upon interaction of µOR with various agonists as well as with a G-protein mimetic, we could propose a model of event propagation during activation.

GPCR Agonist binding promotes primary structural changes in the first intracellular loop and the H8 helix, whereas conformational adaption in TM5 and TM6 is limited compared to the full-active state obtained in presence of agonist and G-protein.

 Coll. Sébastien Granier, (IGF); Christiane Mendre, (IGF); Bernard Mouillac, (IGF)

 

 

• Structure and interactions of bacterial antiterminators •

Coordinators: Hélène Déméné

The Bacillus substilis LicT antiterminator protein represents the prototype in gram+ bacteries of widespread regulators of the BglG antitermination familiy. LicT regulates expression of the bglS gene and bglPH operons involved in the transport and metabolim of b glucosides. When activated, these transcriptional regulators bind to a ribonucleotidic antiterminator (RAT) sequence in targets mRNAs, preventing the formation of an antitermination hairpin associated with premature arrest of transcription. All members of the LicT family present a modular structure composed of a RNA binding domain (CAT) and two regulatory homologous domains PRD1 and PRD2. These two domains are the subject of concurrent phosphorylations by enzymes of the PTS (phosphoenolpyruvate PhosphoTransferase System) that control the activation (RNA binding capacity) of LicT. We have previously established the conditions of stability of truncated proteins (CAT-PRD1) and proposed a model of activation for these proteins. We now investigate on the structure of the whole protein, either alone or in interaction with its PTS partners. Our collaborators focus on the structural mechanism at the RNA level.

Models of activated (closed) and inactive (open) LicT-CAT-PRD1. The degree of opening of the RNA binding domain determines the level of RNA binding activity. 

LICT

NMR Staff : Yang Yinshan

Coll.: Nathalie Declerck (CBS)

 

 

• NMR Platform Examples •

Coordinators: André Padilla & Christian Roumestand

Technical manager: Karine de Guillen

Researchers and Engineers of the NMR team are involved in the platform projects.

 

Structure of the Mycobacterium tuberculosis OmpATb

NMR Platform Staff: Yang Y. & Roumestand C.

Protein Size : 256 a.a. 15N and 13C labeled

The pore-forming outer membrane protein OmpATb from Mycobacterium tuberculosis is a virulence factor shown to be required for acid resistance in host phagosomes. NMR studies show that OmpATb is composed of two independent domains separated by a proline-rich hinge region. The results revealed the N-terminal domain of OmpATb can assemble into multiple oligomeric forms and is responsable to form channels in planar lipid bilayers.

omptb

15N-HSQC spectrum 256 a.a.

ompatb

N-terminal domain structure

pentamer

HADDOCK model of the heptamer

External Contact : Nathalie Saint (INSERM U1046) Email: Cette adresse e-mail est protégée contre les robots spammeurs. Vous devez activer le JavaScript pour la visualiser.

Yang Y, Auguin D, Delbecq S, Dumas E, Molle G, Molle V, Roumestand C, Saint N (2011) Structure of the Mycobacterium tuberculosis OmpATb protein: a model of an oligomeric channel in the mycobacterial cell wall, Proteins 79 (2) 645-661 . doi: 10.1002/prot.22912.

 

NMR Structure of an Antimicrobial peptide

NMR Platform Staff : André Padilla                   pipeline from CBS RX platform

Peptide : GGLKKLGKKLEGAGKRVFKASEKALPVVVGIKAIGK Unlabeled

Aedesin is a cecropin-like anti-microbial peptide that was recently isolated from dengue virus-infected salivary glands of the Aedes aegypti mosquito. In the present study, we have refined the analysis of its structural characteristics. Aedesin has a helix-bend-helix structure typical for a member of the family of alpha-helix anti-microbial peptides.

COSY

Spectra overlay : TOCSY (green) NOESY (yellow)

chenille

Surface coloured by the charge, blue for positive red for negative and grey for hydrophobic residues

 

External Contact: D. Missé (MIVEGEC, UMR224 IRD/CNRS/UM) Email: Cette adresse e-mail est protégée contre les robots spammeurs. Vous devez activer le JavaScript pour la visualiser.

Godreuil S, Leban N, Padilla A, Hamel R, Luplertlop N, Chauffour A, et al. Aedesin: Structure and Antimicrobial Activity against Multidrug Resistant Bacterial Strains. PLoS ONE 2014;9:e105441. doi:10.1371/journal.pone.0105441

 

NMR structure of Bc28.1

NMR Platform Staff: Yang Y. & Roumestand C.

Protein Size : 223 a.a. 15N and 13C labeled

Babesia canis is the agent of the canine babesiosis in Europe. The major merozoite surface antigens of Babesia canis have been described as a 28-kDa membrane protein family, anchored at the surface of the merozoite. The resolution of the structure of Bc28.1 (223 a.a) represents a milestone for the characterization of the parasite erythrocyte binding and its interaction with the host immune system.

 

 bc28total

bc28 

Left Panel : 15N - HSQC and zooms of lightly crowded areas

 

 External Contact : Stéphane Delbecq EA4558, Vaccination Antiparasitaire, Montpellier.

 

Yang YS, Murciano B, Moubri K, Cibrelus P, Schetters T, Gorenflot A, Delbecq S, Roumestand C (2012) Structural and functional characterization of Bc28.1, major erythrocyte-binding protein from Babesia canis merozoite surface, J Biol Chem 287 (12) 9495-9508

 

TGAM_1934, an ORFan protein from the archeon Thermococcus gammatolerans.

NMR Platform Staff: de Guillen K., Yang Y. & Roumestand C.

Protein Size : 148 a.a. 15N and 13C labeled

ORFans are proteins found when annotating new genomes by comparative genomics. TGAM_1934, a 122 amino acid polypeptide from the hyper-radioresistant T. gammatolerans archaeon, was selected as the most abundant hypothetical protein amongst the low molecular weight proteome. The NMR results highlight the potential of structural proteogenomics, i.e. prioritizing ORFan targets for structure determination based on quantitative proteomics data.

tgamhsqc tgam 

 

External Contact : Jean Armengaud , Cette adresse e-mail est protégée contre les robots spammeurs. Vous devez activer le JavaScript pour la visualiser. CEA, DSV, IBEB, Bagnols-sur-Cèze

Yang YS, Fernandez B, Lagorce A, Aloin V, De Guillen KM, Boyer JB, Dedieu A, Confalonieri F, Armengaud J, Roumestand C (2014) Prioritizing targets for structural biology through the lens of proteomics: The archaeal protein TGAM_1934 from Thermococcus gammatolerans, Proteomics. PMID = 25359407

 

 

Structure and dynamics of RYMV viral encoded P1 protein

NMR Staff: Yang Yinshan, Hélène Déméné H.

Coll.: Florence Vignols and Christophe Brugidou (IRD)

The P1 protein is a crucial protein of the RYMV (Rice Mottle Yellow) virus that infects the most productive rice plants in Africa. Using an integrative approach combining X-Ray and NMR spectroscopy at the CBS, we have characterized the structure and revealed the dynamics of the RYMV P1 protein that are linked to the mode of viral activation.

 

 

 

Coordinators: André Padilla & Christian Roumestand

Connexion