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Dulon D, de Monvel JB, Plion B, Mallet A, Petit C, Condamine S, Bouleau Y, Safieddine S. A free intravesicular C-terminal of otoferlin is essential for synaptic vesicle docking and fusion at auditory inner hair cell ribbon synapses. Prog Neurobiol 2024; 240:102658. [PMID: 39103114 DOI: 10.1016/j.pneurobio.2024.102658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 07/27/2024] [Accepted: 07/30/2024] [Indexed: 08/07/2024]
Abstract
Our understanding of how otoferlin, the major calcium sensor in inner hair cells (IHCs) synaptic transmission, contributes to the overall dynamics of synaptic vesicle (SV) trafficking remains limited. To address this question, we generated a knock-in mouse model expressing an otoferlin-GFP protein, where GFP was fused to its C-terminal transmembrane domain. Similar to the wild type protein, the GFP-tagged otoferlin showed normal expression and was associated with IHC SV. Surprisingly, while the heterozygote Otof+/GFP mice exhibited a normal hearing function, homozygote OtofGFP/GFP mice were profoundly deaf attributed to severe reduction in SV exocytosis. Fluorescence recovery after photobleaching revealed a markedly increased mobile fraction of the otof-GFP-associated SV in Otof GFP/GFP IHCs. Correspondingly, 3D-electron tomographic of the ribbon synapses indicated a reduced density of SV attached to the ribbon active zone. Collectively, these results indicate that otoferlin requires a free intravesicular C-terminal end for normal SV docking and fusion.
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Affiliation(s)
- Didier Dulon
- Institut Pasteur, Université Paris Cité, Inserm U06, Institut de l'Audition, Paris, France; Bordeaux Neurocampus, Université de Bordeaux, Bordeaux 33076, France.
| | | | - Baptiste Plion
- Institut Pasteur, Université Paris Cité, Inserm U06, Institut de l'Audition, Paris, France
| | - Adeline Mallet
- Institut Pasteur, Université Paris Cité, Inserm U06, Institut de l'Audition, Paris, France
| | - Christine Petit
- Institut Pasteur, Université Paris Cité, Inserm U06, Institut de l'Audition, Paris, France
| | - Steven Condamine
- Institut Pasteur, Université Paris Cité, Inserm U06, Institut de l'Audition, Paris, France; Bordeaux Neurocampus, Université de Bordeaux, Bordeaux 33076, France
| | - Yohan Bouleau
- Institut Pasteur, Université Paris Cité, Inserm U06, Institut de l'Audition, Paris, France; Bordeaux Neurocampus, Université de Bordeaux, Bordeaux 33076, France
| | - Saaid Safieddine
- Institut Pasteur, Université Paris Cité, Inserm U06, Institut de l'Audition, Paris, France; Centre National de la Recherche Scientifique, Paris, France.
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2
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Lenard AJ, Mulder FAA, Madl T. Solvent paramagnetic relaxation enhancement as a versatile method for studying structure and dynamics of biomolecular systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:113-139. [PMID: 36496256 DOI: 10.1016/j.pnmrs.2022.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 06/17/2023]
Abstract
Solvent paramagnetic relaxation enhancement (sPRE) is a versatile nuclear magnetic resonance (NMR)-based method that allows characterization of the structure and dynamics of biomolecular systems through providing quantitative experimental information on solvent accessibility of NMR-active nuclei. Addition of soluble paramagnetic probes to the solution of a biomolecule leads to paramagnetic relaxation enhancement in a concentration-dependent manner. Here we review recent progress in the sPRE-based characterization of structural and dynamic properties of biomolecules and their complexes, and aim to deliver a comprehensive illustration of a growing number of applications of the method to various biological systems. We discuss the physical principles of sPRE measurements and provide an overview of available co-solute paramagnetic probes. We then explore how sPRE, in combination with complementary biophysical techniques, can further advance biomolecular structure determination, identification of interaction surfaces within protein complexes, and probing of conformational changes and low-population transient states, as well as deliver insights into weak, nonspecific, and transient interactions between proteins and co-solutes. In addition, we present examples of how the incorporation of solvent paramagnetic probes can improve the sensitivity of NMR experiments and discuss the prospects of applying sPRE to NMR metabolomics, drug discovery, and the study of intrinsically disordered proteins.
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Affiliation(s)
- Aneta J Lenard
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria.
| | - Frans A A Mulder
- Interdisciplinary Nanoscience Center and Department of Chemistry, University of Aarhus, DK-8000 Aarhus, Denmark; Institute of Biochemistry, Johannes Kepler Universität Linz, 4040 Linz, Austria.
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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3
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Li Q, Huang Q, Kang C. Secondary Structures of the Transmembrane Domain of SARS-CoV-2 Spike Protein in Detergent Micelles. Int J Mol Sci 2022; 23:ijms23031040. [PMID: 35162961 PMCID: PMC8834715 DOI: 10.3390/ijms23031040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/08/2022] [Accepted: 01/14/2022] [Indexed: 01/11/2023] Open
Abstract
Spike protein of SARS-CoV-2 contains a single-span transmembrane (TM) domain and plays roles in receptor binding, viral attachment and viral entry to the host cells. The TM domain of spike protein is critical for viral infectivity. Herein, the TM domain of spike protein of SARS-CoV-2 was reconstituted in detergent micelles and subjected to structural analysis using solution NMR spectroscopy. The results demonstrate that the TM domain of the protein forms a helical structure in detergent micelles. An unstructured linker is identified between the TM helix and heptapeptide repeat 2 region. The linker is due to the proline residue at position 1213. Side chains of the three tryptophan residues preceding to and within the TM helix important for the function of S-protein might adopt multiple conformations which may be critical for their function. The side chain of W1212 was shown to be exposed to solvent and the side chains of residues W1214 and W1217 are buried in micelles. Relaxation study shows that the TM helix is rigid in solution while several residues have exchanges. The secondary structure and dynamics of the TM domain in this study provide insights into the function of the TM domain of spike protein.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510316, China;
| | - Qiwei Huang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore 138670, Singapore;
| | - Congbao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore 138670, Singapore;
- Correspondence:
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4
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Seiffert P, Bugge K, Nygaard M, Haxholm GW, Martinsen JH, Pedersen MN, Arleth L, Boomsma W, Kragelund BB. Orchestration of signaling by structural disorder in class 1 cytokine receptors. Cell Commun Signal 2020; 18:132. [PMID: 32831102 PMCID: PMC7444064 DOI: 10.1186/s12964-020-00626-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/08/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Class 1 cytokine receptors (C1CRs) are single-pass transmembrane proteins responsible for transmitting signals between the outside and the inside of cells. Remarkably, they orchestrate key biological processes such as proliferation, differentiation, immunity and growth through long disordered intracellular domains (ICDs), but without having intrinsic kinase activity. Despite these key roles, their characteristics remain rudimentarily understood. METHODS The current paper asks the question of why disorder has evolved to govern signaling of C1CRs by reviewing the literature in combination with new sequence and biophysical analyses of chain properties across the family. RESULTS We uncover that the C1CR-ICDs are fully disordered and brimming with SLiMs. Many of these short linear motifs (SLiMs) are overlapping, jointly signifying a complex regulation of interactions, including network rewiring by isoforms. The C1CR-ICDs have unique properties that distinguish them from most IDPs and we forward the perception that the C1CR-ICDs are far from simple strings with constitutively bound kinases. Rather, they carry both organizational and operational features left uncovered within their disorder, including mechanisms and complexities of regulatory functions. CONCLUSIONS Critically, the understanding of the fascinating ability of these long, completely disordered chains to orchestrate complex cellular signaling pathways is still in its infancy, and we urge a perceptional shift away from the current simplistic view towards uncovering their full functionalities and potential. Video abstract.
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Affiliation(s)
- Pernille Seiffert
- REPIN, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Katrine Bugge
- REPIN, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Mads Nygaard
- REPIN, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Gitte W. Haxholm
- REPIN, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Jacob H. Martinsen
- REPIN, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Martin N. Pedersen
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark
| | - Lise Arleth
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
| | - Birthe B. Kragelund
- REPIN, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
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5
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Li Q, Kang C. A Practical Perspective on the Roles of Solution NMR Spectroscopy in Drug Discovery. Molecules 2020; 25:molecules25132974. [PMID: 32605297 PMCID: PMC7411973 DOI: 10.3390/molecules25132974] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/21/2020] [Accepted: 06/26/2020] [Indexed: 11/26/2022] Open
Abstract
Solution nuclear magnetic resonance (NMR) spectroscopy is a powerful tool to study structures and dynamics of biomolecules under physiological conditions. As there are numerous NMR-derived methods applicable to probe protein–ligand interactions, NMR has been widely utilized in drug discovery, especially in such steps as hit identification and lead optimization. NMR is frequently used to locate ligand-binding sites on a target protein and to determine ligand binding modes. NMR spectroscopy is also a unique tool in fragment-based drug design (FBDD), as it is able to investigate target-ligand interactions with diverse binding affinities. NMR spectroscopy is able to identify fragments that bind weakly to a target, making it valuable for identifying hits targeting undruggable sites. In this review, we summarize the roles of solution NMR spectroscopy in drug discovery. We describe some methods that are used in identifying fragments, understanding the mechanism of action for a ligand, and monitoring the conformational changes of a target induced by ligand binding. A number of studies have proven that 19F-NMR is very powerful in screening fragments and detecting protein conformational changes. In-cell NMR will also play important roles in drug discovery by elucidating protein-ligand interactions in living cells.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou 510316, China
- Correspondence: (Q.L.); (C.K.); Tel.: +86-020-84168436 (Q.L.); +65-64070602 (C.K.)
| | - CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, #05-01, Singapore 138670, Singapore
- Correspondence: (Q.L.); (C.K.); Tel.: +86-020-84168436 (Q.L.); +65-64070602 (C.K.)
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6
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Probing Surfaces in Dynamic Protein Interactions. J Mol Biol 2020; 432:2949-2972. [DOI: 10.1016/j.jmb.2020.02.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 02/22/2020] [Accepted: 02/24/2020] [Indexed: 01/09/2023]
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7
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Wilmes S, Hafer M, Vuorio J, Tucker JA, Winkelmann H, Löchte S, Stanly TA, Pulgar Prieto KD, Poojari C, Sharma V, Richter CP, Kurre R, Hubbard SR, Garcia KC, Moraga I, Vattulainen I, Hitchcock IS, Piehler J. Mechanism of homodimeric cytokine receptor activation and dysregulation by oncogenic mutations. Science 2020; 367:643-652. [PMID: 32029621 PMCID: PMC8117407 DOI: 10.1126/science.aaw3242] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 10/08/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022]
Abstract
Homodimeric class I cytokine receptors are assumed to exist as preformed dimers that are activated by ligand-induced conformational changes. We quantified the dimerization of three prototypic class I cytokine receptors in the plasma membrane of living cells by single-molecule fluorescence microscopy. Spatial and spatiotemporal correlation of individual receptor subunits showed ligand-induced dimerization and revealed that the associated Janus kinase 2 (JAK2) dimerizes through its pseudokinase domain. Oncogenic receptor and hyperactive JAK2 mutants promoted ligand-independent dimerization, highlighting the formation of receptor dimers as the switch responsible for signal activation. Atomistic modeling and molecular dynamics simulations based on a detailed energetic analysis of the interactions involved in dimerization yielded a mechanistic blueprint for homodimeric class I cytokine receptor activation and its dysregulation by individual mutations.
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Affiliation(s)
- Stephan Wilmes
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Maximillian Hafer
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Joni Vuorio
- Department of Physics, University of Helsinki, Helsinki, Finland
- Computational Physics Laboratory, Tampere University, Tampere, Finland
| | - Julie A Tucker
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Hauke Winkelmann
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Sara Löchte
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Tess A Stanly
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Katiuska D Pulgar Prieto
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Chetan Poojari
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Christian P Richter
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Rainer Kurre
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Stevan R Hubbard
- Skirball Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ignacio Moraga
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, Helsinki, Finland.
- Computational Physics Laboratory, Tampere University, Tampere, Finland
| | - Ian S Hitchcock
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK.
| | - Jacob Piehler
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany.
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8
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Li Q, Ng HQ, Kang C. Secondary structure and topology of the transmembrane domain of Syndecan‐2 in detergent micelles. FEBS Lett 2019; 593:554-561. [DOI: 10.1002/1873-3468.13335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 02/03/2019] [Accepted: 02/07/2019] [Indexed: 01/18/2023]
Affiliation(s)
- Qingxin Li
- Institute of Chemical and Engineering Sciences Agency for Science, Technology and Research (A*STAR) Jurong Island Singapore
| | - Hui Qi Ng
- Experimental Therapeutics Centre Experimental Drug Development Centre (EDDC) Agency for Science, Technology and Research (A*STAR) Singapore Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre Experimental Drug Development Centre (EDDC) Agency for Science, Technology and Research (A*STAR) Singapore Singapore
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9
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Ng EY, Loh YR, Li Y, Li Q, Kang C. Expression, purification of Zika virus membrane protein-NS2B in detergent micelles for NMR studies. Protein Expr Purif 2019; 154:1-6. [DOI: 10.1016/j.pep.2018.09.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 09/17/2018] [Accepted: 09/20/2018] [Indexed: 12/15/2022]
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10
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Ferrao RD, Wallweber HJ, Lupardus PJ. Receptor-mediated dimerization of JAK2 FERM domains is required for JAK2 activation. eLife 2018; 7:38089. [PMID: 30044226 PMCID: PMC6078494 DOI: 10.7554/elife.38089] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/24/2018] [Indexed: 12/11/2022] Open
Abstract
Cytokines and interferons initiate intracellular signaling via receptor dimerization and activation of Janus kinases (JAKs). How JAKs structurally respond to changes in receptor conformation induced by ligand binding is not known. Here, we present two crystal structures of the human JAK2 FERM and SH2 domains bound to Leptin receptor (LEPR) and Erythropoietin receptor (EPOR), which identify a novel dimeric conformation for JAK2. This 2:2 JAK2/receptor dimer, observed in both structures, identifies a previously uncharacterized receptor interaction essential to dimer formation that is mediated by a membrane-proximal peptide motif called the ‘switch’ region. Mutation of the receptor switch region disrupts STAT phosphorylation but does not affect JAK2 binding, indicating that receptor-mediated formation of the JAK2 FERM dimer is required for kinase activation. These data uncover the structural and molecular basis for how a cytokine-bound active receptor dimer brings together two JAK2 molecules to stimulate JAK2 kinase activity.
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Affiliation(s)
- Ryan D Ferrao
- Department of Structural Biology, Genentech, Inc., South San Francisco, United States
| | - Heidi Ja Wallweber
- Department of Structural Biology, Genentech, Inc., South San Francisco, United States
| | - Patrick J Lupardus
- Department of Structural Biology, Genentech, Inc., South San Francisco, United States
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11
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Pasquier F, Marty C, Balligand T, Verdier F, Grosjean S, Gryshkova V, Raslova H, Constantinescu SN, Casadevall N, Vainchenker W, Bellanné-Chantelot C, Plo I. New pathogenic mechanisms induced by germline erythropoietin receptor mutations in primary erythrocytosis. Haematologica 2018; 103:575-586. [PMID: 29269524 PMCID: PMC5865417 DOI: 10.3324/haematol.2017.176370] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/21/2017] [Indexed: 12/19/2022] Open
Abstract
Primary familial and congenital polycythemia is characterized by erythropoietin hypersensitivity of erythroid progenitors due to germline nonsense or frameshift mutations in the erythropoietin receptor gene. All mutations so far described lead to the truncation of the C-terminal receptor sequence that contains negative regulatory domains. Their removal is presented as sufficient to cause the erythropoietin hypersensitivity phenotype. Here we provide evidence for a new mechanism whereby the presence of novel sequences generated by frameshift mutations is required for the phenotype rather than just extensive truncation resulting from nonsense mutations. We show that the erythropoietin hypersensitivity induced by a new erythropoietin receptor mutant, p.Gln434Profs*11, could not be explained by the loss of negative signaling and of the internalization domains, but rather by the appearance of a new C-terminal tail. The latter, by increasing erythropoietin receptor dimerization, stability and cell-surface localization, causes pre-activation of erythropoietin receptor and JAK2, constitutive signaling and hypersensitivity to erythropoietin. Similar results were obtained with another mutant, p.Pro438Metfs*6, which shares the same last five amino acid residues (MDTVP) with erythropoietin receptor p.Gln434Profs*11, confirming the involvement of the new peptide sequence in the erythropoietin hypersensitivity phenotype. These results suggest a new mechanism that might be common to erythropoietin receptor frameshift mutations. In summary, we show that primary familial and congenital polycythemia is more complex than expected since distinct mechanisms are involved in the erythropoietin hypersensitivity phenotype, according to the type of erythropoietin receptor mutation.
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Affiliation(s)
- Florence Pasquier
- INSERM, UMR 1170, Gustave Roussy, Laboratoire d'Excellence GR-Ex, Villejuif, France
- Université Paris-Sud, UMR 1170, Gustave Roussy, Villejuif, France
- Service d'Hématologie, Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
- Laboratoire d'Excellence GR-Ex, Paris, France
| | - Caroline Marty
- INSERM, UMR 1170, Gustave Roussy, Laboratoire d'Excellence GR-Ex, Villejuif, France
- Université Paris-Sud, UMR 1170, Gustave Roussy, Villejuif, France
- Laboratoire d'Excellence GR-Ex, Paris, France
| | - Thomas Balligand
- Ludwig Institute for Cancer Research, and Université Catholique de Louvain, de Duve Institute, Brussels, Belgium
| | - Frédérique Verdier
- Laboratoire d'Excellence GR-Ex, Paris, France
- INSERM U1016, Institut Cochin, CNRS UMR8104, Université Paris Descartes, France
| | - Sarah Grosjean
- INSERM, UMR 1170, Gustave Roussy, Laboratoire d'Excellence GR-Ex, Villejuif, France
- Université Paris-Sud, UMR 1170, Gustave Roussy, Villejuif, France
- Laboratoire d'Excellence GR-Ex, Paris, France
| | - Vitalina Gryshkova
- Ludwig Institute for Cancer Research, and Université Catholique de Louvain, de Duve Institute, Brussels, Belgium
| | - Hana Raslova
- INSERM, UMR 1170, Gustave Roussy, Laboratoire d'Excellence GR-Ex, Villejuif, France
- Université Paris-Sud, UMR 1170, Gustave Roussy, Villejuif, France
- Laboratoire d'Excellence GR-Ex, Paris, France
| | - Stefan N Constantinescu
- Ludwig Institute for Cancer Research, and Université Catholique de Louvain, de Duve Institute, Brussels, Belgium
| | - Nicole Casadevall
- INSERM, UMR 1170, Gustave Roussy, Laboratoire d'Excellence GR-Ex, Villejuif, France
- Laboratoire d'Hématologie, Hôpital Saint Antoine, Assistance Publique Hôpitaux de Paris, France
| | - William Vainchenker
- INSERM, UMR 1170, Gustave Roussy, Laboratoire d'Excellence GR-Ex, Villejuif, France
- Université Paris-Sud, UMR 1170, Gustave Roussy, Villejuif, France
- Laboratoire d'Excellence GR-Ex, Paris, France
| | - Christine Bellanné-Chantelot
- INSERM, UMR 1170, Gustave Roussy, Laboratoire d'Excellence GR-Ex, Villejuif, France
- Département de Génétique, Hôpital Universitaire Pitié-Salpêtrière, Assistance Publique Hôpitaux de Paris, France
| | - Isabelle Plo
- INSERM, UMR 1170, Gustave Roussy, Laboratoire d'Excellence GR-Ex, Villejuif, France
- Université Paris-Sud, UMR 1170, Gustave Roussy, Villejuif, France
- Laboratoire d'Excellence GR-Ex, Paris, France
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12
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Wang Y, Bugge K, Kragelund BB, Lindorff-Larsen K. Role of protein dynamics in transmembrane receptor signalling. Curr Opin Struct Biol 2018; 48:74-82. [DOI: 10.1016/j.sbi.2017.10.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/16/2017] [Accepted: 10/19/2017] [Indexed: 10/18/2022]
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13
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14
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Uversky VN, Redwan EM. Erythropoietin and co.: intrinsic structure and functional disorder. MOLECULAR BIOSYSTEMS 2017; 13:56-72. [PMID: 27833947 DOI: 10.1039/c6mb00657d] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Erythropoietin (Epo) is a heavily glycosylated protein, with its main function being related to erythropoiesis, where it controls red blood cell production via interaction with the Epo receptor (EpoR). It also plays a number of important roles in various hormonal, growth factor, and cytokine pathways. These roles are defined by Epo partners, such as the homodimeric (EpoR)2 receptor, the heterodimeric EpoR/βCR receptor and hypoxia inducing factor (HIF). Although the main structural features of both Epo and EpoR are conserved in vertebrates, the secretion sites of Epo in mammals are different from those in other vertebrates. Both biosynthetic and synthetic analogues of this protein are available on the market. Several side effects, such as pure red cells aplaisa, increase the rate of cancer-related death in patients treated with recombinant Epo. The multifunctionality of Epo and the ability of this protein to serve as a hormone, a cytokine, and a growth factor suggest the presence of functional disorder, which is a typical "structural" feature of moonlighting proteins. The goal of this article is to evaluate the roles of intrinsic disorder in the functions of Epo and its primary interactors, EpoR, βCR, and HIF-1α.
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Affiliation(s)
- Vladimir N Uversky
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia. and Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia and Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Elrashdy M Redwan
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia. and Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg EL-Arab 21934, Alexandria, Egypt
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15
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Corbett MSP, Mark AE, Poger D. Do All X-ray Structures of Protein-Ligand Complexes Represent Functional States? EPOR, a Case Study. Biophys J 2017; 112:595-604. [PMID: 28256220 PMCID: PMC5340159 DOI: 10.1016/j.bpj.2016.12.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/20/2016] [Accepted: 12/28/2016] [Indexed: 10/20/2022] Open
Abstract
Based on differences between the x-ray crystal structures of ligand-bound and unbound forms, the activation of the erythropoietin receptor (EPOR) was initially proposed to involve a cross-action scissorlike motion. However, the validity of the motions involved in the scissorlike model has been recently challenged. Here, atomistic molecular dynamics simulations are used to examine the structure of the extracellular domain of the EPOR dimer in the presence and absence of erythropoietin and a series of agonistic or antagonistic mimetic peptides free in solution. The simulations suggest that in the absence of crystal packing effects, the EPOR chains in the different dimers adopt very similar conformations with no clear distinction between the agonist and antagonist-bound complexes. This questions whether the available x-ray crystal structures of EPOR truly represent active or inactive conformations. The study demonstrates the difficulty in using such structures to infer a mechanism of action, especially in the case of membrane receptors where just part of the structure has been considered in addition to potential confounding effects that arise from the comparison of structures in a crystal as opposed to a membrane environment. The work highlights the danger of assigning functional significance to small differences between structures of proteins bound to different ligands in a crystal environment without consideration of the effects of the crystal lattice and thermal motion.
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Affiliation(s)
- Michael S P Corbett
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Alan E Mark
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
| | - David Poger
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
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16
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Trenker R, Call MJ, Call ME. Progress and prospects for structural studies of transmembrane interactions in single-spanning receptors. Curr Opin Struct Biol 2016; 39:115-123. [DOI: 10.1016/j.sbi.2016.07.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/20/2016] [Accepted: 07/01/2016] [Indexed: 11/28/2022]
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17
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Bugge K, Lindorff-Larsen K, Kragelund BB. Understanding single-pass transmembrane receptor signaling from a structural viewpoint-what are we missing? FEBS J 2016; 283:4424-4451. [PMID: 27350538 DOI: 10.1111/febs.13793] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 06/10/2016] [Accepted: 06/27/2016] [Indexed: 11/30/2022]
Abstract
Single-pass transmembrane receptors are involved in essential processes of both physiological and pathological nature and represent more than 1300 proteins in the human genome. Despite the high biological relevance of these receptors, the mechanisms of the signal transductions they facilitate are incompletely understood. One major obstacle is the lack of structures of the transmembrane domains that connect the extracellular ligand-binding domains to the intracellular signaling platforms. Over a period of almost 20 years since the first structure was reported, only 21 of these receptors have become represented by a transmembrane domain structure. This scarceness stands in strong contrast to the significance of these transmembrane α-helices for receptor functionality. In this review, we explore the properties and qualities of the current set of structures, as well as the methodological difficulties associated with their characterization and the challenges left to be overcome. Without an increased and focused effort to bring this class of proteins on par with the remaining membrane protein field, a serious lag in their biological understanding looms. Design of pharmaceutical agents, prediction of mutational affects in relation to disease, and deciphering of functional mechanisms require high-resolution structural information, especially when dealing with a domain carrying so much functionality in so few residues.
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Affiliation(s)
- Katrine Bugge
- Department of Biology, Structural Biology and NMR Laboratory, University of Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, Structural Biology and NMR Laboratory, University of Copenhagen, Denmark
| | - Birthe B Kragelund
- Department of Biology, Structural Biology and NMR Laboratory, University of Copenhagen, Denmark
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18
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Bugge K, Papaleo E, Haxholm GW, Hopper JTS, Robinson CV, Olsen JG, Lindorff-Larsen K, Kragelund BB. A combined computational and structural model of the full-length human prolactin receptor. Nat Commun 2016; 7:11578. [PMID: 27174498 PMCID: PMC4869255 DOI: 10.1038/ncomms11578] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 04/11/2016] [Indexed: 12/13/2022] Open
Abstract
The prolactin receptor is an archetype member of the class I cytokine receptor family, comprising receptors with fundamental functions in biology as well as key drug targets. Structurally, each of these receptors represent an intriguing diversity, providing an exceptionally challenging target for structural biology. Here, we access the molecular architecture of the monomeric human prolactin receptor by combining experimental and computational efforts. We solve the NMR structure of its transmembrane domain in micelles and collect structural data on overlapping fragments of the receptor with small-angle X-ray scattering, native mass spectrometry and NMR spectroscopy. Along with previously published data, these are integrated by molecular modelling to generate a full receptor structure. The result provides the first full view of a class I cytokine receptor, exemplifying the architecture of more than 40 different receptor chains, and reveals that the extracellular domain is merely the tip of a molecular iceberg.
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Affiliation(s)
- Katrine Bugge
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Elena Papaleo
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Gitte W. Haxholm
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Jonathan T. S. Hopper
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Johan G. Olsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Birthe B. Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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19
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Li Y, Liew LSY, Li Q, Kang C. Structure of the transmembrane domain of human nicastrin-a component of γ-secretase. Sci Rep 2016; 6:19522. [PMID: 26776682 PMCID: PMC4726005 DOI: 10.1038/srep19522] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/09/2015] [Indexed: 02/04/2023] Open
Abstract
Nicastrin is the largest component of γ-secretase that is an intramembrane protease important in the development of Alzheimer's disease. Nicastrin contains a large extracellular domain, a single transmembrane (TM) domain, and a short C-terminus. Its TM domain is important for the γ-secretase complex formation. Here we report nuclear magnetic resonance (NMR) studies of the TM and C-terminal regions of human nicastrin in both sodium dodecyl sulfate (SDS) and dodecylphosphocholine (DPC) micelles. Structural study and dynamic analysis reveal that the TM domain is largely helical and stable under both SDS and DPC micelles with its N-terminal region undergoing intermediate time scale motion. The TM helix contains a hydrophilic patch that is important for TM-TM interactions. The short C-terminus is not structured in solution and a region formed by residues V697-A702 interacts with the membrane, suggesting that these residues may play a role in the γ-secretase complex formation. Our study provides structural insight into the function of the nicastrin TM domain and the C-terminus in γ-secretase complex.
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Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
| | - Lynette Sin Yee Liew
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
| | - Qingxin Li
- Institute of Chemical &Engineering Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
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20
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Li Y, Li Q, Wong YL, Liew LSY, Kang C. Membrane topology of NS2B of dengue virus revealed by NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2244-52. [DOI: 10.1016/j.bbamem.2015.06.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/20/2015] [Accepted: 06/09/2015] [Indexed: 12/27/2022]
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21
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Li Q, Wong YL, Yueqi Lee M, Li Y, Kang C. Solution structure of the transmembrane domain of the mouse erythropoietin receptor in detergent micelles. Sci Rep 2015; 5:13586. [PMID: 26316120 PMCID: PMC4551963 DOI: 10.1038/srep13586] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 07/31/2015] [Indexed: 12/19/2022] Open
Abstract
Erythropoiesis is regulated by the erythropoietin receptor (EpoR) binding to its ligand. The transmembrane domain (TMD) and the juxtamembrane (JM) regions of the EpoR are important for signal transduction across the cell membrane. We report a solution NMR study of the mouse erythropoietin receptor (mEpoR) comprising the TMD and the JM regions reconstituted in dodecylphosphocholine (DPC) micelles. The TMD and the C-terminal JM region of the mEpoR are mainly α-helical, adopting a similar structure to those of the human EpoR. Residues from S216 to T219 in mEpoR form a short helix. Relaxation study demonstrates that the TMD of the mEpoR is rigid whilst the N-terminal region preceding the TMD is flexible. Fluorescence spectroscopy and sequence analysis indicate that the C-terminal JM region is exposed to the solvent. Helix wheel result shows that there is hydrophilic patch in the TMD of the mEpoR formed by residues S231, S238 and T242, and these residues might be important for the receptor dimerization.
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Affiliation(s)
- Qingxin Li
- Institute of Chemical &Engineering Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Ying Lei Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
| | - Michelle Yueqi Lee
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
| | - Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
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22
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Determinants of Dengue Virus NS4A Protein Oligomerization. J Virol 2015; 89:6171-83. [PMID: 25833044 DOI: 10.1128/jvi.00546-15] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 03/23/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Flavivirus NS4A protein induces host membrane rearrangement and functions as a replication complex component. The molecular details of how flavivirus NS4A exerts these functions remain elusive. Here, we used dengue virus (DENV) as a model to characterize and demonstrate the biological relevance of flavivirus NS4A oligomerization. DENV type 2 (DENV-2) NS4A protein forms oligomers in infected cells or when expressed alone. Deletion mutagenesis mapped amino acids 50 to 76 (spanning the first transmembrane domain [TMD1]) of NS4A as the major determinant for oligomerization, while the N-terminal 50 residues contribute only slightly to the oligomerization. Nuclear magnetic resonance (NMR) analysis of NS4A amino acids 17 to 80 suggests that residues L31, L52, E53, G66, and G67 could participate in oligomerization. Ala substitution for 15 flavivirus conserved NS4A residues revealed that these amino acids are important for viral replication. Among the 15 mutated NS4A residues, 2 amino acids (E50A and G67A) are located within TMD1. Both E50A and G67A attenuated viral replication, decreased NS4A oligomerization, and reduced NS4A protein stability. In contrast, NS4A oligomerization was not affected by the replication-defective mutations (R12A, P49A, and K80A) located outside TMD1. trans complementation experiments showed that expression of wild-type NS4A alone was not sufficient to rescue the replication-lethal NS4A mutants. However, the presence of DENV-2 replicons could partially restore the replication defect of some lethal NS4A mutants (L26A and K80A), but not others (L60A and E122A), suggesting an unidentified mechanism governing the outcome of complementation in a mutant-dependent manner. Collectively, the results have demonstrated the importance of TMD1-mediated NS4A oligomerization in flavivirus replication. IMPORTANCE We report that DENV NS4A forms oligomers. Such NS4A oligomerization is mediated mainly through amino acids 50 to 76 (spanning the first transmembrane domain [TMD1]). The biological importance of NS4A oligomerization is demonstrated by results showing that mutations of flavivirus conserved residues (E50A and G67A located within TMD1) reduced the oligomerization and stability of the NS4A protein, leading to attenuated viral replication. A systematic mutagenesis analysis demonstrated that flavivirus conserved NS4A residues are important for DENV replication. A successful trans complementation of replication-lethal NS4A mutant virus requires wild-type NS4A in the context of the viral replication complex. The wild-type NS4A protein alone is not sufficient to rescue the replication defect of NS4A mutants. Intriguingly, distinct NS4A mutants yielded different complementation outcomes in the replicon-containing cells. Overall, the study has enhanced our understanding of flavivirus NS4A at the molecular level. The results also suggest that inhibitor blocking of NS4A oligomerization could be explored for antiviral drug discovery.
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