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Ruedas R, Vuillemot R, Tubiana T, Winter JM, Pieri L, Arteni AA, Samson C, Jonic S, Mathieu M, Bressanelli S. Structure and conformational variability of the HER2-trastuzumab-pertuzumab complex. J Struct Biol 2024; 216:108095. [PMID: 38723875 DOI: 10.1016/j.jsb.2024.108095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 03/11/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024]
Abstract
Single particle analysis from cryogenic transmission electron microscopy (cryo-EM) is particularly attractive for complexes for which structure prediction remains intractable, such as antibody-antigen complexes. Here we obtain the detailed structure of a particularly difficult complex between human epidermal growth factor receptor 2 (HER2) and the antigen-binding fragments from two distinct therapeutic antibodies binding to distant parts of the flexible HER2, pertuzumab and trastuzumab (HTP). We highlight the strengths and limitations of current data processing software in dealing with various kinds of heterogeneities, particularly continuous conformational heterogeneity, and in describing the motions that can be extracted from our dataset. Our HTP structure provides a more detailed view than the one previously available for this ternary complex. This allowed us to pinpoint a previously overlooked loop in domain IV that may be involved both in binding of trastuzumab and in HER2 dimerization. This finding may contribute to explain the synergistic anticancer effect of the two antibodies. We further propose that the flexibility of the HTP complex, beyond the difficulties it causes for cryo-EM analysis, actually reflects regulation of HER2 signaling and its inhibition by therapeutic antibodies. Notably we obtain our best data with ultra-thin continuous carbon grids, showing that with current cameras their use to alleviate particle misdistribution is compatible with a protein complex of only 162 kDa. Perhaps most importantly, we provide here a dataset for such a smallish protein complex for further development of software accounting for continuous conformational heterogeneity in cryo-EM images.
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Affiliation(s)
- Rémi Ruedas
- Université Paris-Saclay, CEA, CNRS - Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France; Sanofi, Integrated Drug Discovery, 13, quai Jules Guesde 94403, Vitry-sur-Seine, France
| | - Rémi Vuillemot
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, 75005, Paris, France
| | - Thibault Tubiana
- Université Paris-Saclay, CEA, CNRS - Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Jean-Marie Winter
- NanoImaging Core Facility, Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, 75015, Paris, France
| | - Laura Pieri
- Université Paris-Saclay, CEA, CNRS - Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Ana-Andreea Arteni
- Université Paris-Saclay, CEA, CNRS - Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Camille Samson
- Sanofi, Integrated Drug Discovery, 13, quai Jules Guesde 94403, Vitry-sur-Seine, France
| | - Slavica Jonic
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, 75005, Paris, France
| | - Magali Mathieu
- Sanofi, Integrated Drug Discovery, 13, quai Jules Guesde 94403, Vitry-sur-Seine, France
| | - Stéphane Bressanelli
- Université Paris-Saclay, CEA, CNRS - Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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Beratto-Ramos A, Dagnino-Leone J, Martínez-Oyanedel J, Fernández M, Aranda M, Bórquez R. Optimization of detergents in solubilization and reconstitution of Aquaporin Z: A structural approach. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184101. [PMID: 36535340 DOI: 10.1016/j.bbamem.2022.184101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/03/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND The exceptional capacities of aquaporins in terms of water permeation and selectivity have made them an interesting system for membrane applications. Despite the multiple attempts for immobilizing the aquaporins over a porous substrate, there is a lack of studies related to the purification and reconstitution steps, principally associated with the use of detergents in solubilization and destabilization steps. This study analyzed the effect of detergents in Aquaporin Z solubilization, considering the purity and structural homogeneity of the protein. METHODS The extraction process was optimized by the addition of detergent at the sonication step, which enabled the omission of the ultracentrifugation and resuspension steps. Two detergents, Triton X-100, and octyl-glucoside were also evaluated. Destabilization mediated by detergents was used as reconstitution method. Saturation and solubilization points were defined by detergent concentration and both, liposomes and proteoliposomes, were analyzed by size distribution and permeability assays. Detergent removal with Bio-beads was also analyzed. RESULTS Octyl glucoside ensures structural stability and homogeneity of Aquaporin Z. However, high concentrations of detergents induce the presence of defects in proteoliposomes. While saturated liposomes create homogeneous and functional structures, solubilized liposomes get affected by a reassembly process, creating vesicle defects with anomalous permeability profiles. CONCLUSIONS Detergent concentration affects the structural conformation of proteoliposomes in the reconstitution process. GENERAL SIGNIFICANCE Since the destabilization process is dependent on vesicle, detergent, and buffer composition, optimization of this process should be mandatory for further studies. All these considerations will allow achieving the potential of Aquaporins and any other integral membrane protein in their applications for industrial purposes.
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Affiliation(s)
| | | | - José Martínez-Oyanedel
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - Marcos Fernández
- Departamento de Farmacia, Facultad de Farmacia, Universidad de Concepción, Chile
| | - Mario Aranda
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Chile
| | - Rodrigo Bórquez
- Department of Chemical Engineering, Universidad de Concepción, Chile.
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Robert C, Kerff F, Bouillenne F, Gavage M, Vandevenne M, Filée P, Matagne A. Structural analysis of the interaction between human cytokine BMP-2 and the antagonist Noggin reveals molecular details of cell chondrogenesis inhibition. J Biol Chem 2023; 299:102892. [PMID: 36642181 PMCID: PMC9929448 DOI: 10.1016/j.jbc.2023.102892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/04/2023] [Accepted: 01/06/2023] [Indexed: 01/14/2023] Open
Abstract
Bone morphogenetic proteins (BMPs) are secreted cytokines belonging to the transforming growth factor-β superfamily. New therapeutic approaches based on BMP activity, particularly for cartilage and bone repair, have sparked considerable interest; however, a lack of understanding of their interaction pathways and the side effects associated with their use as biopharmaceuticals have dampened initial enthusiasm. Here, we used BMP-2 as a model system to gain further insight into both the relationship between structure and function in BMPs and the principles that govern affinity for their cognate antagonist Noggin. We produced BMP-2 and Noggin as inclusion bodies in Escherichia coli and developed simple and efficient protocols for preparing pure and homogeneous (in terms of size distribution) solutions of the native dimeric forms of the two proteins. The identity and integrity of the proteins were confirmed using mass spectrometry. Additionally, several in vitro cell-based assays, including enzymatic measurements, RT-qPCR, and matrix staining, demonstrated their biological activity during cell chondrogenic and hypertrophic differentiation. Furthermore, we characterized the simple 1:1 noncovalent interaction between the two ligands (KDca. 0.4 nM) using bio-layer interferometry and solved the crystal structure of the complex using X-ray diffraction methods. We identified the residues and binding forces involved in the interaction between the two proteins. Finally, results obtained with the BMP-2 N102D mutant suggest that Noggin is remarkably flexible and able to accommodate major structural changes at the BMP-2 level. Altogether, our findings provide insights into BMP-2 activity and reveal the molecular details of its interaction with Noggin.
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Affiliation(s)
- Charly Robert
- Laboratory of Enzymology and Protein Folding, University of Liège, Liège, Belgium,Centre for Protein Engineering, InBioS Research Unit, University of Liège, Liège, Belgium
| | - Frédéric Kerff
- Centre for Protein Engineering, InBioS Research Unit, University of Liège, Liège, Belgium,Biological Macromolecule Crystallography, University of Liège, Liège, Belgium
| | - Fabrice Bouillenne
- Centre for Protein Engineering, InBioS Research Unit, University of Liège, Liège, Belgium
| | - Maxime Gavage
- Analytical Laboratory, CER Groupe, rue du Point du Jour, Marloie, Belgium
| | - Marylène Vandevenne
- Laboratory of Enzymology and Protein Folding, University of Liège, Liège, Belgium,Centre for Protein Engineering, InBioS Research Unit, University of Liège, Liège, Belgium
| | - Patrice Filée
- Laboratory of immuno-biology, CER Groupe, Novalis Science Park, Aye, Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, University of Liège, Liège, Belgium; Centre for Protein Engineering, InBioS Research Unit, University of Liège, Liège, Belgium.
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Remans K, Lebendiker M, Abreu C, Maffei M, Sellathurai S, May MM, Vaněk O, de Marco A. Protein purification strategies must consider downstream applications and individual biological characteristics. Microb Cell Fact 2022; 21:52. [PMID: 35392897 PMCID: PMC8991485 DOI: 10.1186/s12934-022-01778-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Proteins are used as reagents in a broad range of scientific fields. The reliability and reproducibility of experimental data will largely depend on the quality of the (recombinant) proteins and, consequently, these should undergo thorough structural and functional controls. Depending on the downstream application and the biochemical characteristics of the protein, different sets of specific features will need to be checked. RESULTS A number of examples, representative of recurrent issues and previously published strategies, has been reported that illustrate real cases of recombinant protein production in which careful strategy design at the start of the project combined with quality controls throughout the production process was imperative to obtain high-quality samples compatible with the planned downstream applications. Some proteins possess intrinsic properties (e.g., prone to aggregation, rich in cysteines, or a high affinity for nucleic acids) that require certain precautions during the expression and purification process. For other proteins, the downstream application might demand specific conditions, such as for proteins intended for animal use that need to be endotoxin-free. CONCLUSIONS This review has been designed to act as a practical reference list for researchers who wish to produce and evaluate recombinant proteins with certain specific requirements or that need particular care for their preparation and storage.
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Affiliation(s)
- Kim Remans
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Mario Lebendiker
- Protein Purification Facility, The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Celeste Abreu
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840, Prague, Czech Republic
| | - Mariano Maffei
- Evvivax Biotech, Via di Castel Romano 100, 00128, Rome, Italy
| | | | - Marina M May
- AiCuris Anti-Infective Cures AG, Friedrich-Ebert-Str. 475, 42117, Wuppertal, Germany
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840, Prague, Czech Republic
| | - Ario de Marco
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, 5000, Rožna Dolina-Nova Gorica, Slovenia.
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England P, Jowitt TA. Community-building and promotion of technological excellence in molecular biophysics: the ARBRE-MOBIEU network. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:307-311. [PMID: 34057541 DOI: 10.1007/s00249-021-01550-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Patrick England
- Molecular Biophysics Facility, Institut Pasteur, 25-28 rue du Docteur Roux, 75724, Paris cedex 15, France.
| | - Thomas A Jowitt
- Biomolecular Analysis Core Facility, Faculty of Biology Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
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de Marco A, Berrow N, Lebendiker M, Garcia-Alai M, Knauer SH, Lopez-Mendez B, Matagne A, Parret A, Remans K, Uebel S, Raynal B. Quality control of protein reagents for the improvement of research data reproducibility. Nat Commun 2021; 12:2795. [PMID: 33990604 PMCID: PMC8121922 DOI: 10.1038/s41467-021-23167-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 04/19/2021] [Indexed: 11/23/2022] Open
Abstract
Proteins and peptides are amongst the most widely used research reagents but often their quality is inadequate and can result in poor data reproducibility. Here we propose a simple set of guidelines that, when correctly applied to protein reagents should provide more reliable experimental data.
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Affiliation(s)
- Ario de Marco
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipava, Vipava, Slovenia
| | - Nick Berrow
- Protein Expression Core Facility, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mario Lebendiker
- Protein Purification Facility, Wolfson Centre for Applied Structural Biology, Edmund J. Safra Campus - The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Maria Garcia-Alai
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Hamburg, Germany
| | - Stefan H Knauer
- Biochemistry IV - Biopolymers, University of Bayreuth, Bayreuth, Germany
| | - Blanca Lopez-Mendez
- Protein Production and Characterization Platform, Novo Nordisk Foundation Center for Protein Research, Copenhagen, Denmark
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Department of Life Sciences, University of Liège, Building B6C, Allée du 6 Août, 13, Liège, Belgium
| | - Annabel Parret
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Hamburg, Germany
| | - Kim Remans
- Protein Expression and Purification Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | | | - Bertrand Raynal
- Institut Pasteur, Plateforme de Biophysique moléculaire, Department of Structural Biology and Chemistry, Paris, France.
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