1
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Jacquemmoz C, Mishra R, Guduff L, van Heijenoort C, Dumez JN. Optimisation of spatially-encoded diffusion-ordered NMR spectroscopy for the analysis of mixtures. Magn Reson Chem 2022; 60:121-138. [PMID: 34269476 DOI: 10.1002/mrc.5194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/25/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Diffusion-ordered NMR spectroscopy (DOSY NMR) is a widely used method for the analysis of mixtures. It can be used to separate the spectra of a mixture's components and to analyse interactions. The classic implementation of DOSY experiments, based on an incrementation of the diffusion-encoding gradient area, requires several minutes or more to collect a 2D data set. Spatially-encoded (SPEN) DOSY makes it possible to collect a complete data set in less than 1 s, by spatial parallelisation of the effective gradient area. While several short descriptions of SPEN DOSY experiments have been reported, a thorough characterisation of its features and its practical use is missing, and this hinders the use of the method. Here, we present the unusual principles and implementation of the SPEN DOSY experiment, an understanding of which is useful to make optimal use of the method. The encoding and acquisition steps are described, and the parameter relations that govern the setup of SPEN DOSY experiments are discussed. The influence of key parameters, including on sensitivity, is illustrated experimentally on mixtures of small molecules. This study should be useful for the setup of SPEN DOSY experiments, which are particularly useful for systems that evolve in time.
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Affiliation(s)
| | - Rituraj Mishra
- Université de Nantes, CNRS, CEISAM, UMR 6230, Nantes, France
| | - Ludmilla Guduff
- Université Paris-Saclay, CNRS, ICSN, UPR 2301, Gif-sur-Yvette, France
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2
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Lesma J, Bizet F, Berardet C, Tonali N, Pellegrino S, Taverna M, Khemtemourian L, Soulier JL, van Heijenoort C, Halgand F, Ha-Duong T, Kaffy J, Ongeri S. β-Hairpin Peptide Mimics Decrease Human Islet Amyloid Polypeptide (hIAPP) Aggregation. Front Cell Dev Biol 2021; 9:729001. [PMID: 34604227 PMCID: PMC8481668 DOI: 10.3389/fcell.2021.729001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022] Open
Abstract
Amyloid diseases are degenerative pathologies, highly prevalent today because they are closely related to aging, that have in common the erroneous folding of intrinsically disordered proteins (IDPs) which aggregate and lead to cell death. Type 2 Diabetes involves a peptide called human islet amyloid polypeptide (hIAPP), which undergoes a conformational change, triggering the aggregation process leading to amyloid aggregates and fibers rich in β-sheets mainly found in the pancreas of all diabetic patients. Inhibiting the aggregation of amyloid proteins has emerged as a relevant therapeutic approach and we have recently developed the design of acyclic flexible hairpins based on peptidic recognition sequences of the amyloid β peptide (Aβ1–42) as a successful strategy to inhibit its aggregation involved in Alzheimer’s disease. The present work reports the extension of our strategy to hIAPP aggregation inhibitors. The design, synthesis, conformational analyses, and biophysical evaluations of dynamic β-hairpin like structures built on a piperidine-pyrrolidine β-turn inducer are described. By linking to this β-turn inducer three different arms (i) pentapeptide, (ii) tripeptide, and (iii) α/aza/aza/pseudotripeptide, we demonstrate that the careful selection of the peptide-based arms from the sequence of hIAPP allowed to selectively modulate its aggregation, while the peptide character can be decreased. Biophysical assays combining, Thioflavin-T fluorescence, transmission electronic microscopy, capillary electrophoresis, and mass spectrometry showed that the designed compounds inhibit both the oligomerization and the fibrillization of hIAPP. They are also capable to decrease the aggregation process in the presence of membrane models and to strongly delay the membrane-leakage induced by hIAPP. More generally, this work provides the proof of concept that our rational design is a versatile and relevant strategy for developing efficient and selective inhibitors of aggregation of amyloidogenic proteins.
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Affiliation(s)
- Jacopo Lesma
- BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Faustine Bizet
- BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Corentin Berardet
- BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France.,Institute Galien Paris-Saclay, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Nicolo Tonali
- BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Sara Pellegrino
- DISFARM, Sezione di Chimica Generale e Organica "A. Marchesini," Università degli Studi di Milano, Milan, Italy
| | - Myriam Taverna
- Institute Galien Paris-Saclay, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Lucie Khemtemourian
- Institute of Chemistry and Biology of Membranes and Nanoobjects, Institut Polytechnique Bordeaux, CNRS UMR 5248, Université de Bordeaux, Pessac, France
| | | | - Carine van Heijenoort
- ICSN, Equipe Biologie et Chimie Structurales, Département de Chimie et Biologie Structurales et Analytiques, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Frédéric Halgand
- Institut de Chimie Physique, Equipe Chimie Analytique Physicochimie Réactivité des Ions, CNRS, Université Paris-Saclay, Orsay, France
| | - Tâp Ha-Duong
- BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Julia Kaffy
- BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Sandrine Ongeri
- BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
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3
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Pinet L, Wang YH, Deville C, Lescop E, Guerlesquin F, Badache A, Bontems F, Morellet N, Durand D, Assrir N, van Heijenoort C. Structural and dynamic characterization of the C-terminal tail of ErbB2: Disordered but not random. Biophys J 2021; 120:1869-1882. [PMID: 33741354 DOI: 10.1016/j.bpj.2021.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 01/23/2023] Open
Abstract
ErbB2 (or HER2) is a receptor tyrosine kinase overexpressed in some breast cancers and associated with poor prognosis. Treatments targeting the receptor extracellular and kinase domains have greatly improved disease outcome in the last 20 years. In parallel, the structures of these domains have been described, enabling better mechanistic understanding of the receptor function and targeted inhibition. However, the ErbB2 disordered C-terminal cytoplasmic tail (CtErbB2) remains very poorly characterized in terms of structure, dynamics, and detailed functional mechanism. Yet, it is where signal transduction is triggered via phosphorylation of tyrosine residues and carried out via interaction with adaptor proteins. Here, we report the first description, to our knowledge, of the ErbB2 disordered tail at atomic resolution using NMR, complemented by small-angle x-ray scattering. We show that although no part of CtErbB2 has any fully populated secondary or tertiary structure, it contains several transient α-helices and numerous transient polyproline II helices, populated up to 20 and 40%, respectively, and low but significant compaction. The presence of some structural elements suggests, along the lines of the results obtained for EGFR (ErbB1), that they may have a functional role in ErbB2's autoregulation processes. In addition, the transient formation of polyproline II helices is compliant with previously suggested interactions with SH3 domains. All in all, our in-depth structural study opens perspectives in the mechanistic understanding of ErbB2.
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Affiliation(s)
- Louise Pinet
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France; Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Ying-Hui Wang
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France; SGS Taiwan LTD, New Taipei City, Taiwan
| | - Célia Deville
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France; IGBMC, University of Strasbourg, CNRS UMR, Illkirch, France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Françoise Guerlesquin
- LISM, Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille University, Marseille, France
| | - Ali Badache
- Centre de Recherche en Cancérologie de Marseille, Aix-Marseille Univ, INSERM, Institut Paoli-Calmettes, CNRS, Marseille, France
| | - François Bontems
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France; Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France
| | - Nelly Morellet
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Dominique Durand
- I2BC, Université Paris-Saclay, CNRS UMR 9198, Gif-sur-Yvette, France
| | - Nadine Assrir
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Carine van Heijenoort
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France.
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4
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Pinet L, Wang YH, Vogel A, Guerlesquin F, Assrir N, Heijenoort CV. [Formula: see text]H, [Formula: see text]C and [Formula: see text]N assignments of human Grb2 free of ligands. Biomol NMR Assign 2020; 14:323-327. [PMID: 32844357 PMCID: PMC7462913 DOI: 10.1007/s12104-020-09970-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Growth factor receptor-bound 2 (Grb2) is an important link in the receptor tyrosine kinase signaling cascades. It is involved in crucial processes, both physiological (mainly embryogenesis) and pathological (different types of cancer). Several binding partners of all three domains (SH3-SH2-SH3) of this adaptor protein are well described, such as ErbB family members for the SH2 domain and Sos for the SH3 domains. How the different domains interact with each other, both structurally and functionally, is still unclear. These interactions could be essential for regulation processes, and therefore are of great interest. Although a lot of structural data on Grb2 exist, they describe either individual domains, ligand-bound conformations, or frozen pictures of the protein captured by crystallography. Here we report the assignment of backbone and of [Formula: see text] chemical shifts of full-length, apo-Grb2 in solution. In addition to the assigned conformation corresponding to three well-folded domains, a set of peaks compatible with the presence of an unfolded conformation of the N-terminal SH3 domain is observed. This assignment paves the way for future studies of inter-domain interactions and dynamics that have to be taken into account when studying the regulation of Grb2 interactions and signaling pathways.
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Affiliation(s)
- Louise Pinet
- Department of Analytical and Structural Chemistry and Biology, Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, 1, av. de la terrasse, 91190 Gif-sur-Yvette, France
- Present Address: Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Ying-Hui Wang
- Department of Analytical and Structural Chemistry and Biology, Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, 1, av. de la terrasse, 91190 Gif-sur-Yvette, France
- Present Address: SGS Taiwan LTD, No.38, Wu Chyuan 7th Rd., New Taipei Industrial Park, Wu Ku District, New Taipei City, 24890 Taiwan
| | - Anaïs Vogel
- Department of Analytical and Structural Chemistry and Biology, Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, 1, av. de la terrasse, 91190 Gif-sur-Yvette, France
- Present Address: NG Biotech, ZI Courbouton, 35480 Guipry, France
| | - Françoise Guerlesquin
- LISM, Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille University, Marseille, France
| | - Nadine Assrir
- Department of Analytical and Structural Chemistry and Biology, Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, 1, av. de la terrasse, 91190 Gif-sur-Yvette, France
| | - Carine van Heijenoort
- Department of Analytical and Structural Chemistry and Biology, Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, 1, av. de la terrasse, 91190 Gif-sur-Yvette, France
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5
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Rivière G, Oueslati S, Gayral M, Créchet JB, Nhiri N, Jacquet E, Cintrat JC, Giraud F, van Heijenoort C, Lescop E, Pethe S, Iorga BI, Naas T, Guittet E, Morellet N. NMR Characterization of the Influence of Zinc(II) Ions on the Structural and Dynamic Behavior of the New Delhi Metallo-β-Lactamase-1 and on the Binding with Flavonols as Inhibitors. ACS Omega 2020; 5:10466-10480. [PMID: 32426604 PMCID: PMC7226869 DOI: 10.1021/acsomega.0c00590] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/15/2020] [Indexed: 05/22/2023]
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1) has recently emerged as a global threat because of its ability to confer resistance to all common β-lactam antibiotics. Understanding the molecular basis of β-lactam hydrolysis by NDM is crucial for designing NDM inhibitors or β-lactams resistant to their hydrolysis. In this study, for the first time, NMR was used to study the influence of Zn(II) ions on the dynamic behavior of NDM-1. Our results highlighted that the binding of Zn(II) in the NDM-1 active site induced several structural and dynamic changes on active site loop 2 (ASL2) and L9 loops and on helix α2. We subsequently studied the interaction of several flavonols: morin, quercetin, and myricetin were identified as natural and specific inhibitors of NDM-1. Quercetin conjugates were also synthesized in an attempt to increase the solubility and bioavailability. Our NMR investigations on NDM-1/flavonol interactions highlighted that both Zn(II) ions and the residues of the NDM-1 ASL1, ASL2, and ASL4 loops are involved in the binding of flavonols. This is the first NMR interaction study of NDM-1/inhibitors, and the models generated using HADDOCK will be useful for the rational design of more active inhibitors, directed against NDM-1.
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Affiliation(s)
- Gwladys Rivière
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Saoussen Oueslati
- EA7361
“Structure, Dynamic, Function and Expression of Broad Spectrum
β-Lactamases”, Faculty of Medicine, Université Paris-Sud, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France
| | - Maud Gayral
- Institut
de Chimie Moléculaire et des Matériaux d’Orsay
(ICMMO), CNRS, Université Paris Sud, Université Paris-Saclay, 15 rue Georges Clemenceau, 91405 Orsay Cedex, France
| | | | - Naïma Nhiri
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Eric Jacquet
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Jean-Christophe Cintrat
- Service
de Chimie Bio-organique et Marquage (SCBM), CEA, Université Paris-Saclay, LabEx LERMIT, 91191 Gif/Yvette, France
| | - François Giraud
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Carine van Heijenoort
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Ewen Lescop
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Stéphanie Pethe
- EA7361
“Structure, Dynamic, Function and Expression of Broad Spectrum
β-Lactamases”, Faculty of Medicine, Université Paris-Sud, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France
| | - Bogdan I. Iorga
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Thierry Naas
- EA7361
“Structure, Dynamic, Function and Expression of Broad Spectrum
β-Lactamases”, Faculty of Medicine, Université Paris-Sud, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France
- . Phone:(33)145212019 or (33)145213030. Fax: (33)145216340
| | - Eric Guittet
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Nelly Morellet
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
- . Phone:(33)169823762. Fax: (33)169823784
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6
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Chan-Yao-Chong M, Deville C, Pinet L, van Heijenoort C, Durand D, Ha-Duong T. Structural Characterization of N-WASP Domain V Using MD Simulations with NMR and SAXS Data. Biophys J 2019; 116:1216-1227. [PMID: 30878202 DOI: 10.1016/j.bpj.2019.02.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/14/2019] [Accepted: 02/19/2019] [Indexed: 11/19/2022] Open
Abstract
Because of their large conformational heterogeneity, structural characterization of intrinsically disordered proteins (IDPs) is very challenging using classical experimental methods alone. In this study, we use NMR and small-angle x-ray scattering (SAXS) data with multiple molecular dynamics (MD) simulations to describe the conformational ensemble of the fully disordered verprolin homology domain of the neural Aldrich syndrome protein involved in the regulation of actin polymerization. First, we studied several back-calculation software of SAXS scattering intensity and optimized the adjustable parameters to accurately calculate the SAXS intensity from an atomic structure. We also identified the most appropriate force fields for MD simulations of this IDP. Then, we analyzed four conformational ensembles of neural Aldrich syndrome protein verprolin homology domain, two generated with the program flexible-meccano with or without NMR-derived information as input and two others generated by MD simulations with two different force fields. These four conformational ensembles were compared to available NMR and SAXS data for validation. We found that MD simulations with the AMBER-03w force field and the TIP4P/2005s water model are able to correctly describe the conformational ensemble of this 67-residue IDP at both local and global level.
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Affiliation(s)
- Maud Chan-Yao-Chong
- BioCIS, University Paris-Sud, CNRS UMR 8076, University Paris-Saclay, Châtenay-Malabry, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Célia Deville
- IGBMC, University of Strasbourg, CNRS UMR 7104, Illkirch, France
| | - Louise Pinet
- ICSN, CNRS UPR 2301, University Paris-Saclay, Gif-sur-Yvette, France
| | | | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
| | - Tâp Ha-Duong
- BioCIS, University Paris-Sud, CNRS UMR 8076, University Paris-Saclay, Châtenay-Malabry, France.
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7
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Wang Y, Pinet L, Assrir N, Elantak L, Guerlesquin F, Badache A, Lescop E, van Heijenoort C. 1H, 13C and 15N assignments of the C-terminal intrinsically disordered cytosolic fragment of the receptor tyrosine kinase ErbB2. Biomol NMR Assign 2018; 12:23-26. [PMID: 28905237 DOI: 10.1007/s12104-017-9773-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 08/29/2017] [Indexed: 06/07/2023]
Abstract
ErbB2 (or HER2) is a receptor tyrosine kinase that is involved in signaling pathways controlling cell division, motility and apoptosis. Though important in development and cell growth homeostasis, this protein, when overexpressed, participates in triggering aggressive HER2+ breast cancers. It is composed of an extracellular part and a transmembrane domain, both important for activation by dimerization, and a cytosolic tyrosine kinase, which activates its intrinsically disordered C-terminal end (CtErbB2). Little is known about this C-terminal part of 268 residues, despite its crucial role in interacting with adaptor proteins involved in signaling. Understanding its structural and dynamic characteristics could eventually lead to the design of new interaction inhibitors, and treatments complementary to those already targeting other parts of ErbB2. Here we report backbone and side-chain assignment of CtErbB2, which, together with structural predictions, confirms its intrinsically disordered nature.
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Affiliation(s)
- YingHui Wang
- Institut de Chimie des Substances Naturelles, Structural Chemistry and Biology team, CNRS, Université Paris-Saclay, 1 av. de la terrasse, 91190, Gif-sur-Yvette, France
| | - Louise Pinet
- Institut de Chimie des Substances Naturelles, Structural Chemistry and Biology team, CNRS, Université Paris-Saclay, 1 av. de la terrasse, 91190, Gif-sur-Yvette, France
| | - Nadine Assrir
- Institut de Chimie des Substances Naturelles, Structural Chemistry and Biology team, CNRS, Université Paris-Saclay, 1 av. de la terrasse, 91190, Gif-sur-Yvette, France
| | - Latifa Elantak
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS UMR 7255, 13402, Marseille, France
| | - Françoise Guerlesquin
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS UMR 7255, 13402, Marseille, France
| | - Ali Badache
- Centre de Recherche en Cancérologie de Marseille, INSERM U 1068, 13402, Marseille, France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, Structural Chemistry and Biology team, CNRS, Université Paris-Saclay, 1 av. de la terrasse, 91190, Gif-sur-Yvette, France
| | - Carine van Heijenoort
- Institut de Chimie des Substances Naturelles, Structural Chemistry and Biology team, CNRS, Université Paris-Saclay, 1 av. de la terrasse, 91190, Gif-sur-Yvette, France.
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8
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Hamdoun G, Guduff L, van Heijenoort C, Bour C, Gandon V, Dumez JN. Spatially encoded diffusion-ordered NMR spectroscopy of reaction mixtures in organic solvents. Analyst 2018; 143:3458-3464. [DOI: 10.1039/c8an00434j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Using a spatial encoding of the diffusion dimension, DOSY NMR data are acquired in less than one second for reaction mixtures in organic solvents.
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Affiliation(s)
- Ghanem Hamdoun
- Institut de Chimie des Substances Naturelles
- CNRS UPR2301
- Univ. Paris Sud
- Université Paris-Saclay
- 91190 Gif-Sur-Yvette
| | - Ludmilla Guduff
- Institut de Chimie des Substances Naturelles
- CNRS UPR2301
- Univ. Paris Sud
- Université Paris-Saclay
- 91190 Gif-Sur-Yvette
| | - Carine van Heijenoort
- Institut de Chimie des Substances Naturelles
- CNRS UPR2301
- Univ. Paris Sud
- Université Paris-Saclay
- 91190 Gif-Sur-Yvette
| | - Christophe Bour
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- CNRS UMR 8182
- Univ. Paris Sud
- Université Paris-Saclay
- 91405 Orsay
| | - Vincent Gandon
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- CNRS UMR 8182
- Univ. Paris Sud
- Université Paris-Saclay
- 91405 Orsay
| | - Jean-Nicolas Dumez
- Institut de Chimie des Substances Naturelles
- CNRS UPR2301
- Univ. Paris Sud
- Université Paris-Saclay
- 91190 Gif-Sur-Yvette
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9
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Abstract
The separation of 2D spectra of components in mixtures is accelerated with spatial encoding.
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Affiliation(s)
- Ludmilla Guduff
- Institut de Chimie des Substances Naturelles
- CNRS UPR2301
- Univ. Paris Sud
- Université Paris-Saclay
- 91190 Gif-sur-Yvette
| | - Ilya Kuprov
- School of Chemistry
- University of Southampton
- Southampton SO17 1BJ
- UK
| | - Carine van Heijenoort
- Institut de Chimie des Substances Naturelles
- CNRS UPR2301
- Univ. Paris Sud
- Université Paris-Saclay
- 91190 Gif-sur-Yvette
| | - Jean-Nicolas Dumez
- Institut de Chimie des Substances Naturelles
- CNRS UPR2301
- Univ. Paris Sud
- Université Paris-Saclay
- 91190 Gif-sur-Yvette
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10
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Guduff L, Allami AJ, van Heijenoort C, Dumez JN, Kuprov I. Efficient simulation of ultrafast magnetic resonance experiments. Phys Chem Chem Phys 2017; 19:17577-17586. [DOI: 10.1039/c7cp03074f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We present a convenient and powerful simulation formalism for ultrafast NMR spectroscopy. The formalism is based on the Fokker–Planck equation that supports systems with complicated combinations of classical spatial dynamics and quantum mechanical spin dynamics.
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Affiliation(s)
- Ludmilla Guduff
- Institut de Chimie des Substances Naturelles
- CNRS UPR2301
- Université Paris Sud
- Université Paris-Saclay
- 91190 Gif-sur-Yvette
| | | | - Carine van Heijenoort
- Institut de Chimie des Substances Naturelles
- CNRS UPR2301
- Université Paris Sud
- Université Paris-Saclay
- 91190 Gif-sur-Yvette
| | - Jean-Nicolas Dumez
- Institut de Chimie des Substances Naturelles
- CNRS UPR2301
- Université Paris Sud
- Université Paris-Saclay
- 91190 Gif-sur-Yvette
| | - Ilya Kuprov
- School of Chemistry
- University of Southampton
- Southampton
- UK
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11
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Deville C, Girard-Blanc C, Assrir N, Nhiri N, Jacquet E, Bontems F, Renault L, Petres S, van Heijenoort C. Mutations in actin used for structural studies partially disrupt β-thymosin/WH2 domains interaction. FEBS Lett 2016; 590:3690-3699. [PMID: 27680677 DOI: 10.1002/1873-3468.12423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/25/2016] [Accepted: 09/06/2016] [Indexed: 11/10/2022]
Abstract
Understanding the structural basis of actin cytoskeleton remodeling requires stabilization of actin monomers, oligomers, and filaments in complex with partner proteins, using various biochemical strategies. Here, we report a dramatic destabilization of the dynamic interaction with a model β-thymosin/WH2 domain induced by mutations in actin. This result underlines that mutant actins should be used with prudence to characterize interactions with intrinsically disordered partners as destabilization of dynamic interactions, although identifiable by NMR, may be invisible to other structural techniques. It also highlights how both β-thymosin/WH2 domains and actin tune local structure and dynamics in regulatory processes involving intrinsically disordered domains.
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Affiliation(s)
- Célia Deville
- Structural Chemistry and Biology Team, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Nadine Assrir
- Structural Chemistry and Biology Team, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Naïma Nhiri
- Structural Chemistry and Biology Team, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Eric Jacquet
- Structural Chemistry and Biology Team, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - François Bontems
- Structural Chemistry and Biology Team, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Louis Renault
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Carine van Heijenoort
- Structural Chemistry and Biology Team, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.
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12
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Renault L, Deville C, van Heijenoort C. Structural features and interfacial properties of WH2, β-thymosin domains and other intrinsically disordered domains in the regulation of actin cytoskeleton dynamics. Cytoskeleton (Hoboken) 2013; 70:686-705. [DOI: 10.1002/cm.21140] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 08/28/2013] [Accepted: 09/01/2013] [Indexed: 01/12/2023]
Affiliation(s)
- Louis Renault
- Laboratoire d'Enzymologie et Biochimie Structurales; Centre de Recherche de Gif, CNRS; Gif-sur-Yvette France
| | - Célia Deville
- Laboratoire de Chimie et Biologie Structurales; Institut de Chimie des Substances Naturelles, Centre de Recherche de Gif, CNRS; Gif-sur-Yvette France
| | - Carine van Heijenoort
- Laboratoire de Chimie et Biologie Structurales; Institut de Chimie des Substances Naturelles, Centre de Recherche de Gif, CNRS; Gif-sur-Yvette France
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13
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Catoire LJ, Damian M, Giusti F, Martin A, van Heijenoort C, Popot JL, Guittet E, Banères JL. Structure of a GPCR ligand in its receptor-bound state: leukotriene B4 adopts a highly constrained conformation when associated to human BLT2. J Am Chem Soc 2010; 132:9049-57. [PMID: 20552979 DOI: 10.1021/ja101868c] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
G protein-coupled receptors (GPCRs) are key players in signal recognition and cell communication and are among the most important targets for drug development. Direct structural information on the conformation of GPCR ligands bound to their receptors is scarce. Using a leukotriene receptor, BLT2, expressed under a perdeuterated form in Escherichia coli , purified in milligram amounts, and folded to its native state using amphipols, we have solved, by (1)H NMR, the structure of receptor-bound leukotriene B4 (LTB4). Upon binding, LTB4 adopts a highly constrained seahorse conformation, at variance with the free state, where it explores a wide range of conformations. This structure provides an experimentally determined template of a pro-inflammatory compound for further pharmacological studies. The novel approach used for its determination could prove powerful to investigate ligand binding to GPCRs and membrane proteins in general.
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Affiliation(s)
- Laurent J Catoire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université Paris-7, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, F-75005 Paris, France.
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14
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Buosi V, Placial JP, Leroy JL, Cherfils J, Guittet É, van Heijenoort C. Insight into the role of dynamics in the conformational switch of the small GTP-binding protein Arf1. J Biol Chem 2010; 285:37987-94. [PMID: 20861011 DOI: 10.1074/jbc.m110.134445] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Activation of the small GTP-binding protein Arf1, a major regulator of cellular traffic, follows an ordered sequence of structural events, which have been pictured by crystallographic snapshots. Combined with biochemical analysis, these data lead to a model of Arf1 activation, in which opening of its N-terminal helix first translocates Arf1-GDP to membranes, where it is then secured by a register shift of the interswitch β-strands, before GDP is eventually exchanged for GTP. However, how Arf1 rearranges its central β-sheet, an event that involves the loss and re-formation of H-bonds deep within the protein core, is not explained by available structural data. Here, we used Δ17Arf1, in which the N-terminal helix has been deleted, to address this issue by NMR structural and dynamics analysis. We first completed the assignment of Δ17Arf1 bound to GDP, GTP, and GTPγS and established that NMR data are fully consistent with the crystal structures of Arf1-GDP and Δ17Arf1-GTP. Our assignments allowed us to analyze the kinetics of both protein conformational transitions and nucleotide exchange by real-time NMR. Analysis of the dynamics over a very large range of timescale by (15)N relaxation, CPMG relaxation dispersion and H/D exchange reveals that while Δ17Arf1-GTP and full-length Arf1-GDP dynamics is restricted to localized fast motions, Δ17Arf1-GDP features unique intermediate and slow motions in the interswitch region. Altogether, the NMR data bring insight into how that membrane-bound Arf1-GDP, which is mimicked by the truncation of the N-terminal helix, acquires internal motions that enable the toggle of the interswitch.
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Affiliation(s)
- Vanessa Buosi
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette Cedex, France
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15
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Nunez M, Guittet E, Pompon D, van Heijenoort C, Truan G. NMR structure note: oxidized microsomal human cytochrome b5. J Biomol NMR 2010; 47:289-295. [PMID: 20532590 DOI: 10.1007/s10858-010-9428-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Accepted: 05/11/2010] [Indexed: 05/29/2023]
Affiliation(s)
- Marcela Nunez
- Centre de Génétique Moléculaire, CNRS, Gif-sur-Yvette, France
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16
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Stratmann D, Guittet E, van Heijenoort C. Robust structure-based resonance assignment for functional protein studies by NMR. J Biomol NMR 2010; 46:157-73. [PMID: 20024602 PMCID: PMC2813526 DOI: 10.1007/s10858-009-9390-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 11/04/2009] [Indexed: 05/20/2023]
Abstract
High-throughput functional protein NMR studies, like protein interactions or dynamics, require an automated approach for the assignment of the protein backbone. With the availability of a growing number of protein 3D structures, a new class of automated approaches, called structure-based assignment, has been developed quite recently. Structure-based approaches use primarily NMR input data that are not based on J-coupling and for which connections between residues are not limited by through bonds magnetization transfer efficiency. We present here a robust structure-based assignment approach using mainly H(N)-H(N) NOEs networks, as well as (1)H-(15) N residual dipolar couplings and chemical shifts. The NOEnet complete search algorithm is robust against assignment errors, even for sparse input data. Instead of a unique and partly erroneous assignment solution, an optimal assignment ensemble with an accuracy equal or near to 100% is given by NOEnet. We show that even low precision assignment ensembles give enough information for functional studies, like modeling of protein-complexes. Finally, the combination of NOEnet with a low number of ambiguous J-coupling sequential connectivities yields a high precision assignment ensemble. NOEnet will be available under: http://www.icsn.cnrs-gif.fr/download/nmr.
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Affiliation(s)
- Dirk Stratmann
- NMR, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Eric Guittet
- Centre de Recherche de Gif, Laboratoire de Chimie et Biologie Structurales ICSN-CNRS, 1, av. de la terrasse, 91190 Gif-sur-Yvette, France
| | - Carine van Heijenoort
- Centre de Recherche de Gif, Laboratoire de Chimie et Biologie Structurales ICSN-CNRS, 1, av. de la terrasse, 91190 Gif-sur-Yvette, France
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17
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Catoire LJ, Zoonens M, van Heijenoort C, Giusti F, Guittet E, Popot JL. Solution NMR mapping of water-accessible residues in the transmembrane beta-barrel of OmpX. Eur Biophys J 2009; 39:623-30. [PMID: 19639312 DOI: 10.1007/s00249-009-0513-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Revised: 06/19/2009] [Accepted: 06/22/2009] [Indexed: 12/11/2022]
Abstract
The atomic structure of OmpX, the smallest member of the bacterial outer membrane protein family, has been previously established by X-ray crystallography and NMR spectroscopy. In apparent conflict with electrophysiological studies, the lumen of its transmembrane beta-barrel appears too tightly packed with amino acid side chains to let any solute flow through. In the present study, high-resolution solution NMR spectra were obtained of OmpX kept water-soluble by either amphipol A8-35 or the detergent dihexanoylphosphatidylcholine. Hydrogen/deuterium exchange measurements performed after prolonged equilibration show that, whatever the surfactant used, some of the amide protons of the membrane-spanning region exchange much more readily than others, which likely reflects the dynamics of the barrel.
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Affiliation(s)
- Laurent J Catoire
- Laboratoire de Physico-Chimie Moléculaire des Protéines Membranaires, UMR 7099, CNRS/Université Paris-7, Institut de Biologie Physico-Chimique (FRC 550), 75005 Paris, France.
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18
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Catoire LJ, Zoonens M, van Heijenoort C, Giusti F, Popot JL, Guittet E. Inter- and intramolecular contacts in a membrane protein/surfactant complex observed by heteronuclear dipole-to-dipole cross-relaxation. J Magn Reson 2009; 197:91-95. [PMID: 19101186 DOI: 10.1016/j.jmr.2008.11.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Revised: 11/17/2008] [Accepted: 11/18/2008] [Indexed: 05/27/2023]
Abstract
Heteronuclear dipole-to-dipole cross-relaxation has been applied to exploring intermolecular interactions and intramolecular spatial proximities in a large supramolecular structure comprised of a beta-barrel membrane protein, OmpX, in complex with a polymeric surfactant, amphipol A8-35. The experiments, performed in either the laboratory or the rotating frame, reveal the existence of intermolecular contacts between aromatic amino acids and specific groups of the polymer, in addition to intra-protein dipolar interactions, some of them involving carbonyl carbons. This study opens the perspective of collecting by NMR spectroscopy a new kind of through-space structural information involving aromatic and carbonyl (13)C atoms of large proteins.
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Affiliation(s)
- Laurent J Catoire
- Laboratoire de Physico-Chimie Moléculaire des Membranes Biologiques, UMR 7099 CNRS/Université Paris-7, IBPC, 13 rue Pierre et Marie Curie, F-75005 Paris, France.
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19
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Abstract
Motivation: A prerequisite for any protein study by NMR is the assignment of the resonances from the 15N−1H HSQC spectrum to their corresponding atoms of the protein backbone. Usually, this assignment is obtained by analyzing triple resonance NMR experiments. An alternative assignment strategy exploits the information given by an already available 3D structure of the same or a homologous protein. Up to now, the algorithms that have been developed around the structure-based assignment strategy have the important drawbacks that they cannot guarantee a high assignment accuracy near to 100%. Results: We propose here a new program, called NOEnet, implementing an efficient complete search algorithm that ensures the correctness of the assignment results. NOEnet exploits the network character of unambiguous NOE constraints to realize an exhaustive search of all matching possibilities of the NOE network onto the structural one. NOEnet has been successfully tested on EIN, a large protein of 28 kDa, using only NOE data. The complete search of NOEnet finds all possible assignments compatible with experimental data that can be defined as an assignment ensemble. We show that multiple assignment possibilities of large NOE networks are restricted to a small spatial assignment range (SAR), so that assignment ensembles, obtained from accessible experimental data, are precise enough to be used for functional proteins studies, like protein–ligand interaction or protein dynamics studies. We believe that NOEnet can become a major tool for the structure-based backbone resonance assignment strategy in NMR. Availability: The NOEnet program will be available under: http://www.icsn.cnrs-gif.fr/download/nmr Contact:carine@icsn.cnrs-gif.fr; eric.guittet@icsn.cnrs-gif.fr Supplementary Information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Dirk Stratmann
- Laboratoire de Chimie et Biologie Structurales, ICSN-CNRS, Gif-sur-Yvette, France
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20
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Cabal S, van Heijenoort C, Guittet E. (1)H, (13)C and (15)N resonance assignment of the first N-terminal RNA recognition motif (RRM) of the human heterogeneous nuclear ribonucleoprotein H (hnRNP H). Biomol NMR Assign 2007; 1:221-223. [PMID: 19636870 DOI: 10.1007/s12104-007-9061-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Accepted: 10/18/2007] [Indexed: 05/28/2023]
Abstract
Human heterogeneous nuclear ribonucleoprotein H (hnRNP H) regulates alternative splicing of HIV-1 Tat pre-mRNA. The structure of the first N-terminal domain (residues 1-104) of hnRNP H was solved and its binding to an exonic splicing silencer (pESS2) studied. For this, all backbone and 85% of side-chain resonance frequencies were assigned.
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21
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Agez M, Chen J, Guerois R, van Heijenoort C, Thuret JY, Mann C, Ochsenbein F. Structure of the histone chaperone ASF1 bound to the histone H3 C-terminal helix and functional insights. Structure 2007; 15:191-9. [PMID: 17292837 DOI: 10.1016/j.str.2007.01.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2006] [Revised: 12/29/2006] [Accepted: 01/07/2007] [Indexed: 12/01/2022]
Abstract
Asf1 is a histone chaperone that favors histone H3/H4 assembly and disassembly. We solved the structure of the conserved domain of human ASF1A in complex with the C-terminal helix of histone H3 using nuclear magnetic resonance spectroscopy. This structure is fully compatible with an association of ASF1 with the heterodimeric form of histones H3/H4. In our model, ASF1 substitutes for the second H3/H4 heterodimer that is normally found in heterotetrameric H3/H4 complexes. This result constitutes an essential step in the fundamental understanding of the mechanisms of nucleosome assembly by histone chaperones. Point mutations that perturb the Asf1/histone interface were designed from the structure. The decreased binding affinity of the Asf1-H3/H4 complex correlates with decreased levels of H3-K56 acetylation and phenotypic defects in vivo.
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Affiliation(s)
- Morgane Agez
- Institut de Biologie et de Technologie de Saclay, Commissariat à l'Energie Atomique/Saclay, F-91191 Gif-sur-Yvette Cedex, France
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22
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Domanski M, Hertzog M, Coutant J, Gutsche-Perelroizen I, Bontems F, Carlier MF, Guittet E, van Heijenoort C. Coupling of Folding and Binding of Thymosin β4 upon Interaction with Monomeric Actin Monitored by Nuclear Magnetic Resonance. J Biol Chem 2004; 279:23637-45. [PMID: 15039431 DOI: 10.1074/jbc.m311413200] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Thymosin beta4 is a major actin-sequestering protein, yet the structural basis for its biological function is still unknown. This study provides insight regarding the way this 43-amino acid peptide, mostly unstructured in solution, binds to monomeric actin and prevents its assembly in filaments. We show here that the whole backbone of thymosin beta4 is highly affected upon binding to G-actin. The assignment of all amide protons and nitrogens of thymosin in the bound state, obtained using a combination of NMR experiments and selective labelings, shows that thymosin folds completely upon binding and displays a central extended region flanked by two N- and C-terminal helices. The cleavage of actin by subtilisin in the DNase I binding loop does not modify the structure of thymosin beta4 in the complex, showing that the backbone of the peptide is not in close proximity to segment 42-47 of actin. The combination of our NMR results and previously published mutation and cross-link data allows a better characterization of the binding mode of thymosins on G-actin.
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Affiliation(s)
- Michael Domanski
- Institut de Chimie des Substances Naturelles, Laboratoire de Chimie et Biologie Structurales, CNRS, 1 Avenue de la Terrasse, F-91190 Gif sur Yvette, France
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23
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Hertzog M, van Heijenoort C, Didry D, Gaudier M, Coutant J, Gigant B, Didelot G, Préat T, Knossow M, Guittet E, Carlier MF. The β-Thymosin/WH2 Domain. Cell 2004; 117:611-23. [PMID: 15163409 DOI: 10.1016/s0092-8674(04)00403-9] [Citation(s) in RCA: 181] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2003] [Revised: 03/12/2004] [Accepted: 03/23/2004] [Indexed: 11/27/2022]
Abstract
The widespread beta-thymosin/WH2 actin binding domain has versatile regulatory properties in actin dynamics and motility. beta-thymosins (isolated WH2 domain) maintain monomeric actin in a "sequestered" nonpolymerizable form. In contrast, when repeated in tandem or inserted in modular proteins, the beta-thymosin/WH2 domain promotes actin assembly at filament barbed ends, like profilin. The structural basis for these opposite functions is addressed using ciboulot, a three beta-thymosin repeat protein. Only the first repeat binds actin and possesses the function of ciboulot. The region that shows the strongest interaction with actin is an amphipathic N-terminal alpha helix, present in all beta-thymosin/WH2 domains, which recognizes the ATP bound actin structure and uses the shear motion of actin linked to ATP hydrolysis to control polymerization. Crystallographic ((1)H, (15)N), NMR, and mutagenetic data reveal that the weaker interaction of the C-terminal region of beta-thymosin/WH2 domain with actin accounts for the switch in function from inhibition to promotion of actin assembly.
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Affiliation(s)
- Maud Hertzog
- Dynamique du Cytosquelette, Laboratoire d'Enzymologie et Biochimie Structurales, Institut Alfred Fessard, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, France
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24
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Gallopin M, Ochsenbein F, Guittet É, van Heijenoort C. Analysis of slow motions in the micro–millisecond range on domain 1 of annexin I. CR CHIM 2004. [DOI: 10.1016/j.crci.2003.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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25
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Ochsenbein F, Neumann JM, Guittet E, van Heijenoort C. Dynamical characterization of residual and non-native structures in a partially folded protein by (15)N NMR relaxation using a model based on a distribution of correlation times. Protein Sci 2002; 11:957-64. [PMID: 11910038 PMCID: PMC2373535 DOI: 10.1110/ps.4000102] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
A spectral density model based on a truncated lorentzian distribution of correlation times is used to analyze the nanosecond time-scale dynamics of the partially unfolded domain 2 of annexin I from its (15)N NMR relaxation parameters measured at three magnetic field strengths. The use of a distribution of correlation times enables the characterization of the dynamical features of the NH bonds of the protein in terms of heterogeneity of dynamical states in the nanosecond range. The variation along the sequence of the two dynamical parameters introduced, namely the center and the width of the distribution, points out the different types of residual secondary structures present in the D2 domain. Moreover, it allows a physically sensible interpretation of the dynamical behavior of the different residual helices and of the non-native structures. Also, a striking correspondence is found between the parameters obtained using an extended Lipari and Szabo model and the parameters obtained using the distribution of correlation times. This result led us to propose a specific interpretation of the model-free order parameter for internal motions in the nanosecond range in the case of unfolded states.
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Affiliation(s)
- Françoise Ochsenbein
- CNRS, Institut de Chimie des Substances Naturelles, F-91190 Gif sur Yvette, France.
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