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Fedry J, Silva J, Vanevic M, Fronik S, Mechulam Y, Schmitt E, des Georges A, Faller WJ, Förster F. Visualization of translation reorganization upon persistent ribosome collision stress in mammalian cells. Mol Cell 2024; 84:1078-1089.e4. [PMID: 38340715 PMCID: PMC7615912 DOI: 10.1016/j.molcel.2024.01.015] [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: 04/21/2023] [Revised: 11/06/2023] [Accepted: 01/18/2024] [Indexed: 02/12/2024]
Abstract
Aberrantly slow ribosomes incur collisions, a sentinel of stress that triggers quality control, signaling, and translation attenuation. Although each collision response has been studied in isolation, the net consequences of their collective actions in reshaping translation in cells is poorly understood. Here, we apply cryoelectron tomography to visualize the translation machinery in mammalian cells during persistent collision stress. We find that polysomes are compressed, with up to 30% of ribosomes in helical polysomes or collided disomes, some of which are bound to the stress effector GCN1. The native collision interface extends beyond the in vitro-characterized 40S and includes the L1 stalk and eEF2, possibly contributing to translocation inhibition. The accumulation of unresolved tRNA-bound 80S and 60S and aberrant 40S configurations identifies potentially limiting steps in collision responses. Our work provides a global view of the translation machinery in response to persistent collisions and a framework for quantitative analysis of translation dynamics in situ.
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Affiliation(s)
- Juliette Fedry
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, the Netherlands; MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
| | - Joana Silva
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mihajlo Vanevic
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Stanley Fronik
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Amédée des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, USA; Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA; Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, City University of New York, New York, NY, USA
| | - William James Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, the Netherlands
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2
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Fedry J, Silva J, Vanevic M, Fronik S, Mechulam Y, Schmitt E, des Georges A, Faller W, Förster F. Visualization of translation reorganization upon persistent collision stress in mammalian cells. bioRxiv 2023:2023.03.23.533914. [PMID: 36993420 PMCID: PMC10055323 DOI: 10.1101/2023.03.23.533914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Aberrantly slow mRNA translation leads to ribosome stalling and subsequent collision with the trailing neighbor. Ribosome collisions have recently been shown to act as stress sensors in the cell, with the ability to trigger stress responses balancing survival and apoptotic cell-fate decisions depending on the stress level. However, we lack a molecular understanding of the reorganization of translation processes over time in mammalian cells exposed to an unresolved collision stress. Here we visualize the effect of a persistent collision stress on translation using in situ cryo electron tomography. We observe that low dose anisomycin collision stress leads to the stabilization of Z-site bound tRNA on elongating 80S ribosomes, as well as to the accumulation of an off-pathway 80S complex possibly resulting from collision splitting events. We visualize collided disomes in situ, occurring on compressed polysomes and revealing a stabilized geometry involving the Z-tRNA and L1 stalk on the stalled ribosome, and eEF2 bound to its collided rotated-2 neighbor. In addition, non-functional post-splitting 60S complexes accumulate in the stressed cells, indicating a limiting Ribosome associated Quality Control clearing rate. Finally, we observe the apparition of tRNA-bound aberrant 40S complexes shifting with the stress timepoint, suggesting a succession of different initiation inhibition mechanisms over time. Altogether, our work visualizes the changes of translation complexes under persistent collision stress in mammalian cells, indicating how perturbations in initiation, elongation and quality control processes contribute to an overall reduced protein synthesis.
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Affiliation(s)
- Juliette Fedry
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Joana Silva
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mihajlo Vanevic
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Stanley Fronik
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Amédée des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, USA
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, City University of New York, New York, NY, USA
| | - William Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands
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3
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Marcink TC, Kicmal T, Armbruster E, Zhang Z, Zipursky G, Golub KL, Idris M, Khao J, Drew-Bear J, McGill G, Gallagher T, Porotto M, des Georges A, Moscona A. Intermediates in SARS-CoV-2 spike-mediated cell entry. Sci Adv 2022; 8:eabo3153. [PMID: 35984891 PMCID: PMC9390989 DOI: 10.1126/sciadv.abo3153] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 07/07/2022] [Indexed: 05/17/2023]
Abstract
SARS-CoV-2 cell entry is completed after viral spike (S) protein-mediated membrane fusion between viral and host cell membranes. Stable prefusion and postfusion S structures have been resolved by cryo-electron microscopy and cryo-electron tomography, but the refolding intermediates on the fusion pathway are transient and have not been examined. We used an antiviral lipopeptide entry inhibitor to arrest S protein refolding and thereby capture intermediates as S proteins interact with hACE2 and fusion-activating proteases on cell-derived target membranes. Cryo-electron tomography imaged both extended and partially folded intermediate states of S2, as well as a novel late-stage conformation on the pathway to membrane fusion. The intermediates now identified in this dynamic S protein-directed fusion provide mechanistic insights that may guide the design of CoV entry inhibitors.
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Affiliation(s)
- Tara C. Marcink
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Thomas Kicmal
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - Emily Armbruster
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, USA
| | - Zhening Zhang
- Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Gillian Zipursky
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Kate L. Golub
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Mohab Idris
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | | | - Jennifer Drew-Bear
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Gael McGill
- Digizyme Inc., Brookline, MA, USA
- Center for Molecular and Cellular Dynamics, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli,” 81100 Caserta, Italy
| | - Amédée des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, USA
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, City University of New York, New York, NY, USA
| | - Anne Moscona
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
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4
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Cheng EL, Cardle II, Kacherovsky N, Bansia H, Wang T, Zhou Y, Raman J, Yen A, Gutierrez D, Salipante SJ, des Georges A, Jensen MC, Pun SH. Discovery of a Transferrin Receptor 1-Binding Aptamer and Its Application in Cancer Cell Depletion for Adoptive T-Cell Therapy Manufacturing. J Am Chem Soc 2022; 144:13851-13864. [PMID: 35875870 PMCID: PMC10024945 DOI: 10.1021/jacs.2c05349] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The clinical manufacturing of chimeric antigen receptor (CAR) T cells includes cell selection, activation, gene transduction, and expansion. While the method of T-cell selection varies across companies, current methods do not actively eliminate the cancer cells in the patient's apheresis product from the healthy immune cells. Alarmingly, it has been found that transduction of a single leukemic B cell with the CAR gene can confer resistance to CAR T-cell therapy and lead to treatment failure. In this study, we report the identification of a novel high-affinity DNA aptamer, termed tJBA8.1, that binds transferrin receptor 1 (TfR1), a receptor broadly upregulated by cancer cells. Using competition assays, high resolution cryo-EM, and de novo model building of the aptamer into the resulting electron density, we reveal that tJBA8.1 shares a binding site on TfR1 with holo-transferrin, the natural ligand of TfR1. We use tJBA8.1 to effectively deplete B lymphoma cells spiked into peripheral blood mononuclear cells with minimal impact on the healthy immune cell composition. Lastly, we present opportunities for affinity improvement of tJBA8.1. As TfR1 expression is broadly upregulated in many cancers, including difficult-to-treat T-cell leukemias and lymphomas, our work provides a facile, universal, and inexpensive approach for comprehensively removing cancerous cells from patient apheresis products for safe manufacturing of adoptive T-cell therapies.
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Affiliation(s)
- Emmeline L Cheng
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Ian I Cardle
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States.,Seattle Children's Therapeutics, Seattle, Washington 98101, United States
| | - Nataly Kacherovsky
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Harsh Bansia
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, New York 10031, United States
| | - Tong Wang
- Nanoscience Initiative, CUNY Advanced Science Research Center, City University of New York, New York, New York 10031, United States
| | - Yunshi Zhou
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Jai Raman
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Albert Yen
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Dominique Gutierrez
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, New York 10031, United States.,Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York (CUNY), New York, New York 10016, United States
| | - Stephen J Salipante
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195-7110, United States
| | - Amédée des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, New York 10031, United States.,Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States.,Department of Chemistry and Biochemistry, City College of New York, New York, New York 10031, United States
| | - Michael C Jensen
- Seattle Children's Therapeutics, Seattle, Washington 98101, United States.,Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
| | - Suzie H Pun
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
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5
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Montemiglio LC, Testi C, Ceci P, Falvo E, Pitea M, Savino C, Arcovito A, Peruzzi G, Baiocco P, Mancia F, Boffi A, des Georges A, Vallone B. Cryo-EM structure of the human ferritin-transferrin receptor 1 complex. Nat Commun 2019; 10:1121. [PMID: 30850661 PMCID: PMC6408514 DOI: 10.1038/s41467-019-09098-w] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [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: 09/18/2018] [Accepted: 02/13/2019] [Indexed: 12/31/2022] Open
Abstract
Human transferrin receptor 1 (CD71) guarantees iron supply by endocytosis upon binding of iron-loaded transferrin and ferritin. Arenaviruses and the malaria parasite exploit CD71 for cell invasion and epitopes on CD71 for interaction with transferrin and pathogenic hosts were identified. Here, we provide the molecular basis of the CD71 ectodomain-human ferritin interaction by determining the 3.9 Å resolution single-particle cryo-electron microscopy structure of their complex and by validating our structural findings in a cellular context. The contact surfaces between the heavy-chain ferritin and CD71 largely overlap with arenaviruses and Plasmodium vivax binding regions in the apical part of the receptor ectodomain. Our data account for transferrin-independent binding of ferritin to CD71 and suggest that select pathogens may have adapted to enter cells by mimicking the ferritin access gate. The human transferrin receptor 1 (CD71) is a transmembrane protein responsible for iron uptake. Here the authors present the 3.9 Å resolution cryo-EM structure of the CD71 ectodomain-human ferritin (H-Ft) complex and find that H-Ft binds a CD71 region different from the transferrin one that overlaps with the surface recognized by select pathogens.
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Affiliation(s)
- Linda Celeste Montemiglio
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy.,Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Claudia Testi
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy.,Center for Life Nano Science @ Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, 00161, Rome, Italy
| | - Pierpaolo Ceci
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy
| | - Elisabetta Falvo
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy
| | - Martina Pitea
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy
| | - Alessandro Arcovito
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Largo F. Vito 1, 00168, Rome, Italy
| | - Giovanna Peruzzi
- Center for Life Nano Science @ Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, 00161, Rome, Italy
| | - Paola Baiocco
- Center for Life Nano Science @ Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, 00161, Rome, Italy
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Russ Berrie Pavilion, Columbia University Medical Center, 1150 St Nicholas Ave, New York, NY, 10032, USA
| | - Alberto Boffi
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy
| | - Amédée des Georges
- Advanced Science Research Center at The Graduate Center of the City University of New York, 85 Saint Nicholas Terrace, New York, NY, 10031, USA. .,Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA. .,Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
| | - Beatrice Vallone
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy. .,Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy.
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6
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Calisti L, Trabuco MC, Boffi A, Testi C, Montemiglio LC, des Georges A, Benni I, Ilari A, Taciak B, Białasek M, Rygiel T, Król M, Baiocco P, Bonamore A. Engineered ferritin for lanthanide binding. PLoS One 2018; 13:e0201859. [PMID: 30102720 PMCID: PMC6089422 DOI: 10.1371/journal.pone.0201859] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 06/07/2018] [Accepted: 07/23/2018] [Indexed: 11/18/2022] Open
Abstract
Ferritin H-homopolymers have been extensively used as nanocarriers for diverse applications in the targeted delivery of drugs and imaging agents, due to their unique ability to bind the transferrin receptor (CD71), highly overexpressed in most tumor cells. In order to incorporate novel fluorescence imaging properties, we have fused a lanthanide binding tag (LBT) to the C-terminal end of mouse H-chain ferritin, HFt. The HFt-LBT possesses one high affinity Terbium binding site per each of the 24 subunits provided by six coordinating aminoacid side chains and a tryptophan residue in its close proximity and is thus endowed with strong FRET sensitization properties. Accordingly, the characteristic Terbium emission band at 544 nm for the HFt-LBT Tb(III) complex was detectable upon excitation of the tag enclosed at two order of magnitude higher intensity with respect to the wtHFt protein. X-ray data at 2.9 Å and cryo-EM at 7 Å resolution demonstrated that HFt-LBT is correctly assembled as a 24-mer both in crystal and in solution. On the basis of the intrinsic Tb(III) binding properties of the wt protein, 32 additional Tb(III) binding sites, located within the natural iron binding sites of the protein, were identified besides the 24 Tb(III) ions coordinated to the LBTs. HFt-LBT Tb(III) was demonstrated to be actively uptaken by selected tumor cell lines by confocal microscopy and FACS analysis of their FITC derivatives, although direct fluorescence from Terbium emission could not be singled out with conventional, 295-375 nm, fluorescence excitation.
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Affiliation(s)
- Lorenzo Calisti
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
| | | | - Alberto Boffi
- Center for Life Nano Science @ Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Claudia Testi
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
| | - Linda Celeste Montemiglio
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Amédée des Georges
- The City University of New York Advanced Science Research Center, New York, NY
| | - Irene Benni
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Bartłomiej Taciak
- Faculty of Veterinary Medicine, Warsaw University of Life Sciences, ul. Nowoursynowska, Warszawa, Poland
- Cellis Ltd., Warsaw, Poland
| | - Maciej Białasek
- Faculty of Veterinary Medicine, Warsaw University of Life Sciences, ul. Nowoursynowska, Warszawa, Poland
| | - Tomasz Rygiel
- Cellis Ltd., Warsaw, Poland
- Department of Immunology, Center for Biostructure Research, Medical University of Warsaw, Warsaw, Poland
| | - Magdalena Król
- Faculty of Veterinary Medicine, Warsaw University of Life Sciences, ul. Nowoursynowska, Warszawa, Poland
- Cellis Ltd., Warsaw, Poland
| | - Paola Baiocco
- Center for Life Nano Science @ Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
- * E-mail:
| | - Alessandra Bonamore
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
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7
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des Georges A, Clarke OB, Zalk R, Yuan Q, Condon KJ, Grassucci RA, Hendrickson WA, Marks AR, Frank J. Structural Basis for Gating and Activation of RyR1. Cell 2016; 167:145-157.e17. [PMID: 27662087 DOI: 10.1016/j.cell.2016.08.075] [Citation(s) in RCA: 256] [Impact Index Per Article: 32.0] [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: 02/29/2016] [Revised: 06/08/2016] [Accepted: 08/30/2016] [Indexed: 10/21/2022]
Abstract
The type-1 ryanodine receptor (RyR1) is an intracellular calcium (Ca(2+)) release channel required for skeletal muscle contraction. Here, we present cryo-EM reconstructions of RyR1 in multiple functional states revealing the structural basis of channel gating and ligand-dependent activation. Binding sites for the channel activators Ca(2+), ATP, and caffeine were identified at interdomain interfaces of the C-terminal domain. Either ATP or Ca(2+) alone induces conformational changes in the cytoplasmic assembly ("priming"), without pore dilation. In contrast, in the presence of all three activating ligands, high-resolution reconstructions of open and closed states of RyR1 were obtained from the same sample, enabling analyses of conformational changes associated with gating. Gating involves global conformational changes in the cytosolic assembly accompanied by local changes in the transmembrane domain, which include bending of the S6 transmembrane segment and consequent pore dilation, displacement, and deformation of the S4-S5 linker and conformational changes in the pseudo-voltage-sensor domain.
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Affiliation(s)
- Amédée des Georges
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
| | - Oliver B Clarke
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Ran Zalk
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Qi Yuan
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Kendall J Condon
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
| | - Robert A Grassucci
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
| | - Wayne A Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA.
| | - Andrew R Marks
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032, USA; Wu Center for Molecular Cardiology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA; Department of Biological Sciences, Columbia University, New York, NY 10032, USA.
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8
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Zalk R, Clarke OB, des Georges A, Grassucci RA, Reiken S, Mancia F, Hendrickson WA, Frank J, Marks AR. Structure of a mammalian ryanodine receptor. Nature 2014; 517:44-9. [PMID: 25470061 PMCID: PMC4300236 DOI: 10.1038/nature13950] [Citation(s) in RCA: 290] [Impact Index Per Article: 29.0] [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: 07/16/2014] [Accepted: 10/08/2014] [Indexed: 12/11/2022]
Abstract
Ryanodine receptors (RyRs) mediate rapid release of calcium (Ca2+) from intracellular stores into the cytosol, which is essential for numerous cellular functions including excitation-contraction coupling in muscle. Lack of sufficient structural detail has impeded understanding of RyR gating and regulation. Here, we report the closed-state structure of the 2.3 MDa complex of the rabbit skeletal muscle type 1 RyR (RyR1), solved by single-particle cryo-electron microscopy at an overall resolution of 4.8 Å. We fitted a polyalanine-level model to all 3939 ordered residues in each protomer, defining the transmembrane pore in unprecedented detail and placing all cytosolic domains as tertiary folds. The cytosolic assembly is built on an extended α-solenoid scaffold connecting key regulatory domains to the pore. The RyR1 pore architecture places it in the six-transmembrane (6TM) ion channel superfamily. A unique domain inserted between the second and third transmembrane helices interacts intimately with paired EF-hands originating from the α-solenoid scaffold, suggesting a mechanism for channel gating by Ca2+.
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Affiliation(s)
- Ran Zalk
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
| | - Oliver B Clarke
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - Amédée des Georges
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - Robert A Grassucci
- 1] Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA [2] Howard Hughes Medical Institute, Columbia University, New York, New York 10032, USA
| | - Steven Reiken
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
| | - Wayne A Hendrickson
- 1] Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA [2] Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - Joachim Frank
- 1] Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA [2] Howard Hughes Medical Institute, Columbia University, New York, New York 10032, USA [3] Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Andrew R Marks
- 1] Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA [2] Department of Medicine, Columbia University, New York, New York 10032, USA [3] Wu Center for Molecular Cardiology, College of Physicians and Surgeons of Columbia University, New York, New York 10032, USA
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9
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des Georges A, Hashem Y, Unbehaun A, Grassucci RA, Taylor D, Hellen CUT, Pestova TV, Frank J. Structure of the mammalian ribosomal pre-termination complex associated with eRF1.eRF3.GDPNP. Nucleic Acids Res 2013; 42:3409-18. [PMID: 24335085 PMCID: PMC3950680 DOI: 10.1093/nar/gkt1279] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Eukaryotic translation termination results from the complex functional interplay between two release factors, eRF1 and eRF3, in which GTP hydrolysis by eRF3 couples codon recognition with peptidyl-tRNA hydrolysis by eRF1. Here, we present a cryo-electron microscopy structure of pre-termination complexes associated with eRF1•eRF3•GDPNP at 9.7 -Å resolution, which corresponds to the initial pre-GTP hydrolysis stage of factor attachment and stop codon recognition. It reveals the ribosomal positions of eRFs and provides insights into the mechanisms of stop codon recognition and triggering of eRF3's GTPase activity.
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Affiliation(s)
- Amédée des Georges
- Howard Hughes Medical Institute, Chevy Chase, MD, USA, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA, Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY, USA, Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA and Department of Biological Sciences, Columbia University, New York, NY, USA
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10
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Abstract
The envelope of the influenza virus undergoes extensive structural change during the viral life cycle. However, it is unknown how lipid and protein components of the viral envelope contribute to its mechanical properties. Using atomic force microscopy, here we show that the lipid envelope of spherical influenza virions is ∼10 times softer (∼0.05 nanonewton nm(-1)) than a viral protein-capsid coat and sustains deformations of one-third of the virion's diameter. Compared with phosphatidylcholine liposomes, it is twice as stiff, due to membrane-attached protein components. We found that virus indentation resulted in a biphasic force-indentation response. We propose that the first phase, including a stepwise reduction in stiffness at ∼10-nm indentation and ∼100 piconewtons of force, is due to mobilization of membrane proteins by the indenting atomic force microscope tip, consistent with the glycoprotein ectodomains protruding ∼13 nm from the bilayer surface. This phase was obliterated for bromelain-treated virions with the ectodomains removed. Following pH 5 treatment, virions were as soft as pure liposomes, consistent with reinforcing proteins detaching from the lipid bilayer. We propose that the soft, pH-dependent mechanical properties of the envelope are critical for the pH-regulated life cycle and support the persistence of the virus inside and outside the host.
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Affiliation(s)
- Iwan A T Schaap
- National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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11
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des Georges A, Katsuki M, Drummond DR, Osei M, Cross RA, Amos LA. Mal3, the Schizosaccharomyces pombe homolog of EB1, changes the microtubule lattice. Nat Struct Mol Biol 2008; 15:1102-8. [PMID: 18794845 DOI: 10.1038/nsmb.1482] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 07/29/2008] [Indexed: 11/09/2022]
Abstract
In vitro studies of pure tubulin have suggested that tubulin heterodimers in cells assemble into B-lattice microtubules, where the 8-nm dimers in adjacent protofilaments are staggered by 0.9 nm. This arrangement requires the tube to close by forming a seam with an A-lattice, in which the protofilaments are staggered by 4.9 nm. Here we show that Mal3, an EB1 family tip-tracking protein, drives tubulin to assemble in vitro into exclusively 13-protofilament microtubules with a high proportion of A-lattice protofilament contacts. We present a three-dimensional cryo-EM reconstruction of a purely A-lattice microtubule decorated with Mal3, in which Mal3 occupies the groove between protofilaments and associates closely with one tubulin monomer. We propose that Mal3 promotes assembly by binding to freshly formed tubulin polymer and particularly favors any with A-lattice arrangement. These results reopen the question of microtubule structure in cells.
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