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Erba EB, Pastore A. The Complementarity of Nuclear Magnetic Resonance and Native Mass Spectrometry in Probing Protein-Protein Interactions. Adv Exp Med Biol 2024; 3234:109-123. [PMID: 38507203 DOI: 10.1007/978-3-031-52193-5_8] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Nuclear magnetic resonance (NMR) and native mass spectrometry (MS) are mature physicochemical techniques with long histories and important applications. NMR spectroscopy provides detailed information about the structure, dynamics, interactions, and chemical environment of biomolecules. MS is an effective approach for determining the mass of biomolecules with high accuracy, sensitivity, and speed. The two techniques offer unique advantages and provide solid tools for structural biology. In the present review, we discuss their individual merits in the context of their applications to structural studies in biology with specific focus on protein interactions and evaluate their limitations. We provide specific examples in which these techniques can complement each other, providing new information on the same scientific case. We discuss how the field may develop and what challenges are expected in the future. Overall, the combination of NMR and MS plays an increasingly important role in integrative structural biology, assisting scientists in deciphering the three-dimensional structure of composite macromolecular assemblies.
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Paris T, Kiss A, Signor L, Lutfalla G, Blaise M, Boeri Erba E, Chaloin L, Yatime L. The IbeA protein from adherent invasive Escherichia coli is a flavoprotein sharing structural homology with FAD-dependent oxidoreductases. FEBS J 2024; 291:177-203. [PMID: 37786987 DOI: 10.1111/febs.16969] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/22/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
Invasion of brain endothelium protein A (IbeA) is a virulence factor specific to pathogenic Escherichia coli. Originally identified in the K1 strain causing neonatal meningitis, it was more recently found in avian pathogenic Escherichia coli (APEC) and adherent invasive Escherichia coli (AIEC). In these bacteria, IbeA facilitates host cell invasion and intracellular survival, in particular, under harsh conditions like oxidative stress. Furthermore, IbeA from AIEC contributes to intramacrophage survival and replication, thus enhancing the inflammatory response within the intestine. Therefore, this factor is a promising drug target for anti-AIEC strategies in the context of Crohn's disease. Despite such an important role, the biological function of IbeA remains largely unknown. In particular, its exact nature and cellular localization, i.e., membrane-bound invasin versus cytosolic factor, are still of debate. Here, we developed an efficient protocol for recombinant expression of IbeA under native conditions and demonstrated that IbeA from AIEC is a soluble, homodimeric flavoprotein. Using mass spectrometry and tryptophan fluorescence measurements, we further showed that IbeA preferentially binds flavin adenine dinucleotide (FAD), with an affinity in the one-hundred nanomolar range and optimal binding under reducing conditions. 3D-modeling with AlphaFold revealed that IbeA shares strong structural homology with FAD-dependent oxidoreductases. Finally, we used ligand docking, mutational analyses, and molecular dynamics simulations to identify the FAD binding pocket within IbeA and characterize possible conformational changes occurring upon ligand binding. Overall, we suggest that the role of IbeA in the survival of AIEC within host cells, notably macrophages, is linked to modulation of redox processes.
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Affiliation(s)
- Théo Paris
- LPHI, Univ. Montpellier, CNRS, INSERM, France
| | - Agneta Kiss
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Luca Signor
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
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Lethier M, Huard K, Hons M, Favier A, Brutscher B, Boeri Erba E, Abbott DW, Cusack S, Pellegrini E. Structure shows that the BIR2 domain of E3 ligase XIAP binds across the RIPK2 kinase dimer interface. Life Sci Alliance 2023; 6:e202201784. [PMID: 37673444 PMCID: PMC10485824 DOI: 10.26508/lsa.202201784] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 09/08/2023] Open
Abstract
RIPK2 is an essential adaptor for NOD signalling and its kinase domain is a drug target for NOD-related diseases, such as inflammatory bowel disease. However, recent work indicates that the phosphorylation activity of RIPK2 is dispensable for signalling and that inhibitors of both RIPK2 activity and RIPK2 ubiquitination prevent the essential interaction between RIPK2 and the BIR2 domain of XIAP, the key RIPK2 ubiquitin E3 ligase. Moreover, XIAP BIR2 antagonists also block this interaction. To reveal the molecular mechanisms involved, we combined native mass spectrometry, NMR, and cryo-electron microscopy to determine the structure of the RIPK2 kinase BIR2 domain complex and validated the interface with in cellulo assays. The structure shows that BIR2 binds across the RIPK2 kinase antiparallel dimer and provides an explanation for both inhibitory mechanisms. It also highlights why phosphorylation of the kinase activation loop is dispensable for signalling while revealing the structural role of RIPK2-K209 residue in the RIPK2-XIAP BIR2 interaction. Our results clarify the features of the RIPK2 conformation essential for its role as a scaffold protein for ubiquitination.
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Affiliation(s)
- Mathilde Lethier
- https://ror.org/01zjc6908 European Molecular Biology Laboratory, Grenoble, France
| | - Karine Huard
- https://ror.org/01zjc6908 European Molecular Biology Laboratory, Grenoble, France
| | - Michael Hons
- https://ror.org/01zjc6908 European Molecular Biology Laboratory, Grenoble, France
| | - Adrien Favier
- University Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Bernhard Brutscher
- University Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Elisabetta Boeri Erba
- University Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Derek W Abbott
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Stephen Cusack
- https://ror.org/01zjc6908 European Molecular Biology Laboratory, Grenoble, France
| | - Erika Pellegrini
- https://ror.org/01zjc6908 European Molecular Biology Laboratory, Grenoble, France
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Iuso D, Garcia-Saez I, Couté Y, Yamaryo-Botté Y, Boeri Erba E, Adrait A, Zeaiter N, Tokarska-Schlattner M, Jilkova ZM, Boussouar F, Barral S, Signor L, Couturier K, Hajmirza A, Chuffart F, Bourova-Flin E, Vitte AL, Bargier L, Puthier D, Decaens T, Rousseaux S, Botté C, Schlattner U, Petosa C, Khochbin S. Nucleoside diphosphate kinases 1 and 2 regulate a protective liver response to a high-fat diet. Sci Adv 2023; 9:eadh0140. [PMID: 37672589 PMCID: PMC10482350 DOI: 10.1126/sciadv.adh0140] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 08/02/2023] [Indexed: 09/08/2023]
Abstract
The synthesis of fatty acids from acetyl-coenzyme A (AcCoA) is deregulated in diverse pathologies, including cancer. Here, we report that fatty acid accumulation is negatively regulated by nucleoside diphosphate kinases 1 and 2 (NME1/2), housekeeping enzymes involved in nucleotide homeostasis that were recently found to bind CoA. We show that NME1 additionally binds AcCoA and that ligand recognition involves a unique binding mode dependent on the CoA/AcCoA 3' phosphate. We report that Nme2 knockout mice fed a high-fat diet (HFD) exhibit excessive triglyceride synthesis and liver steatosis. In liver cells, NME2 mediates a gene transcriptional response to HFD leading to the repression of fatty acid accumulation and activation of a protective gene expression program via targeted histone acetylation. Our findings implicate NME1/2 in the epigenetic regulation of a protective liver response to HFD and suggest a potential role in controlling AcCoA usage between the competing paths of histone acetylation and fatty acid synthesis.
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Affiliation(s)
- Domenico Iuso
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Isabel Garcia-Saez
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble 38000, France
| | - Yohann Couté
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, Grenoble 38000, France
| | - Yoshiki Yamaryo-Botté
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Elisabetta Boeri Erba
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble 38000, France
| | - Annie Adrait
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, Grenoble 38000, France
| | - Nour Zeaiter
- Univ. Grenoble Alpes, INSERM, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France
| | | | - Zuzana Macek Jilkova
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
- CHU Grenoble Alpes, Service d’hépato-gastroentérologie, Pôle Digidune, La Tronche 38700, France
| | - Fayçal Boussouar
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Sophie Barral
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Luca Signor
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble 38000, France
| | - Karine Couturier
- Univ. Grenoble Alpes, INSERM, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France
| | - Azadeh Hajmirza
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Florent Chuffart
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Ekaterina Bourova-Flin
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Anne-Laure Vitte
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Lisa Bargier
- Aix Marseille Université, INSERM, TAGC, TGML, Marseille 13288, France
| | - Denis Puthier
- Aix Marseille Université, INSERM, TAGC, TGML, Marseille 13288, France
| | - Thomas Decaens
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
- CHU Grenoble Alpes, Service d’hépato-gastroentérologie, Pôle Digidune, La Tronche 38700, France
| | - Sophie Rousseaux
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Cyrille Botté
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Uwe Schlattner
- Univ. Grenoble Alpes, INSERM, Institut Universitaire de France, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France
| | - Carlo Petosa
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble 38000, France
| | - Saadi Khochbin
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
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Laroussi H, Juarez‐Martinez AB, Le Roy A, Boeri Erba E, Gabel F, de Massy B, Kadlec J. Characterization of the REC114-MEI4-IHO1 complex regulating meiotic DNA double-strand break formation. EMBO J 2023; 42:e113866. [PMID: 37431931 PMCID: PMC10425845 DOI: 10.15252/embj.2023113866] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
Meiotic recombination is initiated by the formation of DNA double-strand breaks (DSBs), essential for fertility and genetic diversity. In the mouse, DSBs are formed by the catalytic TOPOVIL complex consisting of SPO11 and TOPOVIBL. To preserve genome integrity, the activity of the TOPOVIL complex is finely controlled by several meiotic factors including REC114, MEI4, and IHO1, but the underlying mechanism is poorly understood. Here, we report that mouse REC114 forms homodimers, that it associates with MEI4 as a 2:1 heterotrimer that further dimerizes, and that IHO1 forms coiled-coil-based tetramers. Using AlphaFold2 modeling combined with biochemical characterization, we uncovered the molecular details of these assemblies. Finally, we show that IHO1 directly interacts with the PH domain of REC114 by recognizing the same surface as TOPOVIBL and another meiotic factor ANKRD31. These results provide strong evidence for the existence of a ternary IHO1-REC114-MEI4 complex and suggest that REC114 could act as a potential regulatory platform mediating mutually exclusive interactions with several partners.
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Affiliation(s)
| | | | - Aline Le Roy
- Université Grenoble Alpes, CNRS, CEA, IBSGrenobleFrance
| | | | - Frank Gabel
- Université Grenoble Alpes, CNRS, CEA, IBSGrenobleFrance
| | - Bernard de Massy
- Institut de Génétique Humaine (IGH), Centre National de la Recherche ScientifiqueUniversity of MontpellierMontpellierFrance
| | - Jan Kadlec
- Université Grenoble Alpes, CNRS, CEA, IBSGrenobleFrance
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Linares R, Arnaud CA, Effantin G, Darnault C, Epalle NH, Boeri Erba E, Schoehn G, Breyton C. Structural basis of bacteriophage T5 infection trigger and E. coli cell wall perforation. Sci Adv 2023; 9:eade9674. [PMID: 36961893 PMCID: PMC10038345 DOI: 10.1126/sciadv.ade9674] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Most bacteriophages present a tail allowing host recognition, cell wall perforation, and viral DNA channeling from the capsid to the infected bacterium cytoplasm. The majority of tailed phages bear a long flexible tail (Siphoviridae) at the tip of which receptor binding proteins (RBPs) specifically interact with their host, triggering infection. In siphophage T5, the unique RBP is located at the extremity of a central fiber. We present the structures of T5 tail tip, determined by cryo-electron microscopy before and after interaction with its E. coli receptor, FhuA, reconstituted into nanodisc. These structures bring out the important conformational changes undergone by T5 tail tip upon infection, which include bending of T5 central fiber on the side of the tail tip, tail anchoring to the membrane, tail tube opening, and formation of a transmembrane channel. The data allow to detail the first steps of an otherwise undescribed infection mechanism.
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Vallet A, Martin-Laffon J, Favier A, Revel B, Bonnot T, Vidaud C, Armengaud J, Gaillard JC, Delangle P, Devime F, Figuet S, Serre NBC, Erba EB, Brutscher B, Ravanel S, Bourguignon J, Alban C. The plasma membrane-associated cation-binding protein PCaP1 of Arabidopsis thaliana is a uranyl-binding protein. J Hazard Mater 2023; 446:130668. [PMID: 36608581 DOI: 10.1016/j.jhazmat.2022.130668] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/14/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Uranium (U) is a naturally-occurring radionuclide that is toxic to living organisms. Given that proteins are primary targets of U(VI), their identification is an essential step towards understanding the mechanisms of radionuclide toxicity, and possibly detoxification. Here, we implemented a chromatographic strategy including immobilized metal affinity chromatography to trap protein targets of uranyl in Arabidopsis thaliana. This procedure allowed the identification of 38 uranyl-binding proteins (UraBPs) from root and shoot extracts. Among them, UraBP25, previously identified as plasma membrane-associated cation-binding protein 1 (PCaP1), was further characterized as a protein interacting in vitro with U(VI) and other metals using spectroscopic and structural approaches, and in planta through analyses of the fate of U(VI) in Arabidopsis lines with altered PCaP1 gene expression. Our results showed that recombinant PCaP1 binds U(VI) in vitro with affinity in the nM range, as well as Cu(II) and Fe(III) in high proportions, and that Ca(II) competes with U(VI) for binding. U(VI) induces PCaP1 oligomerization through binding at the monomer interface, at both the N-terminal structured domain and the C-terminal flexible region. Finally, U(VI) translocation in Arabidopsis shoots was affected in pcap1 null-mutant, suggesting a role for this protein in ion trafficking in planta.
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Affiliation(s)
- Alicia Vallet
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, IBS, 38000 Grenoble, France
| | | | - Adrien Favier
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, IBS, 38000 Grenoble, France
| | - Benoît Revel
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France
| | - Titouan Bonnot
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France
| | - Claude Vidaud
- BIAM, CEA, CNRS, Univ. Aix-Marseille, 13108 Saint-Paul-lez-Durance, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, F-F-30200 Bagnols-sur-Cèze, France
| | - Jean-Charles Gaillard
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, F-F-30200 Bagnols-sur-Cèze, France
| | - Pascale Delangle
- Univ. Grenoble Alpes, CEA, CNRS, GRE-INP, IRIG, SyMMES, 38000 Grenoble, France
| | - Fabienne Devime
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France
| | - Sylvie Figuet
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France
| | - Nelson B C Serre
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France
| | | | | | - Stéphane Ravanel
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France
| | | | - Claude Alban
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France.
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Spittler D, Indorato RL, Boeri Erba E, Delaforge E, Signor L, Harris SJ, Garcia-Saez I, Palencia A, Gabel F, Blackledge M, Noirclerc-Savoye M, Petosa C. Binding stoichiometry and structural model of the HIV-1 Rev/importin β complex. Life Sci Alliance 2022; 5:5/10/e202201431. [PMID: 35995566 PMCID: PMC9396022 DOI: 10.26508/lsa.202201431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/24/2022] Open
Abstract
HIV-1 Rev mediates the nuclear export of intron-containing viral RNA transcripts and is essential for viral replication. Rev is imported into the nucleus by the host protein importin β (Impβ), but how Rev associates with Impβ is poorly understood. Here, we report biochemical, mutational, and biophysical studies of the Impβ/Rev complex. We show that Impβ binds two Rev monomers through independent binding sites, in contrast to the 1:1 binding stoichiometry observed for most Impβ cargos. Peptide scanning data and charge-reversal mutations identify the N-terminal tip of Rev helix α2 within Rev's arginine-rich motif (ARM) as a primary Impβ-binding epitope. Cross-linking mass spectrometry and compensatory mutagenesis data combined with molecular docking simulations suggest a structural model in which one Rev monomer binds to the C-terminal half of Impβ with Rev helix α2 roughly parallel to the HEAT-repeat superhelical axis, whereas the other monomer binds to the N-terminal half. These findings shed light on the molecular basis of Rev recognition by Impβ and highlight an atypical binding behavior that distinguishes Rev from canonical cellular Impβ cargos.
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Affiliation(s)
- Didier Spittler
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Rose-Laure Indorato
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Elisabetta Boeri Erba
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Elise Delaforge
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Luca Signor
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Simon J Harris
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Isabel Garcia-Saez
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Andrés Palencia
- Institute for Advanced Biosciences, Structural Biology of Novel Targets in Human Diseases, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Frank Gabel
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Martin Blackledge
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Marjolaine Noirclerc-Savoye
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Carlo Petosa
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
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Ramos J, Laux V, Haertlein M, Boeri Erba E, McAuley KE, Forsyth VT, Mossou E, Larsen S, Langkilde AE. Structural insights into protein folding, stability and activity using in vivo perdeuteration of hen egg-white lysozyme. IUCrJ 2021; 8:372-386. [PMID: 33953924 PMCID: PMC8086161 DOI: 10.1107/s2052252521001299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
This structural and biophysical study exploited a method of perdeuterating hen egg-white lysozyme based on the expression of insoluble protein in Escherichia coli followed by in-column chemical refolding. This allowed detailed comparisons with perdeuterated lysozyme produced in the yeast Pichia pastoris, as well as with unlabelled lysozyme. Both perdeuterated variants exhibit reduced thermal stability and enzymatic activity in comparison with hydrogenated lysozyme. The thermal stability of refolded perdeuterated lysozyme is 4.9°C lower than that of the perdeuterated variant expressed and secreted in yeast and 6.8°C lower than that of the hydrogenated Gallus gallus protein. However, both perdeuterated variants exhibit a comparable activity. Atomic resolution X-ray crystallographic analyses show that the differences in thermal stability and enzymatic function are correlated with refolding and deuteration effects. The hydrogen/deuterium isotope effect causes a decrease in the stability and activity of the perdeuterated analogues; this is believed to occur through a combination of changes to hydrophobicity and protein dynamics. The lower level of thermal stability of the refolded perdeuterated lysozyme is caused by the unrestrained Asn103 peptide-plane flip during the unfolded state, leading to a significant increase in disorder of the Lys97-Gly104 region following subsequent refolding. An ancillary outcome of this study has been the development of an efficient and financially viable protocol that allows stable and active perdeuterated lysozyme to be more easily available for scientific applications.
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Affiliation(s)
- Joao Ramos
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Valerie Laux
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michael Haertlein
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Elisabetta Boeri Erba
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Institut de Biologie Structurale, Université de Grenoble Alpes, CEA, CNRS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Katherine E. McAuley
- Diamond Light Source, Didcot OX11 0DE, United Kingdom
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - V. Trevor Forsyth
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, United Kingdom
| | - Estelle Mossou
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, United Kingdom
| | - Sine Larsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Annette E. Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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10
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Giachin G, Jessop M, Bouverot R, Acajjaoui S, Saïdi M, Chretien A, Bacia‐Verloop M, Signor L, Mas PJ, Favier A, Borel Meneroud E, Hons M, Hart DJ, Kandiah E, Boeri Erba E, Buisson A, Leonard G, Gutsche I, Soler‐Lopez M. Assembly of The Mitochondrial Complex I Assembly Complex Suggests a Regulatory Role for Deflavination. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Gabriele Giachin
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Matthew Jessop
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Romain Bouverot
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Samira Acajjaoui
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Melissa Saïdi
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Anaïs Chretien
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Maria Bacia‐Verloop
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Luca Signor
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Philippe J. Mas
- Integrated Structural Biology Grenoble (ISBG) CNRS CEA, Université Grenoble Alpes 71 avenue des Martyrs 38042 Grenoble France
| | - Adrien Favier
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Eve Borel Meneroud
- Grenoble Institut des Neurosciences (GIN) Centre Inserm U1216 Equipe Neuropathologies et Dysfonctions Synaptiques Université Grenoble Alpes 31 Chemin Fortuné Ferrini 38700 La Tronche France
| | - Michael Hons
- European Molecular Biology Laboratory (EMBL) Grenoble Outstation 71 avenue des Martyrs 38042 Grenoble France
| | - Darren J. Hart
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Eaazhisai Kandiah
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Elisabetta Boeri Erba
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Alain Buisson
- Grenoble Institut des Neurosciences (GIN) Centre Inserm U1216 Equipe Neuropathologies et Dysfonctions Synaptiques Université Grenoble Alpes 31 Chemin Fortuné Ferrini 38700 La Tronche France
| | - Gordon Leonard
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Irina Gutsche
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Montserrat Soler‐Lopez
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
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11
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Giachin G, Jessop M, Bouverot R, Acajjaoui S, Saïdi M, Chretien A, Bacia-Verloop M, Signor L, Mas PJ, Favier A, Borel Meneroud E, Hons M, Hart DJ, Kandiah E, Boeri Erba E, Buisson A, Leonard G, Gutsche I, Soler-Lopez M. Assembly of The Mitochondrial Complex I Assembly Complex Suggests a Regulatory Role for Deflavination. Angew Chem Int Ed Engl 2021; 60:4689-4697. [PMID: 33320993 PMCID: PMC7986633 DOI: 10.1002/anie.202011548] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Indexed: 01/01/2023]
Abstract
Fatty acid β‐oxidation (FAO) and oxidative phosphorylation (OXPHOS) are mitochondrial redox processes that generate ATP. The biogenesis of the respiratory Complex I, a 1 MDa multiprotein complex that is responsible for initiating OXPHOS, is mediated by assembly factors including the mitochondrial complex I assembly (MCIA) complex. However, the organisation and the role of the MCIA complex are still unclear. Here we show that ECSIT functions as the bridging node of the MCIA core complex. Furthermore, cryo‐electron microscopy together with biochemical and biophysical experiments reveal that the C‐terminal domain of ECSIT directly binds to the vestigial dehydrogenase domain of the FAO enzyme ACAD9 and induces its deflavination, switching ACAD9 from its role in FAO to an MCIA factor. These findings provide the structural basis for the MCIA complex architecture and suggest a unique molecular mechanism for coordinating the regulation of the FAO and OXPHOS pathways to ensure an efficient energy production.
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Affiliation(s)
- Gabriele Giachin
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Matthew Jessop
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Romain Bouverot
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Samira Acajjaoui
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Melissa Saïdi
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Anaïs Chretien
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Maria Bacia-Verloop
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Luca Signor
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Philippe J Mas
- Integrated Structural Biology Grenoble (ISBG) CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Adrien Favier
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Eve Borel Meneroud
- Grenoble Institut des Neurosciences (GIN), Centre Inserm U1216, Equipe Neuropathologies et Dysfonctions Synaptiques, Université Grenoble Alpes, 31 Chemin Fortuné Ferrini, 38700, La Tronche, France
| | - Michael Hons
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Darren J Hart
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Eaazhisai Kandiah
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Elisabetta Boeri Erba
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Alain Buisson
- Grenoble Institut des Neurosciences (GIN), Centre Inserm U1216, Equipe Neuropathologies et Dysfonctions Synaptiques, Université Grenoble Alpes, 31 Chemin Fortuné Ferrini, 38700, La Tronche, France
| | - Gordon Leonard
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Irina Gutsche
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Montserrat Soler-Lopez
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
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12
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Favier A, Gans P, Boeri Erba E, Signor L, Muthukumar SS, Pfannschmidt T, Blanvillain R, Cobessi D. The Plastid-Encoded RNA Polymerase-Associated Protein PAP9 Is a Superoxide Dismutase With Unusual Structural Features. Front Plant Sci 2021; 12:668897. [PMID: 34276730 PMCID: PMC8278866 DOI: 10.3389/fpls.2021.668897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/28/2021] [Indexed: 05/09/2023]
Abstract
In Angiosperms, the plastid-encoded RNA polymerase (PEP) is a multimeric enzyme, essential for the proper expression of the plastid genome during chloroplast biogenesis. It is especially required for the light initiated expression of photosynthesis genes and the subsequent build-up of the photosynthetic apparatus. The PEP complex is composed of a prokaryotic-type core of four plastid-encoded subunits and 12 nuclear-encoded PEP-associated proteins (PAPs). Among them, there are two iron superoxide dismutases, FSD2/PAP9 and FSD3/PAP4. Superoxide dismutases usually are soluble enzymes not bound into larger protein complexes. To investigate this unusual feature, we characterized PAP9 using molecular genetics, fluorescence microscopy, mass spectrometry, X-ray diffraction, and solution-state NMR. Despite the presence of a predicted nuclear localization signal within the sequence of the predicted chloroplast transit peptide, PAP9 was mainly observed within plastids. Mass spectrometry experiments with the recombinant Arabidopsis PAP9 suggested that monomers and dimers of PAP9 could be associated to the PEP complex. In crystals, PAP9 occurred as a dimeric enzyme that displayed a similar fold to that of the FeSODs or manganese SOD (MnSODs). A zinc ion, instead of the expected iron, was found to be penta-coordinated with a trigonal-bipyramidal geometry in the catalytic center of the recombinant protein. The metal coordination involves a water molecule and highly conserved residues in FeSODs. Solution-state NMR and DOSY experiments revealed an unfolded C-terminal 34 amino-acid stretch in the stand-alone protein and few internal residues interacting with the rest of the protein. We hypothesize that this C-terminal extension had appeared during evolution as a distinct feature of the FSD2/PAP9 targeting it to the PEP complex. Close vicinity to the transcriptional apparatus may allow for the protection against the strongly oxidizing aerial environment during plant conquering of terrestrial habitats.
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Affiliation(s)
- Adrien Favier
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Pierre Gans
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | | | - Luca Signor
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | | | | | - Robert Blanvillain
- Université Grenoble-Alpes, CNRS, CEA, INRA, IRIG-LPCV, Grenoble, France
- *Correspondence: Robert Blanvillain,
| | - David Cobessi
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
- David Cobessi,
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13
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Liebers M, Gillet FX, Israel A, Pounot K, Chambon L, Chieb M, Chevalier F, Ruedas R, Favier A, Gans P, Boeri Erba E, Cobessi D, Pfannschmidt T, Blanvillain R. Nucleo-plastidic PAP8/pTAC6 couples chloroplast formation with photomorphogenesis. EMBO J 2020; 39:e104941. [PMID: 33001465 DOI: 10.15252/embj.2020104941] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 03/09/2020] [Revised: 09/02/2020] [Accepted: 09/09/2020] [Indexed: 12/29/2022] Open
Abstract
The initial greening of angiosperms involves light activation of photoreceptors that trigger photomorphogenesis, followed by the development of chloroplasts. In these semi-autonomous organelles, construction of the photosynthetic apparatus depends on the coordination of nuclear and plastid gene expression. Here, we show that the expression of PAP8, an essential subunit of the plastid-encoded RNA polymerase (PEP) in Arabidopsis thaliana, is under the control of a regulatory element recognized by the photomorphogenic factor HY5. PAP8 protein is localized and active in both plastids and the nucleus, and particularly required for the formation of late photobodies. In the pap8 albino mutant, phytochrome-mediated signalling is altered, degradation of the chloroplast development repressors PIF1/PIF3 is disrupted, HY5 is not stabilized, and the expression of the photomorphogenesis regulator GLK1 is impaired. PAP8 translocates into plastids via its targeting pre-sequence, interacts with the PEP and eventually reaches the nucleus, where it can interact with another PEP subunit pTAC12/HMR/PAP5. Since PAP8 is required for the phytochrome B-mediated signalling cascade and the reshaping of the PEP activity, it may coordinate nuclear gene expression with PEP-driven chloroplastic gene expression during chloroplast biogenesis.
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Affiliation(s)
- Monique Liebers
- CNRS, CEA, INRA, IRIG-LPCV, Univ. Grenoble-Alpes, Grenoble, France
| | | | - Abir Israel
- CNRS, CEA, INRA, IRIG-LPCV, Univ. Grenoble-Alpes, Grenoble, France
| | - Kevin Pounot
- CNRS, CEA, INRA, IRIG-LPCV, Univ. Grenoble-Alpes, Grenoble, France
| | - Louise Chambon
- CNRS, CEA, INRA, IRIG-LPCV, Univ. Grenoble-Alpes, Grenoble, France
| | - Maha Chieb
- CNRS, CEA, INRA, IRIG-LPCV, Univ. Grenoble-Alpes, Grenoble, France
| | - Fabien Chevalier
- CNRS, CEA, INRA, IRIG-LPCV, Univ. Grenoble-Alpes, Grenoble, France
| | - Rémi Ruedas
- CEA, CNRS, IBS, Univ. Grenoble Alpes, Grenoble, France
| | - Adrien Favier
- CEA, CNRS, IBS, Univ. Grenoble Alpes, Grenoble, France
| | - Pierre Gans
- CEA, CNRS, IBS, Univ. Grenoble Alpes, Grenoble, France
| | | | - David Cobessi
- CEA, CNRS, IBS, Univ. Grenoble Alpes, Grenoble, France
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14
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Puglisi R, Boeri Erba E, Pastore A. A Guide to Native Mass Spectrometry to determine complex interactomes of molecular machines. FEBS J 2020; 287:2428-2439. [PMID: 32142206 PMCID: PMC8647915 DOI: 10.1111/febs.15281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 12/08/2019] [Revised: 02/01/2020] [Accepted: 03/04/2020] [Indexed: 01/17/2023]
Abstract
Native mass spectrometry is an emerging technique in biology that gives the possibility to study noncovalently bound complexes with high sensitivity and accuracy. It thus allows the characterization of macromolecular assemblies, assessing their mass and stoichiometries and mapping the interacting surfaces. In this review, we discuss the application of native mass spectrometry to dynamic molecular machines based on multiple weak interactions. In the study of these machines, it is crucial to understand which and under which conditions various complexes form at any time point. We focus on the specific example of the iron-sulfur cluster biogenesis machine because this is an archetype of a dynamic machine that requires very specific and demanding experimental conditions, such as anaerobicity and the need of retaining the fold of marginally folded proteins. We describe the advantages, challenges and current limitations of the technique by providing examples from our own experience and suggesting possible future solutions.
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Affiliation(s)
- Rita Puglisi
- UK Dementia Research Institute at the Wohl Institute of King's College London, UK
| | - Elisabetta Boeri Erba
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Annalisa Pastore
- UK Dementia Research Institute at the Wohl Institute of King's College London, UK
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15
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Yee AW, Aldeghi M, Blakeley MP, Ostermann A, Mas PJ, Moulin M, de Sanctis D, Bowler MW, Mueller-Dieckmann C, Mitchell EP, Haertlein M, de Groot BL, Boeri Erba E, Forsyth VT. A molecular mechanism for transthyretin amyloidogenesis. Nat Commun 2019; 10:925. [PMID: 30804345 PMCID: PMC6390107 DOI: 10.1038/s41467-019-08609-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 01/14/2019] [Indexed: 01/12/2023] Open
Abstract
Human transthyretin (TTR) is implicated in several fatal forms of amyloidosis. Many mutations of TTR have been identified; most of these are pathogenic, but some offer protective effects. The molecular basis underlying the vastly different fibrillation behaviours of these TTR mutants is poorly understood. Here, on the basis of neutron crystallography, native mass spectrometry and modelling studies, we propose a mechanism whereby TTR can form amyloid fibrils via a parallel equilibrium of partially unfolded species that proceeds in favour of the amyloidogenic forms of TTR. It is suggested that unfolding events within the TTR monomer originate at the C-D loop of the protein, and that destabilising mutations in this region enhance the rate of TTR fibrillation. Furthermore, it is proposed that the binding of small molecule drugs to TTR stabilises non-amyloidogenic states of TTR in a manner similar to that occurring for the protective mutants of the protein.
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Affiliation(s)
- Ai Woon Yee
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Matteo Aldeghi
- Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Matthew P Blakeley
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, 85748, Garching, Germany
| | - Philippe J Mas
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000, Grenoble, France
| | - Martine Moulin
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Daniele de Sanctis
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Matthew W Bowler
- EMBL, Grenoble Outstation, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | | | - Edward P Mitchell
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Michael Haertlein
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Bert L de Groot
- Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | | | - V Trevor Forsyth
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK.
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France.
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16
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Boeri Erba E, Signor L, Oliva MF, Hans F, Petosa C. Erratum to: Characterizing Intact Macromolecular Complexes Using Native Mass Spectrometry. Methods Mol Biol 2018; 1764:E1. [PMID: 30043152 DOI: 10.1007/978-1-4939-7759-8_32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The chapter author provided the below additional text to be added in the acknowledgement section. This has now been updated in the revised version of the book.
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Affiliation(s)
- Elisabetta Boeri Erba
- Institut de Biologie Structurale (IBS), Université de Grenoble Alpes, CEA, CNRS, Grenoble, France.
| | - Luca Signor
- Institut de Biologie Structurale (IBS), Université de Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Mizar F Oliva
- Institut de Biologie Structurale (IBS), Université de Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Fabienne Hans
- Institut de Biologie Structurale (IBS), Université de Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Carlo Petosa
- Institut de Biologie Structurale (IBS), Université de Grenoble Alpes, CEA, CNRS, Grenoble, France
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17
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Abstract
Native mass spectrometry (MS) enables the characterization of macromolecular assemblies with high sensitivity. It can reveal the stoichiometry of subunits as well as their two-dimensional interaction network and provide information regarding the dynamic behavior of macromolecular complexes. Here, we describe the workflow to perform native MS experiments. In addition, we illustrate the quality control analysis of proteins using MS in denaturing conditions.
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Affiliation(s)
- Elisabetta Boeri Erba
- Institut de Biologie Structurale (IBS), Université de Grenoble Alpes, CEA, CNRS, Grenoble, France.
| | - Luca Signor
- Institut de Biologie Structurale (IBS), Université de Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Mizar F Oliva
- Institut de Biologie Structurale (IBS), Université de Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Fabienne Hans
- Institut de Biologie Structurale (IBS), Université de Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Carlo Petosa
- Institut de Biologie Structurale (IBS), Université de Grenoble Alpes, CEA, CNRS, Grenoble, France
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18
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Alfieri A, Sorokina O, Adrait A, Angelini C, Russo I, Morellato A, Matteoli M, Menna E, Boeri Erba E, McLean C, Armstrong JD, Ala U, Buxbaum JD, Brusco A, Couté Y, De Rubeis S, Turco E, Defilippi P. Synaptic Interactome Mining Reveals p140Cap as a New Hub for PSD Proteins Involved in Psychiatric and Neurological Disorders. Front Mol Neurosci 2017; 10:212. [PMID: 28713243 PMCID: PMC5492163 DOI: 10.3389/fnmol.2017.00212] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 03/29/2017] [Accepted: 06/15/2017] [Indexed: 01/21/2023] Open
Abstract
Altered synaptic function has been associated with neurological and psychiatric conditions including intellectual disability, schizophrenia and autism spectrum disorder (ASD). Amongst the recently discovered synaptic proteins is p140Cap, an adaptor that localizes at dendritic spines and regulates their maturation and physiology. We recently showed that p140Cap knockout mice have cognitive deficits, impaired long-term potentiation (LTP) and long-term depression (LTD), and immature, filopodia-like dendritic spines. Only a few p140Cap interacting proteins have been identified in the brain and the molecular complexes and pathways underlying p140Cap synaptic function are largely unknown. Here, we isolated and characterized the p140Cap synaptic interactome by co-immunoprecipitation from crude mouse synaptosomes, followed by mass spectrometry-based proteomics. We identified 351 p140Cap interactors and found that they cluster to sub complexes mostly located in the postsynaptic density (PSD). p140Cap interactors converge on key synaptic processes, including transmission across chemical synapses, actin cytoskeleton remodeling and cell-cell junction organization. Gene co-expression data further support convergent functions: the p140Cap interactors are tightly co-expressed with each other and with p140Cap. Importantly, the p140Cap interactome and its co-expression network show strong enrichment in genes associated with schizophrenia, autism, bipolar disorder, intellectual disability and epilepsy, supporting synaptic dysfunction as a shared biological feature in brain diseases. Overall, our data provide novel insights into the molecular organization of the synapse and indicate that p140Cap acts as a hub for postsynaptic complexes relevant to psychiatric and neurological disorders.
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Affiliation(s)
- Annalisa Alfieri
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, Università di TorinoTorino, Italy
| | - Oksana Sorokina
- The Institute for Adaptive and Neural Computation, School of Informatics, University of EdinburghEdinburgh, United Kingdom
| | - Annie Adrait
- Université Grenoble Alpes, iRTSV-BGEGrenoble, France.,CEA, iRTSV-BGEGrenoble, France.,Institut National de la Santé et de la Recherche Médicale, BGEGrenoble, France
| | - Costanza Angelini
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, Università di TorinoTorino, Italy
| | - Isabella Russo
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, Università di TorinoTorino, Italy
| | - Alessandro Morellato
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, Università di TorinoTorino, Italy
| | - Michela Matteoli
- Institute of Neuroscience, Consiglio Nazionale delle Ricerche (CNR)Milan, Italy.,Humanitas Clinical and Research Center, IRCCSRozzano, Italy
| | - Elisabetta Menna
- Institute of Neuroscience, Consiglio Nazionale delle Ricerche (CNR)Milan, Italy.,Humanitas Clinical and Research Center, IRCCSRozzano, Italy
| | - Elisabetta Boeri Erba
- Institut de Biologie Structurale, Université Grenoble AlpesGrenoble, France.,CEA, DSV, IBSGrenoble, France.,Centre National de la Recherche Scientifique, IBSGrenoble, France
| | - Colin McLean
- The Institute for Adaptive and Neural Computation, School of Informatics, University of EdinburghEdinburgh, United Kingdom
| | - J Douglas Armstrong
- The Institute for Adaptive and Neural Computation, School of Informatics, University of EdinburghEdinburgh, United Kingdom
| | - Ugo Ala
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, Università di TorinoTorino, Italy.,GenoBiToUS-Genomics and Bioinformatics, Università di TorinoTurin, Italy
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount SinaiNew York, NY, United States.,Department of Psychiatry, Icahn School of Medicine at Mount SinaiNew York, NY, United States.,Department of Neuroscience, Icahn School of Medicine at Mount SinaiNew York, NY, United States.,Friedman Brain Institute, Icahn School of Medicine at Mount SinaiNew York, NY, United States.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount SinaiNew York, NY, United States.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount SinaiNew York, NY, United States
| | - Alfredo Brusco
- Department of Medical Sciences, Università di TorinoTurin, Italy.,Medical Genetics Unit, Azienda Ospedaliera Città della Salute e della Scienza di TorinoTurin, Italy
| | - Yohann Couté
- Université Grenoble Alpes, iRTSV-BGEGrenoble, France.,CEA, iRTSV-BGEGrenoble, France.,Institut National de la Santé et de la Recherche Médicale, BGEGrenoble, France
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount SinaiNew York, NY, United States.,Department of Psychiatry, Icahn School of Medicine at Mount SinaiNew York, NY, United States
| | - Emilia Turco
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, Università di TorinoTorino, Italy
| | - Paola Defilippi
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, Università di TorinoTorino, Italy
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19
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Pellegrini E, Signor L, Singh S, Boeri Erba E, Cusack S. Structures of the inactive and active states of RIP2 kinase inform on the mechanism of activation. PLoS One 2017; 12:e0177161. [PMID: 28545134 PMCID: PMC5436651 DOI: 10.1371/journal.pone.0177161] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/24/2017] [Indexed: 12/14/2022] Open
Abstract
Innate immune receptors NOD1 and NOD2 are activated by bacterial peptidoglycans leading to recruitment of adaptor kinase RIP2, which, upon phosphorylation and ubiquitination, becomes a scaffold for downstream effectors. The kinase domain (RIP2K) is a pharmaceutical target for inflammatory diseases caused by aberrant NOD2-RIP2 signalling. Although structures of active RIP2K in complex with inhibitors have been reported, the mechanism of RIP2K activation remains to be elucidated. Here we analyse RIP2K activation by combining crystal structures of the active and inactive states with mass spectrometric characterization of their phosphorylation profiles. The active state has Helix αC inwardly displaced and the phosphorylated Activation Segment (AS) disordered, whilst in the inactive state Helix αC is outwardly displaced and packed against the helical, non-phosphorylated AS. Biophysical measurements show that the active state is a stable dimer whilst the inactive kinase is in a monomer-dimer equilibrium, consistent with the observed structural differences at the dimer interface. We conclude that RIP2 kinase auto-phosphorylation is intimately coupled to dimerization, similar to the case of BRAF. Our results will help drug design efforts targeting RIP2 as a potential treatment for NOD2-RIP2 related inflammatory diseases.
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Affiliation(s)
| | - Luca Signor
- University Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Saurabh Singh
- European Molecular Biology Laboratory, Grenoble, France
| | - Elisabetta Boeri Erba
- University Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble, France
- * E-mail:
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20
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Macek P, Kerfah R, Boeri Erba E, Crublet E, Moriscot C, Schoehn G, Amero C, Boisbouvier J. Unraveling self-assembly pathways of the 468-kDa proteolytic machine TET2. Sci Adv 2017; 3:e1601601. [PMID: 28435872 PMCID: PMC5384809 DOI: 10.1126/sciadv.1601601] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 02/10/2017] [Indexed: 05/03/2023]
Abstract
The spontaneous formation of biological higher-order structures from smaller building blocks, called self-assembly, is a fundamental attribute of life. Although the protein self-assembly is a time-dependent process that occurs at the molecular level, its current understanding originates either from static structures of trapped intermediates or from modeling. Nuclear magnetic resonance (NMR) spectroscopy has the unique ability to monitor structural changes in real time; however, its size limitation and time-resolution constraints remain a challenge when studying the self-assembly of large biological particles. We report the application of methyl-specific isotopic labeling combined with relaxation-optimized NMR spectroscopy to overcome both size- and time-scale limitations. We report for the first time the self-assembly process of a half-megadalton protein complex that was monitored at the structural level, including the characterization of intermediate states, using a mutagenesis-free strategy. NMR was used to obtain individual kinetics data on the different transient intermediates and the formation of final native particle. In addition, complementary time-resolved electron microscopy and native mass spectrometry were used to characterize the low-resolution structures of oligomerization intermediates.
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Affiliation(s)
- Pavel Macek
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Rime Kerfah
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Elisabetta Boeri Erba
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Elodie Crublet
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Christine Moriscot
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Guy Schoehn
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Carlos Amero
- Centro de Investigaciones Químicas, IICBA,
Universidad Autónoma del Estado de Morelos, México
- Corresponding author. (C.A.);
(J.B.)
| | - Jerome Boisbouvier
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- Corresponding author. (C.A.);
(J.B.)
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21
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Yee AW, Moulin M, Breteau N, Haertlein M, Mitchell EP, Cooper JB, Boeri Erba E, Forsyth VT. Impact of Deuteration on the Assembly Kinetics of Transthyretin Monitored by Native Mass Spectrometry and Implications for Amyloidoses. Angew Chem Int Ed Engl 2016; 55:9292-6. [PMID: 27311939 PMCID: PMC5094506 DOI: 10.1002/anie.201602747] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 01/13/2023]
Abstract
It is well established that the formation of transthyretin (TTR) amyloid fibrils is linked to the destabilization and dissociation of its tetrameric structure into insoluble aggregates. Isotope labeling is used for the study of TTR by NMR, neutron diffraction, and mass spectrometry (MS). Here MS, thioflavin T fluorescence, and crystallographic data demonstrate that while the X-ray structures of unlabeled and deuterium-labeled TTR are essentially identical, subunit exchange kinetics and amyloid formation are accelerated for the deuterated protein. However, a slower subunit exchange is noted in deuterated solvent, reflecting the poorer solubility of non-polar protein side chains in such an environment. These observations are important for the interpretation of kinetic studies involving deuteration. The destabilizing effects of TTR deuteration are rather similar in character to those observed for aggressive mutations of TTR such as L55P (associated with familial amyloid polyneuropathy).
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Affiliation(s)
- Ai Woon Yee
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | - Martine Moulin
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | - Nina Breteau
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Michael Haertlein
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Edward P Mitchell
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
- ESRF, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Jonathan B Cooper
- Laboratory of Protein Crystallography, Drug Discovery Group, Wolfson Institute for Biomedical Research, UCL, London, WC1E 6BT, UK
| | - Elisabetta Boeri Erba
- Univ. Grenoble Alpes, IBS, 38044, Grenoble, France.
- CNRS, IBS, 38044, Grenoble, France.
- CEA, IBS, 38044, Grenoble, France.
| | - V Trevor Forsyth
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France.
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK.
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22
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Rasmussen KK, Frandsen KEH, Boeri Erba E, Pedersen M, Varming AK, Hammer K, Kilstrup M, Thulstrup PW, Blackledge M, Jensen MR, Lo Leggio L. Structural and dynamics studies of a truncated variant of CI repressor from bacteriophage TP901-1. Sci Rep 2016; 6:29574. [PMID: 27403839 PMCID: PMC4941734 DOI: 10.1038/srep29574] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/17/2016] [Indexed: 11/28/2022] Open
Abstract
The CI repressor from the temperate bacteriophage TP901-1 consists of two folded domains, an N-terminal helix-turn-helix DNA-binding domain (NTD) and a C-terminal oligomerization domain (CTD), which we here suggest to be further divided into CTD1 and CTD2. Full-length CI is a hexameric protein, whereas a truncated version, CI∆58, forms dimers. We identify the dimerization region of CI∆58 as CTD1 and determine its secondary structure to be helical both within the context of CI∆58 and in isolation. To our knowledge this is the first time that a helical dimerization domain has been found in a phage repressor. We also precisely determine the length of the flexible linker connecting the NTD to the CTD. Using electrophoretic mobility shift assays and native mass spectrometry, we show that CI∆58 interacts with the OL operator site as one dimer bound to both half-sites, and with much higher affinity than the isolated NTD domain thus demonstrating cooperativity between the two DNA binding domains. Finally, using small angle X-ray scattering data and state-of-the-art ensemble selection techniques, we delineate the conformational space sampled by CI∆58 in solution, and we discuss the possible role that the dynamics play in CI-repressor function.
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Affiliation(s)
- Kim Krighaar Rasmussen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen, Denmark
| | - Kristian E. H. Frandsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen, Denmark
| | | | - Margit Pedersen
- Department of Biology, University of Copenhagen, Ole Maaløes vej 5, DK-2200 Copenhagen N, Denmark
| | - Anders K. Varming
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen, Denmark
| | - Karin Hammer
- Metabolic signalling and regulation, Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Mogens Kilstrup
- Metabolic signalling and regulation, Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Peter W. Thulstrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen, Denmark
| | - Martin Blackledge
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | | | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen, Denmark
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23
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Boeri Erba E, Klein PA, Signor L. Combining a NHS ester and glutaraldehyde improves crosslinking prior to MALDI MS analysis of intact protein complexes. J Mass Spectrom 2015; 50:1114-1119. [PMID: 26456778 DOI: 10.1002/jms.3626] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 11/05/2014] [Revised: 06/11/2015] [Accepted: 06/18/2015] [Indexed: 06/05/2023]
Abstract
Protein complexes play pivotal roles in cellular life. Nevertheless, their characterization remains a substantial challenge. Mass spectrometry (MS) is an emerging tool to study protein assemblies, and electrospray ionization (ESI) is often used because it preserves non-covalent interactions. Matrix-assisted laser desorption/ionization (MALDI) represents an important alternative to ESI because it is more tolerant to salts and detergents (e.g. necessary in the case of membrane complex analyses). Prior to MALDI-MS, the subunits should be crosslinked (XLed). Moreover, crosslinking (XLing) is useful when constraint distances are determined to obtain low-resolution structural information. Here we report a novel XLing approach to study protein complexes with MALDI-MS. We investigated two tetramers (i.e. alcohol dehydrogenase and aldolase) larger than 140 kDa at two pH values (7.2 and 8.0). We tested two different crosslinkers (XLers) (i.e. BS(3) and glutaraldehyde), used separately or in combination. We utilized gentle agitation and ultracentrifugation. Our data shows that the pH influenced the XLing when using a single XLer. Combining two XLers was demonstrated to be more efficient than using a reagent alone. In particular, the combination determined a higher degree of XLing and lower mass shift. This could suggest a ranking in target amino acid availability. First residues at specific distances are linked by BS(3) , then glutaraldehyde binds residues that are still available at larger distances. Ultracentrifugation and gentle agitation both provide similar degrees of XLing, but the former method determined a lower mass increment resulting from redundant XLing. To conclude, we present an efficient dual XLing approach for determining mass and stoichiometry of protein assemblies.
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Affiliation(s)
- Elisabetta Boeri Erba
- Univ. Grenoble Alpes, IBS, F-38044, Grenoble, France
- CNRS, IBS, F-38044, Grenoble, France
- CEA, IBS, F-38044, Grenoble, France
| | - Pierre Andre Klein
- Univ. Grenoble Alpes, IBS, F-38044, Grenoble, France
- CNRS, IBS, F-38044, Grenoble, France
- CEA, IBS, F-38044, Grenoble, France
| | - Luca Signor
- Univ. Grenoble Alpes, IBS, F-38044, Grenoble, France
- CNRS, IBS, F-38044, Grenoble, France
- CEA, IBS, F-38044, Grenoble, France
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24
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Boeri Erba E, Petosa C. The emerging role of native mass spectrometry in characterizing the structure and dynamics of macromolecular complexes. Protein Sci 2015; 24:1176-92. [PMID: 25676284 DOI: 10.1002/pro.2661] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [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: 12/29/2014] [Revised: 02/06/2015] [Accepted: 02/06/2015] [Indexed: 12/31/2022]
Abstract
Mass spectrometry (MS) is a powerful tool for determining the mass of biomolecules with high accuracy and sensitivity. MS performed under so-called "native conditions" (native MS) can be used to determine the mass of biomolecules that associate noncovalently. Here we review the application of native MS to the study of protein-ligand interactions and its emerging role in elucidating the structure of macromolecular assemblies, including soluble and membrane protein complexes. Moreover, we discuss strategies aimed at determining the stoichiometry and topology of subunits by inducing partial dissociation of the holo-complex. We also survey recent developments in "native top-down MS", an approach based on Fourier Transform MS, whereby covalent bonds are broken without disrupting non-covalent interactions. Given recent progress, native MS is anticipated to play an increasingly important role for researchers interested in the structure of macromolecular complexes.
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Affiliation(s)
- Elisabetta Boeri Erba
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, F-38044, Grenoble, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), DSV, IBS, F-38044, Grenoble, France.,Centre National de la Recherche Scientifique (CNRS), IBS, F-38044, Grenoble, France
| | - Carlo Petosa
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, F-38044, Grenoble, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), DSV, IBS, F-38044, Grenoble, France.,Centre National de la Recherche Scientifique (CNRS), IBS, F-38044, Grenoble, France
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25
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Boeri Erba E. Investigating macromolecular complexes using top-down mass spectrometry. Proteomics 2014; 14:1259-70. [PMID: 24723549 DOI: 10.1002/pmic.201300333] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [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: 07/31/2013] [Revised: 04/03/2014] [Accepted: 04/08/2014] [Indexed: 12/25/2022]
Abstract
MS has emerged as an important tool to investigate noncovalent interactions between proteins and various ligands (e.g. other proteins, small molecules, or drugs). In particular, ESI under so-called "native conditions" (a.k.a. "native MS") has considerably expanded the scope of such investigations. For instance, ESI quadrupole time of flight (Q-TOF) instruments have been used to probe the precise stoichiometry of protein assemblies, the interactions between subunits and the position of subunits within the complex (i.e. defining core and peripheral subunits). This review highlights several illustrative native Q-TOF-based investigations and recent seminal contributions of top-down MS (i.e. Fourier transform (FT) MS) to the characterization of noncovalent complexes. Combined top-down and native MS, recently demonstrated in "high-mass modified" orbitrap mass spectrometers, and further improvements needed for the enhanced investigation of biologically significant noncovalent interactions by MS will be discussed.
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Affiliation(s)
- Elisabetta Boeri Erba
- Institute of Structural Biology (Institut de Biologie Structurale), Centre National de la Recherche Scientifique (CNRS), University of Grenoble Alpes (Université de Grenoble Alpes), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), DSV, Grenoble, France
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26
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Signor L, Boeri Erba E. Matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometric analysis of intact proteins larger than 100 kDa. J Vis Exp 2013. [PMID: 24056304 PMCID: PMC3857990 DOI: 10.3791/50635] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Effectively determining masses of proteins is critical to many biological studies (e.g. for structural biology investigations). Accurate mass determination allows one to evaluate the correctness of protein primary sequences, the presence of mutations and/or post-translational modifications, the possible protein degradation, the sample homogeneity, and the degree of isotope incorporation in case of labelling (e.g.13C labelling). Electrospray ionisation (ESI) mass spectrometry (MS) is widely used for mass determination of denatured proteins, but its efficiency is affected by the composition of the sample buffer. In particular, the presence of salts, detergents, and contaminants severely undermines the effectiveness of protein analysis by ESI-MS. Matrix-assisted laser desorption/ionization (MALDI) MS is an attractive alternative, due to its salt tolerance and the simplicity of data acquisition and interpretation. Moreover, the mass determination of large heterogeneous proteins (bigger than 100 kDa) is easier by MALDI-MS due to the absence of overlapping high charge state distributions which are present in ESI spectra. Here we present an accessible approach for analysing proteins larger than 100 kDa by MALDI-time of flight (TOF). We illustrate the advantages of using a mixture of two matrices (i.e. 2,5-dihydroxybenzoic acid and α-cyano-4-hydroxycinnamic acid) and the utility of the thin layer method as approach for sample deposition. We also discuss the critical role of the matrix and solvent purity, of the standards used for calibration, of the laser energy, and of the acquisition time. Overall, we provide information necessary to a novice for analysing intact proteins larger than 100 kDa by MALDI-MS.
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Affiliation(s)
- Luca Signor
- Institute of Structural Biology "J.P. Ebel", UMR5075, Commissariat à L'Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Université J. Fourier
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27
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Repetto D, Aramu S, Boeri Erba E, Sharma N, Grasso S, Russo I, Jensen ON, Cabodi S, Turco E, Di Stefano P, Defilippi P. Mapping of p140Cap phosphorylation sites: the EPLYA and EGLYA motifs have a key role in tyrosine phosphorylation and Csk binding, and are substrates of the Abl kinase. PLoS One 2013; 8:e54931. [PMID: 23383002 PMCID: PMC3561454 DOI: 10.1371/journal.pone.0054931] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 12/17/2012] [Indexed: 12/11/2022] Open
Abstract
Protein phosphorylation tightly regulates specific binding of effector proteins that control many diverse biological functions of cells (e. g. signaling, migration and proliferation). p140Cap is an adaptor protein, specifically expressed in brain, testis and epithelial cells, that undergoes phosphorylation and tunes its interactions with other regulatory molecules via post-translation modification. In this work, using mass spectrometry, we found that p140Cap is in vivo phosphorylated on tyrosine (Y) within the peptide GEGLpYADPYGLLHEGR (from now on referred to as EGLYA) as well as on three serine residues. Consistently, EGLYA has the highest score of in silico prediction of p140Cap phosphorylation. To further investigate the p140Cap function, we performed site specific mutagenesis on tyrosines inserted in EGLYA and EPLYA, a second sequence with the same highest score of phosphorylation. The mutant protein, in which both EPLYA/EGLYA tyrosines were converted to phenylalanine, was no longer tyrosine phosphorylated, despite the presence of other tyrosine residues in p140Cap sequence. Moreover, this mutant lost its ability to bind the C-terminal Src kinase (Csk), previously shown to interact with p140Cap by Far Western analysis. In addition, we found that in vitro and in HEK-293 cells, the Abelson kinase is the major kinase involved in p140Cap tyrosine phosphorylation on the EPLYA and EGLYA sequences. Overall, these data represent an original attempt to in vivo characterise phosphorylated residues of p140Cap. Elucidating the function of p140Cap will provide novel insights into its biological activity not only in normal cells, but also in tumors.
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Affiliation(s)
- Daniele Repetto
- Department of Molecular Biotechnology and Health Sciences, Università degli Studi di Torino, Torino, Italy
| | - Simona Aramu
- Department of Molecular Biotechnology and Health Sciences, Università degli Studi di Torino, Torino, Italy
| | | | - Nanaocha Sharma
- Department of Molecular Biotechnology and Health Sciences, Università degli Studi di Torino, Torino, Italy
| | - Silvia Grasso
- Department of Molecular Biotechnology and Health Sciences, Università degli Studi di Torino, Torino, Italy
| | - Isabella Russo
- Department of Molecular Biotechnology and Health Sciences, Università degli Studi di Torino, Torino, Italy
| | - Ole N. Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Sara Cabodi
- Department of Molecular Biotechnology and Health Sciences, Università degli Studi di Torino, Torino, Italy
| | - Emilia Turco
- Department of Molecular Biotechnology and Health Sciences, Università degli Studi di Torino, Torino, Italy
| | - Paola Di Stefano
- Department of Molecular Biotechnology and Health Sciences, Università degli Studi di Torino, Torino, Italy
- * E-mail: (PD); (PDS)
| | - Paola Defilippi
- Department of Molecular Biotechnology and Health Sciences, Università degli Studi di Torino, Torino, Italy
- * E-mail: (PD); (PDS)
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28
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Pellegrino S, Radzimanowski J, de Sanctis D, Boeri Erba E, McSweeney S, Timmins J. Structural and functional characterization of an SMC-like protein RecN: new insights into double-strand break repair. Structure 2012; 20:2076-89. [PMID: 23085075 DOI: 10.1016/j.str.2012.09.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 09/14/2012] [Accepted: 09/18/2012] [Indexed: 01/01/2023]
Abstract
Repair of DNA double-strand breaks (DSBs) is essential for cell survival and maintaining genome integrity. DSBs are repaired in a stepwise manner by homologous recombination. Here, we focused on the early steps of DSB repair, including DSB recognition, which is still only poorly understood. In prokaryotes, this process has been proposed to involve the RecN protein, a member of the structural maintenance of chromosome (SMC) protein family, which include key eukaryotic and prokaryotic proteins such as cohesin, condensin, and Rad50. An extensive high- and low-resolution structural analysis of Deinococcus radiodurans RecN using a combination of protein crystallography and small-angle X-ray scattering enabled us to assemble a quasi-atomic model of the entire RecN protein, representing the complete structure of a SMC-like protein. These results, together with a thorough biochemical and mutational study of RecN, allow us to propose a model for the role of RecN in DSB repair.
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Affiliation(s)
- Simone Pellegrino
- Structural Biology Group, European Synchrotron Radiation Facility, BP 220, 38043 Grenoble Cedex 9, France
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29
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Brand GD, Salbo R, Jørgensen TJD, Bloch C, Boeri Erba E, Robinson CV, Tanjoni I, Moura-da-Silva AM, Roepstorff P, Domont GB, Perales J, Valente RH, Neves-Ferreira AGC. The interaction of the antitoxin DM43 with a snake venom metalloproteinase analyzed by mass spectrometry and surface plasmon resonance. J Mass Spectrom 2012; 47:567-73. [PMID: 22549991 DOI: 10.1002/jms.2990] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
DM43 is a circulating dimeric antitoxin isolated from Didelphis aurita, a South American marsupial naturally immune to snake envenomation. This endogenous inhibitor binds non-covalently to jararhagin, the main hemorrhagic metalloproteinase from Bothrops jararaca snake venom, and efficiently neutralizes its toxicity. The aim of this study was to apply mass spectrometry (MS) and surface plasmon resonance (SPR) to improve the molecular characterization of this heterocomplex. The stoichiometry of the interaction was confirmed by nanoelectrospray ionization-quadrupole-time-of-flight MS; from native solution conditions, the complex showed a molecular mass of ~94 kDa, indicating that one molecule of jararhagin (50 kDa) interacts with one monomer of DM43 (43 kDa). Although readily observed in solution, the dimeric structure of the inhibitor was barely preserved in the gas phase. This result suggests that, in contrast to the toxin-antitoxin complex, hydrophobic interactions are the primary driving force for the inhibitor dimerization. For the real-time interaction analysis, the toxin was captured on a sensor chip derivatized with the anti-jararhagin monoclonal antibody MAJar 2. The sensorgrams obtained after successive injections of DM43 in a concentration series were globally fitted to a simple bimolecular interaction, yielding the following kinetic rates for the DM43/jararhagin interaction: k(a) = 3.54 ± 0.03 × 10(4) M(-1) s(-1) and k(d) = 1.16 ± 0.07 × 10(-5) s(-1), resulting in an equilibrium dissociation constant (K(D) ) of 0.33 ± 0.06 nM. Taken together, MS and SPR results show that DM43 binds to its target toxin with high affinity and constitute the first accurate quantitative study on the extent of the interaction between a natural inhibitor and a metalloproteinase toxin, with unequivocal implications for the use of this kind of molecule as template for the rational development of novel antivenom therapies.
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Affiliation(s)
- Guilherme D Brand
- Laboratório de Espectrometria de Massa, Embrapa-Recursos Genéticos e Biotecnologia, Estação Parque Biológico, Final W5, Asa Norte, 70770-900, Brasília, DF, Brazil
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Mädler S, Barylyuk K, Boeri Erba E, Nieckarz RJ, Zenobi R. Compelling advantages of negative ion mode detection in high-mass MALDI-MS for homomeric protein complexes. J Am Soc Mass Spectrom 2012; 23:213-224. [PMID: 22131225 DOI: 10.1007/s13361-011-0274-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 10/04/2011] [Accepted: 10/08/2011] [Indexed: 05/31/2023]
Abstract
Chemical cross-linking in combination with high-mass MALDI mass spectrometry allows for the rapid identification of interactions and determination of the complex stoichiometry of noncovalent protein-protein interactions. As the molecular weight of these complexes increases, the fraction of multiply charged species typically increases. In the case of homomeric complexes, signals from multiply charged multimers overlap with singly charged subunits. Remarkably, spectra recorded in negative ion mode show lower abundances of multiply charged species, lower background, higher reproducibility, and, thus, overall cleaner spectra compared with positive ion mode spectra. In this work, a dedicated high-mass detector was applied for measuring high-mass proteins (up to 200 kDa) by negative ion mode MALDI-MS. The influences of sample preparation and instrumental parameters were carefully investigated. Relative signal integrals of multiply charged anions were relatively independent of any of the examined parameters and could thus be approximated easily for the spectra of cross-linked complexes. For example, the fraction of doubly charged anions signals overlapping with the signals of singly charged subunits could be more precisely estimated than in positive ion mode. Sinapinic acid was found to be an excellent matrix for the analysis of proteins and cross-linked protein complexes in both ion modes. Our results suggest that negative ion mode data of chemically cross-linked protein complexes are complementary to positive ion mode data and can in some cases represent the solution phase situation better than positive ion mode.
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Affiliation(s)
- Stefanie Mädler
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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Abstract
Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been demonstrated to be a valuable tool to investigate noncovalent interactions of biomolecules. The direct detection of noncovalent assemblies is often more troublesome than with electrospray ionization. Using dedicated sample preparation techniques and carefully optimized instrumental parameters, a number of biomolecule assemblies were successfully analyzed. For complexes dissociating under MALDI conditions, covalent stabilization with chemical cross-linking is a suitable alternative. Indirect methods allow the detection of noncovalent assemblies by monitoring the fading of binding partners or altered H/D exchange patterns.
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Affiliation(s)
- Stefanie Mädler
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
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Boeri Erba E, Barylyuk K, Yang Y, Zenobi R. Quantifying Protein–Protein Interactions Within Noncovalent Complexes Using Electrospray Ionization Mass Spectrometry. Anal Chem 2011; 83:9251-9. [DOI: 10.1021/ac201576e] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Elisabetta Boeri Erba
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Konstantin Barylyuk
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Yang Yang
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
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Erba EB, Ruotolo BT, Barsky D, Robinson CV. Ion Mobility-Mass Spectrometry Reveals the Influence of Subunit Packing and Charge on the Dissociation of Multiprotein Complexes. Anal Chem 2010; 82:9702-10. [DOI: 10.1021/ac101778e] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Elisabetta Boeri Erba
- University Chemistry Department, University of Cambridge, Cambridge, United Kingdom, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, Lawrence Livermore National Laboratory, Livermore, California, and Department of Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Brandon T. Ruotolo
- University Chemistry Department, University of Cambridge, Cambridge, United Kingdom, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, Lawrence Livermore National Laboratory, Livermore, California, and Department of Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Daniel Barsky
- University Chemistry Department, University of Cambridge, Cambridge, United Kingdom, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, Lawrence Livermore National Laboratory, Livermore, California, and Department of Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Carol V. Robinson
- University Chemistry Department, University of Cambridge, Cambridge, United Kingdom, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, Lawrence Livermore National Laboratory, Livermore, California, and Department of Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
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Sharon M, Mao H, Boeri Erba E, Stephens E, Zheng N, Robinson CV. Symmetrical modularity of the COP9 signalosome complex suggests its multifunctionality. Structure 2009; 17:31-40. [PMID: 19141280 DOI: 10.1016/j.str.2008.10.012] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Revised: 09/10/2008] [Accepted: 10/13/2008] [Indexed: 10/21/2022]
Abstract
The COP9 signalosome (CSN) is an eight-subunit protein complex that is found in all eukaryotes. Accumulating evidence indicates its diverse biological functions that are often linked to ubiquitin-mediated proteolysis. Here we applied an emerging mass spectrometry approach to gain insight into the structure of the CSN complex. Our results indicate that the catalytically active human complex, reconstituted in vitro, is composed of a single copy of each of the eight subunits. By forming a total of 35 subcomplexes, we are able to build a comprehensive interaction map that shows two symmetrical modules, Csn1/2/3/8 and Csn4/5/6/7, connected by interactions between Csn1-Csn6. Overall the stable modules and multiple subcomplexes observed here are in agreement with the "mini-CSN" complexes reported previously. This suggests that the propensity of the CSN complex to change and adapt its subunit composition might underlie its ability to perform multiple functions in vivo.
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Affiliation(s)
- Michal Sharon
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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Levy ED, Boeri Erba E, Robinson CV, Teichmann SA. Assembly reflects evolution of protein complexes. Nature 2008; 453:1262-5. [PMID: 18563089 DOI: 10.1038/nature06942] [Citation(s) in RCA: 323] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Accepted: 03/20/2008] [Indexed: 02/03/2023]
Abstract
A homomer is formed by self-interacting copies of a protein unit. This is functionally important, as in allostery, and structurally crucial because mis-assembly of homomers is implicated in disease. Homomers are widespread, with 50-70% of proteins with a known quaternary state assembling into such structures. Despite their prevalence, their role in the evolution of cellular machinery and the potential for their use in the design of new molecular machines, little is known about the mechanisms that drive formation of homomers at the level of evolution and assembly in the cell. Here we present an analysis of over 5,000 unique atomic structures and show that the quaternary structure of homomers is conserved in over 70% of protein pairs sharing as little as 30% sequence identity. Where quaternary structure is not conserved among the members of a protein family, a detailed investigation revealed well-defined evolutionary pathways by which proteins transit between different quaternary structure types. Furthermore, we show by perturbing subunit interfaces within complexes and by mass spectrometry analysis, that the (dis)assembly pathway mimics the evolutionary pathway. These data represent a molecular analogy to Haeckel's evolutionary paradigm of embryonic development, where an intermediate in the assembly of a complex represents a form that appeared in its own evolutionary history. Our model of self-assembly allows reliable prediction of evolution and assembly of a complex solely from its crystal structure.
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Affiliation(s)
- Emmanuel D Levy
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
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Boeri Erba E, Matthiesen R, Bunkenborg J, Schulze WX, Di Stefano P, Cabodi S, Tarone G, Defilippi P, Jensen ON. Quantitation of Multisite EGF Receptor Phosphorylation Using Mass Spectrometry and a Novel Normalization Approach. J Proteome Res 2007; 6:2768-85. [PMID: 17523611 DOI: 10.1021/pr060675m] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [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: 01/21/2023]
Abstract
Using stable isotope labeling and mass spectrometry, we performed a sensitive, quantitative analysis of multiple phosphorylation sites of the epidermal growth factor (EGF) receptor. Phosphopeptide detection efficiency was significantly improved by using the tyrosine phosphatase inhibitor sodium pervanadate to boost the abundance of phosphorylation of the EGF receptor. Nine phosphorylation sites (pT669, pS967, pS1002, pY845, pY974, pY1045, pY1086, pY1148, and pY1173) of EGF receptor were quantified from EGF-stimulated cells in suspension and adherent conditions. Our data sets revealed that EGF stimulation of adherent cells induced higher levels of tyrosine phosphorylation relative to EGF stimulation of suspended cells. In contrast, EGF stimulation of adherent cells induced lower levels of serine and threonine phosphorylation relative to EGF stimulation of suspended cells. These findings are consistent with the hypothesis that cellular adhesion modulates phosphorylation of plasma membrane receptor tyrosine kinases relevant for EGF-induced signal transduction processes. Furthermore, our results suggest that strong phosphatase inhibitors should be used to generate reference datasets in comparative phosphoproteomics experiments.
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Affiliation(s)
- Elisabetta Boeri Erba
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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Voena C, Conte C, Ambrogio C, Boeri Erba E, Boccalatte F, Mohammed S, Jensen ON, Palestro G, Inghirami G, Chiarle R. The tyrosine phosphatase Shp2 interacts with NPM-ALK and regulates anaplastic lymphoma cell growth and migration. Cancer Res 2007; 67:4278-86. [PMID: 17483340 DOI: 10.1158/0008-5472.can-06-4350] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Anaplastic large cell lymphomas (ALCL) are mainly characterized by the reciprocal translocation t(2;5)(p23;q35) that involves the anaplastic lymphoma kinase (ALK) gene and generates the fusion protein NPM-ALK with intrinsic tyrosine kinase activity. NPM-ALK triggers several signaling cascades, leading to increased cell growth, resistance to apoptosis, and changes in morphology and migration of transformed cells. To search for new NPM-ALK interacting molecules, we developed a mass spectrometry-based proteomic approach in HEK293 cells expressing an inducible NPM-ALK and identified the tyrosine phosphatase Shp2 as a candidate substrate. We found that NPM-ALK was able to bind Shp2 in coprecipitation experiments and to induce its phosphorylation in the tyrosine residues Y542 and Y580 both in HEK293 cells and ALCL cell lines. In primary lymphomas, antibodies against the phosphorylated tyrosine Y542 of Shp2 mainly stained ALK-positive cells. In ALCL cell lines, Shp2-constitutive phosphorylation was dependent on NPM-ALK, as it significantly decreased after short hairpin RNA (shRNA)-mediated NPM-ALK knock down. In addition, only the constitutively active NPM-ALK, but not the kinase dead NPM-ALK(K210R), formed a complex with Shp2, Gab2, and growth factor receptor binding protein 2 (Grb2), where Grb2 bound to the phosphorylated Shp2 through its SH2 domain. Shp2 knock down by specific shRNA decreased the phosphorylation of extracellular signal-regulated kinase 1/2 and of the tyrosine residue Y416 in the activation loop of Src, resulting in impaired ALCL cell proliferation and growth disadvantage. Finally, migration of ALCL cells was reduced by Shp2 shRNA. These findings show a direct involvement of Shp2 in NPM-ALK lymphomagenesis, highlighting its critical role in lymphoma cell proliferation and migration.
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Affiliation(s)
- Claudia Voena
- Department of Biomedical Sciences and Human Oncology, University of Turin, Turin, Italy
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Ambrogio C, Voena C, Manazza AD, Piva R, Riera L, Barberis L, Costa C, Tarone G, Defilippi P, Hirsch E, Boeri Erba E, Mohammed S, Jensen ON, Palestro G, Inghirami G, Chiarle R. p130Cas mediates the transforming properties of the anaplastic lymphoma kinase. Blood 2005; 106:3907-16. [PMID: 16105984 PMCID: PMC1895100 DOI: 10.1182/blood-2005-03-1204] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Translocations of the anaplastic lymphoma kinase (ALK) gene have been described in anaplastic large-cell lymphomas (ALCLs) and in stromal tumors. The most frequent translocation, t(2;5), generates the fusion protein nucleophosmin (NPM)-ALK with intrinsic tyrosine kinase activity. Along with transformation, NPM-ALK induces morphologic changes in fibroblasts and lymphoid cells, suggesting a direct role of ALK in cell shaping. In this study, we used a mass-spectrometry-based proteomic approach to search for proteins involved in cytoskeleton remodeling and identified p130Cas (p130 Crk-associated substrate) as a novel interactor of NPM-ALK. In 293 cells and in fibroblasts as well as in human ALK-positive lymphoma cell lines, NPM-ALK was able to bind p130Cas and to induce its phosphorylation. Both of the effects were dependent on ALK kinase activity and on the adaptor protein growth factor receptor-bound protein 2 (Grb2), since no binding or phosphorylation was found with the kinase-dead mutant NPM-ALK(K210R) or in the presence of a Grb2 dominant-negative protein. Phosphorylation of p130Cas by NPM-ALK was partially independent from Src (tyrosine kinase pp60c-src) kinase activity, as it was still detectable in Syf-/- cells. Finally, p130Cas-/- (also known as Bcar1-/-) fibroblasts expressing NPM-ALK showed impaired actin filament depolymerization and were no longer transformed compared with wild-type cells, indicating an essential role of p130Cas activation in ALK-mediated transformation.
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Affiliation(s)
- Chiara Ambrogio
- Center for Experimental Research and Medical Studies and Department of Biomedical Sciences and Human Oncology, University of Turin, Turin, Italy
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Boeri Erba E, Bergatto E, Cabodi S, Silengo L, Tarone G, Defilippi P, Jensen ON. Systematic Analysis of the Epidermal Growth Factor Receptor by Mass Spectrometry Reveals Stimulation-dependent Multisite Phosphorylation. Mol Cell Proteomics 2005; 4:1107-21. [DOI: 10.1074/mcp.m500070-mcp200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Di Stefano P, Cabodi S, Boeri Erba E, Margaria V, Bergatto E, Giuffrida MG, Silengo L, Tarone G, Turco E, Defilippi P. P130Cas-associated protein (p140Cap) as a new tyrosine-phosphorylated protein involved in cell spreading. Mol Biol Cell 2003; 15:787-800. [PMID: 14657239 PMCID: PMC329393 DOI: 10.1091/mbc.e03-09-0689] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [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: 12/27/2022] Open
Abstract
Integrin-mediated cell adhesion stimulates a cascade of signaling pathways that control cell proliferation, migration, and survival, mostly through tyrosine phosphorylation of signaling molecules. p130Cas, originally identified as a major substrate of v-Src, is a scaffold molecule that interacts with several proteins and mediates multiple cellular events after cell adhesion and mitogen treatment. Here, we describe a novel p130Cas-associated protein named p140Cap (Cas-associated protein) as a new tyrosine phosphorylated molecule involved in integrin- and epidermal growth factor (EGF)-dependent signaling. By affinity chromatography of human ECV304 cell extracts on a MBP-p130Cas column followed by mass spectrometry matrix-assisted laser desorption ionization/time of flight analysis, we identified p140Cap as a protein migrating at 140 kDa. We detected its expression in human, mouse, and rat cells and in different mouse tissues. Endogenous and transfected p140Cap proteins coimmunoprecipitate with p130Cas in ECV304 and in human embryonic kidney 293 cells and associate with p130Cas through their carboxy-terminal region. By immunofluorescence analysis, we demonstrated that in ECV304 cells plated on fibronectin, the endogenous p140Cap colocalizes with p130Cas in the perinuclear region as well as in lamellipodia. In addition p140Cap codistributes with cortical actin and actin stress fibers but not with focal adhesions. We also show that p140Cap is tyrosine phosphorylated within 15 min of cell adhesion to integrin ligands. p140Cap tyrosine phosphorylation is also induced in response to EGF through an EGF receptor dependent-mechanism. Interestingly expression of p140Cap in NIH3T3 and in ECV304 cells delays the onset of cell spreading in the early phases of cell adhesion to fibronectin. Therefore, p140Cap is a novel protein associated with p130Cas and actin cytoskeletal structures. Its tyrosine phosphorylation by integrin-mediated adhesion and EGF stimulation and its involvement in cell spreading on matrix proteins suggest that p140Cap plays a role in controlling actin cytoskeleton organization in response to adhesive and growth factor signaling.
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Affiliation(s)
- Paola Di Stefano
- Dipartimento di Genetica, Biologia e Biochimica, Università di Torino, 10126 Turin, Italy
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Moro L, Dolce L, Cabodi S, Bergatto E, Boeri Erba E, Smeriglio M, Turco E, Retta SF, Giuffrida MG, Venturino M, Godovac-Zimmermann J, Conti A, Schaefer E, Beguinot L, Tacchetti C, Gaggini P, Silengo L, Tarone G, Defilippi P. Integrin-induced epidermal growth factor (EGF) receptor activation requires c-Src and p130Cas and leads to phosphorylation of specific EGF receptor tyrosines. J Biol Chem 2002; 277:9405-14. [PMID: 11756413 DOI: 10.1074/jbc.m109101200] [Citation(s) in RCA: 283] [Impact Index Per Article: 12.9] [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
Integrin-mediated cell adhesion cooperates with growth factor receptors in the control of cell proliferation, cell survival, and cell migration. One mechanism to explain these synergistic effects is the ability of integrins to induce phosphorylation of growth factor receptors, for instance the epidermal growth factor (EGF) receptor. Here we define some aspects of the molecular mechanisms regulating integrin-dependent EGF receptor phosphorylation. We show that in the early phases of cell adhesion integrins associate with EGF receptors on the cell membrane in a macromolecular complex including the adaptor protein p130Cas and the c-Src kinase, the latter being required for adhesion-dependent assembly of the macromolecular complex. We also show that the integrin cytoplasmic tail, c-Src kinase, and the p130Cas adaptor protein are required for phosphorylation of EGF receptor in response to integrin-mediated adhesion. We show that integrins induce phosphorylation of EGF receptor on tyrosine residues 845, 1068, 1086, and 1173, but not on residue 1148, a major site of phosphorylation in response to EGF. In addition we find that integrin-mediated adhesion increases the amount of EGF receptor expressed on the cell surface. Therefore these data indicate that integrin-mediated adhesion induces assembly of a macromolecular complex containing c-Src and p130Cas and leads to phosphorylation of specific EGF receptor tyrosine residues.
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Affiliation(s)
- Laura Moro
- Dipartimento di Scienze Mediche, Università del Piemonte Orientale, Novara 28100, Italy
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