1
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Wolters RM, Ferguson JA, Nuñez IA, Chen EE, Sornberger T, Myers L, Oeverdieck S, Raghavan SSR, Kona C, Handal LS, Esilu TE, Davidson E, Doranz BJ, Engdahl TB, Kose N, Williamson LE, Creech CB, Gibson-Corley KN, Ward AB, Crowe JE. Isolation of human antibodies against influenza B neuraminidase and mechanisms of protection at the airway interface. Immunity 2024:S1074-7613(24)00253-X. [PMID: 38823390 DOI: 10.1016/j.immuni.2024.05.002] [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: 09/19/2023] [Revised: 01/16/2024] [Accepted: 05/06/2024] [Indexed: 06/03/2024]
Abstract
Influenza B viruses (IBVs) comprise a substantial portion of the circulating seasonal human influenza viruses. Here, we describe the isolation of human monoclonal antibodies (mAbs) that recognized the IBV neuraminidase (NA) glycoprotein from an individual following seasonal vaccination. Competition-binding experiments suggested the antibodies recognized two major antigenic sites. One group, which included mAb FluB-393, broadly inhibited IBV NA sialidase activity, protected prophylactically in vivo, and bound to the lateral corner of NA. The second group contained an active site mAb, FluB-400, that broadly inhibited IBV NA sialidase activity and virus replication in vitro in primary human respiratory epithelial cell cultures and protected against IBV in vivo when administered systemically or intranasally. Overall, the findings described here shape our mechanistic understanding of the human immune response to the IBV NA glycoprotein through the demonstration of two mAb delivery routes for protection against IBV and the identification of potential IBV therapeutic candidates.
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Affiliation(s)
- Rachael M Wolters
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James A Ferguson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ivette A Nuñez
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Elaine E Chen
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ty Sornberger
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Luke Myers
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Svearike Oeverdieck
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sai Sundar Rajan Raghavan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chandrahaas Kona
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Laura S Handal
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | | | | | - Taylor B Engdahl
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nurgun Kose
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Lauren E Williamson
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - C Buddy Creech
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Katherine N Gibson-Corley
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - James E Crowe
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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2
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Serbynovskyi V, Wang J, Chua EYD, Ishemgulova A, Alink LM, Budell WC, Johnston JD, Dubbeldam C, Gonzalez FA, Rozovsky S, Eng ET, de Marco A, Noble AJ. CryoCycle your grids: Plunge vitrifying and reusing clipped grids to advance cryoEM democratization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576763. [PMID: 38328036 PMCID: PMC10849629 DOI: 10.1101/2024.01.23.576763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
CryoEM democratization is hampered by access to costly plunge-freezing supplies. We introduce methods, called CryoCycle, for reliably blotting, vitrifying, and reusing clipped cryoEM grids. We demonstrate that vitreous ice may be produced by plunging clipped grids with purified proteins into liquid ethane and that clipped grids may be reused several times for different protein samples. Furthermore, we demonstrate the vitrification of thin areas of cells prepared on gold-coated, pre-clipped grids.
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Affiliation(s)
| | - Jing Wang
- Simons Electron Microscopy Center, New York Structural Biology Center, NY, NY, USA
| | - Eugene YD Chua
- Simons Electron Microscopy Center, New York Structural Biology Center, NY, NY, USA
| | - Aygul Ishemgulova
- Simons Electron Microscopy Center, New York Structural Biology Center, NY, NY, USA
| | - Lambertus M. Alink
- Simons Electron Microscopy Center, New York Structural Biology Center, NY, NY, USA
| | - William C. Budell
- Simons Electron Microscopy Center, New York Structural Biology Center, NY, NY, USA
| | - Jake D. Johnston
- Simons Electron Microscopy Center, New York Structural Biology Center, NY, NY, USA
- Department of Cellular and Molecular Physiology & Biophysics
| | - Charlie Dubbeldam
- Simons Electron Microscopy Center, New York Structural Biology Center, NY, NY, USA
| | - Fabio A. Gonzalez
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Edward T. Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, NY, NY, USA
| | - Alex de Marco
- Simons Electron Microscopy Center, New York Structural Biology Center, NY, NY, USA
- Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Alex J. Noble
- Simons Electron Microscopy Center, New York Structural Biology Center, NY, NY, USA
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3
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Jia L, Ruben EA, Suarez HJ, Olsen SK, Wasmuth EV. Single particle cryo-electron microscopy with an enhanced 200 kV cryo-TEM configuration achieves near-atomic resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.593029. [PMID: 38766263 PMCID: PMC11100677 DOI: 10.1101/2024.05.07.593029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Single particle cryogenic electron microscopy (cryo-EM) as a structural biology methodology has become increasingly attractive and accessible to investigators in both academia and industry as this ever-advancing technology enables successful structural determination of a wide range of protein and nucleic acid targets. Although data for many high resolution cryo-EM structures are still obtained using a 300 kV cryogenic transmission electron microscope (cryo-TEM), a modern 200 kV cryo-TEM equipped with an advanced direct electron detector and energy filter is a cost-effective choice for most single particle applications, routinely achieving sub 3 angstrom (Å) resolution. Here, we systematically evaluate performance of one such high-end configuration - a 200 kV Glacios microscope coupled with a Falcon 4 direct electron detector and Selectris energy filter (Glacios-F4-S). First, we evaluated data quality on the standard benchmarking sample, rabbit muscle aldolase, using three of the most frequently used cryo-EM data collection software: SerialEM, Leginon and EPU, and found that - despite sample heterogeneity - all final reconstructions yield same overall resolutions of 2.6 Å and map quality when using either of the three software. Furthermore, comparison between Glacios-F4-S and a 300 kV cryo-TEM (Titan Krios with Falcon 4) revealed nominal resolution differences in overall reconstructions of a reconstituted human nucleosome core particle, achieving 2.8 and 2.5 Å, respectively. Finally, we performed comparative data analysis on the human RAD51 paralog complex, BCDX2, a four-protein complex of approximately 150 kilodaltons, and found that a small dataset (≤1,000 micrographs) was sufficient to generate a 3.3 Å reconstruction, with sufficient detail to resolve co-bound ligands, AMP-PNP and Mg +2 . In summary, this study provides evidence that the Glacios-F4-S operates equally well with all standard data collection software, and is sufficient to obtain high resolution structural information of novel macromolecular complexes, readily acquiring single particle data rivaling that of 300 kV cryo-TEMs.
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4
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Tomris I, van der Woude R, de Paiva Froes Rocha R, Torrents de la Peña A, Ward AB, de Vries RP. Viral envelope proteins fused to multiple distinct fluorescent reporters to probe receptor binding. Protein Sci 2024; 33:e4974. [PMID: 38533540 DOI: 10.1002/pro.4974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/04/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
Enveloped viruses carry one or multiple proteins with receptor-binding functionalities. Functional receptors can be glycans, proteinaceous, or both; therefore, recombinant protein approaches are instrumental in attaining new insights regarding viral envelope protein receptor-binding properties. Visualizing and measuring receptor binding typically entails antibody detection or direct labeling, whereas direct fluorescent fusions are attractive tools in molecular biology. Here, we report a suite of distinct fluorescent fusions, both N- and C-terminal, for influenza A virus hemagglutinins and SARS-CoV-2 spike RBD. The proteins contained three or six fluorescent protein barrels and were applied directly to cells to assess receptor binding properties.
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Affiliation(s)
- Ilhan Tomris
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
| | - Roosmarijn van der Woude
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
| | - Rebeca de Paiva Froes Rocha
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Alba Torrents de la Peña
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Robert P de Vries
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
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5
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Aiyer S, Baldwin PR, Tan SM, Shan Z, Oh J, Mehrani A, Bowman ME, Louie G, Passos DO, Đorđević-Marquardt S, Mietzsch M, Hull JA, Hoshika S, Barad BA, Grotjahn DA, McKenna R, Agbandje-McKenna M, Benner SA, Noel JAP, Wang D, Tan YZ, Lyumkis D. Overcoming resolution attenuation during tilted cryo-EM data collection. Nat Commun 2024; 15:389. [PMID: 38195598 PMCID: PMC10776679 DOI: 10.1038/s41467-023-44555-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting "preferred orientations" on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60° are virtually indistinguishable. These strategies allowed the reconstruction to 3 Å resolution of a bacterial RNA polymerase with preferred orientation, containing an unnatural nucleotide for studying novel base pair recognition. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle during data acquisition. These results reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.
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Affiliation(s)
- Sriram Aiyer
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Philip R Baldwin
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shi Min Tan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Zelin Shan
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- College of Pharmacy, Kyung Hee University, Seoul, 02247, Republic of Korea
| | - Atousa Mehrani
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Marianne E Bowman
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Gordon Louie
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Dario Oliveira Passos
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | | | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Joshua A Hull
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd Box 7, Alachua, FL, 32615, USA
| | - Benjamin A Barad
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Danielle A Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd Box 7, Alachua, FL, 32615, USA
| | - Joseph A P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yong Zi Tan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.
- Disease Intervention Technology Laboratory (DITL), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore, 138648, Singapore.
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore.
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA, 92093, USA.
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6
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Cuervo A, Losana P, Carrascosa JL. Observation of Bacteriophage Ultrastructure by Cryo-Electron Microscopy. Methods Mol Biol 2024; 2734:13-25. [PMID: 38066360 DOI: 10.1007/978-1-0716-3523-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Transmission electron microscopy (TEM) is an ideal method to observe and determine the structure of bacteriophages. From early studies by negative staining to the present atomic structure models derived from cryo-TEM, bacteriophage detection, classification, and structure determination have been mostly done by electron microscopy. Although embedding in metal salts has been a routine method for virus observation for many years, the preservation of bacteriophages in a thin layer of fast frozen buffer has proven to be the most convenient preparation method for obtaining images using cryo-electron microscopy (cryo-EM). In this technique, frozen samples are observed at liquid nitrogen temperature, and the images are acquired using different recording media. The incorporation of direct electron detectors has been a fundamental step in achieving atomic resolution images of a number of viruses. These projection images can be numerically combined using different approaches to render a three-dimensional model of the virus. For those viral components exhibiting any symmetry, averaging can nowadays achieve atomic structures in most cases. Image processing methods have also evolved to improve the resolution in asymmetric viral components or regions showing different types of symmetries (symmetry mismatch).
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Affiliation(s)
- Ana Cuervo
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología, CSIC, Madrid, Spain.
| | - Patricia Losana
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - José L Carrascosa
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
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7
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de la Cruz MJ, Eng ET. Scaling up cryo-EM for biology and chemistry: The journey from niche technology to mainstream method. Structure 2023; 31:1487-1498. [PMID: 37820731 PMCID: PMC10841453 DOI: 10.1016/j.str.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/31/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023]
Abstract
Cryoelectron microscopy (cryo-EM) methods have made meaningful contributions in a wide variety of scientific research fields. In structural biology, cryo-EM routinely elucidates molecular structure from isolated biological macromolecular complexes or in a cellular context by harnessing the high-resolution power of the electron in order to image samples in a frozen, hydrated environment. For structural chemistry, the cryo-EM method popularly known as microcrystal electron diffraction (MicroED) has facilitated atomic structure generation of peptides and small molecules from their three-dimensional crystal forms. As cryo-EM has grown from an emerging technology, it has undergone modernization to enable multimodal transmission electron microscopy (TEM) techniques becoming more routine, reproducible, and accessible to accelerate research across multiple disciplines. We review recent advances in modern cryo-EM and assess how they are contributing to the future of the field with an eye to the past.
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Affiliation(s)
- M Jason de la Cruz
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Edward T Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA.
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8
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Turner HL, Jackson AM, Richey ST, Sewall LM, Antanasijevic A, Hangartner L, Ward AB. Protocol for analyzing antibody responses to glycoprotein antigens using electron-microscopy-based polyclonal epitope mapping. STAR Protoc 2023; 4:102476. [PMID: 37516970 PMCID: PMC10400963 DOI: 10.1016/j.xpro.2023.102476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/09/2023] [Accepted: 06/30/2023] [Indexed: 08/01/2023] Open
Abstract
Electron microscopy-based polyclonal epitope mapping (EMPEM) can delineate epitope specificities of serum antibodies to a given antigen following vaccination or infection. Here, we present a protocol for the EMPEM method for rapid high-throughput assessment of antibody responses to glycoprotein antigens in vaccination and infection studies. We describe steps for antibody isolation and digestion, antigen complex and purification, and electron microscope imaging. We then detail procedures for processing and analysis of EMPEM data. For complete details on the use and execution of this protocol, please refer to Bianchi et al. (2018).1.
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Affiliation(s)
- Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Abigail M Jackson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sara T Richey
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Leigh M Sewall
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lars Hangartner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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9
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Roy A, Shi L, Chang A, Dong X, Fernandez A, Kraft JC, Li J, Le VQ, Winegar RV, Cherf GM, Slocum D, Poulson PD, Casper GE, Vallecillo-Zúniga ML, Valdoz JC, Miranda MC, Bai H, Kipnis Y, Olshefsky A, Priya T, Carter L, Ravichandran R, Chow CM, Johnson MR, Cheng S, Smith M, Overed-Sayer C, Finch DK, Lowe D, Bera AK, Matute-Bello G, Birkland TP, DiMaio F, Raghu G, Cochran JR, Stewart LJ, Campbell MG, Van Ry PM, Springer T, Baker D. De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8. Nat Commun 2023; 14:5660. [PMID: 37704610 PMCID: PMC10500007 DOI: 10.1038/s41467-023-41272-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/18/2023] [Indexed: 09/15/2023] Open
Abstract
The RGD (Arg-Gly-Asp)-binding integrins αvβ6 and αvβ8 are clinically validated cancer and fibrosis targets of considerable therapeutic importance. Compounds that can discriminate between homologous αvβ6 and αvβ8 and other RGD integrins, stabilize specific conformational states, and have high thermal stability could have considerable therapeutic utility. Existing small molecule and antibody inhibitors do not have all these properties, and hence new approaches are needed. Here we describe a generalized method for computationally designing RGD-containing miniproteins selective for a single RGD integrin heterodimer and conformational state. We design hyperstable, selective αvβ6 and αvβ8 inhibitors that bind with picomolar affinity. CryoEM structures of the designed inhibitor-integrin complexes are very close to the computational design models, and show that the inhibitors stabilize specific conformational states of the αvβ6 and the αvβ8 integrins. In a lung fibrosis mouse model, the αvβ6 inhibitor potently reduced fibrotic burden and improved overall lung mechanics, demonstrating the therapeutic potential of de novo designed integrin binding proteins with high selectivity.
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Affiliation(s)
- Anindya Roy
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Lei Shi
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Encodia Inc, 5785 Oberlin Drive, San Diego, CA, 92121, USA
| | - Ashley Chang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Xianchi Dong
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA, USA
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, China
| | - Andres Fernandez
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - John C Kraft
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Jing Li
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA, USA
| | - Viet Q Le
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA, USA
| | - Rebecca Viazzo Winegar
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Gerald Maxwell Cherf
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Denali Therapeutics, South San Francisco, CA, USA
| | - Dean Slocum
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA, USA
| | - P Daniel Poulson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Garrett E Casper
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | | | - Jonard Corpuz Valdoz
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Marcos C Miranda
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Hua Bai
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Yakov Kipnis
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Audrey Olshefsky
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Tanu Priya
- Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98195, USA
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Lauren Carter
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Cameron M Chow
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Max R Johnson
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Suna Cheng
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - McKaela Smith
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Catherine Overed-Sayer
- Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Bioscience COPD/IPF, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Donna K Finch
- Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Alchemab Therapeutics Ltd, Cambridge, UK
| | - David Lowe
- Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Evox Therapeutics Limited, Oxford Science Park, Medawar Centre, East Building, Robert Robinson Avenue, Oxford, OX4 4HG, England
| | - Asim K Bera
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Gustavo Matute-Bello
- Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, USA
| | - Timothy P Birkland
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Frank DiMaio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Ganesh Raghu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
- Dept of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Lance J Stewart
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Melody G Campbell
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA.
| | - Pam M Van Ry
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA.
| | - Timothy Springer
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA, USA.
| | - David Baker
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
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10
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Cleeve P, Dierickx D, Naegele L, Kannachel R, Burne L, Buckley G, Gorelick S, Whisstock JC, de Marco A. OpenFIBSEM: A universal API for FIBSEM control. J Struct Biol 2023; 215:107967. [PMID: 37105276 DOI: 10.1016/j.jsb.2023.107967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023]
Abstract
This paper introduces OpenFIBSEM, a universal API to control Focused Ion Beam Scanning Electron Microscopes (FIBSEM). OpenFIBSEM aims to improve the programmability and automation of electron microscopy workflows in structural biology research. The API is designed to be cross-platform, composable, and extendable: allowing users to use any portion of OpenFIBSEM to develop or integrate with other software tools. The package provides core functionality such as imaging, movement, milling, and manipulator control, as well as system calibration, alignment, and image analysis modules. Further, a library of reusable user interface components integrated with napari is provided, ensuring easy and efficient application development. OpenFIBSEM currently supports ThermoFisher and TESCAN hardware, with support for other manufacturers planned. To demonstrate the improved automation capabilities enabled by OpenFIBSEM, several example applications that are compatible with multiple hardware manufacturers are discussed. We argue that OpenFIBSEM provides the foundation for a cross-platform operating system and development ecosystem for FIBSEM systems. The API and applications are open-source and available on GitHub (https://github.com/DeMarcoLab/fibsem).
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Affiliation(s)
- Patrick Cleeve
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia
| | - David Dierickx
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia
| | - Lucile Naegele
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia
| | - Rohit Kannachel
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia
| | - Lachlan Burne
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia
| | - Genevieve Buckley
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, 3800 Clayton, Victoria, Australia
| | - Sergey Gorelick
- Monash Centre for Electron Microscopy, Monash University, 3800 Clayton, Victoria, Australia
| | - James C Whisstock
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia; EMBL Australia, Monash University, 3800 Clayton, Victoria, Australia.
| | - Alex de Marco
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia.
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11
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Aiyer S, Baldwin PR, Tan SM, Shan Z, Oh J, Mehrani A, Bowman ME, Louie G, Passos DO, Đorđević-Marquardt S, Mietzsch M, Hull JA, Hoshika S, Barad BA, Grotjahn DA, McKenna R, Agbandje-McKenna M, Benner SA, Noel JAP, Wang D, Tan YZ, Lyumkis D. Overcoming Resolution Attenuation During Tilted Cryo-EM Data Collection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.548955. [PMID: 37503021 PMCID: PMC10369999 DOI: 10.1101/2023.07.14.548955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting "preferred orientations" on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60° are virtually indistinguishable. These strategies allowed the reconstruction to 3 Å resolution of a bacterial RNA polymerase with preferred orientation. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle for dataset acquisition. These data reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.
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12
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Torrez RM, Nagaraja S, Menon A, Chang L, Ohi MD, Garner AL. Comparative Biochemical Studies of Disease-Associated Human Dicer Mutations on Processing of a Pre-microRNA and snoRNA. Biochemistry 2023. [PMID: 37130292 DOI: 10.1021/acs.biochem.2c00687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Dicer is an RNase III enzyme that is responsible for the maturation of small RNAs such as microRNAs. As Dicer's cleavage products play key roles in promoting cellular homeostasis through the fine-tuning of gene expression, dysregulation of Dicer activity can lead to several human diseases, including cancers. Mutations in Dicer have been found to induce tumorigenesis and lead to the development of a rare pleiotropic tumor predisposition syndrome found in children and young adults called DICER1 syndrome. These patients harbor germline and somatic mutations in Dicer that lead to defective microRNA processing and activity. While most mutations occur within Dicer's catalytic RNase III domains, alterations within the Platform-PAZ (Piwi-Argonaute-Zwille) domain also cause loss of microRNA production. Using a combination of in vitro biochemical and cellular studies, we characterized the effect of disease-relevant Platform-PAZ-associated mutations on the processing of a well-studied oncogenic microRNA, pre-microRNA-21. We then compared these results to those of a representative from another Dicer substrate class, the small nucleolar RNA, snord37. From this analysis, we provide evidence that mutations within the Platform-PAZ domain result in differential impacts on RNA binding and processing, adding new insights into the complexities of Dicer processing of small RNA substrates.
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Affiliation(s)
- Rachel M Torrez
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Shruti Nagaraja
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
| | - Arya Menon
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
| | - Louise Chang
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Melanie D Ohi
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109, United States
| | - Amanda L Garner
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
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13
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Radić L, Sliepen K, Yin V, Brinkkemper M, Capella-Pujol J, Schriek AI, Torres JL, Bangaru S, Burger JA, Poniman M, Bontjer I, Bouhuijs JH, Gideonse D, Eggink D, Ward AB, Heck AJ, Van Gils MJ, Sanders RW, Schinkel J. Bispecific antibodies combine breadth, potency, and avidity of parental antibodies to neutralize sarbecoviruses. iScience 2023; 26:106540. [PMID: 37063468 PMCID: PMC10065043 DOI: 10.1016/j.isci.2023.106540] [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: 11/17/2022] [Revised: 02/07/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
SARS-CoV-2 variants evade current monoclonal antibody therapies. Bispecific antibodies (bsAbs) combine the specificities of two distinct antibodies taking advantage of the avidity and synergy provided by targeting different epitopes. Here we used controlled Fab-arm exchange to produce bsAbs that neutralize SARS-CoV and SARS-CoV-2 variants, including Omicron and its subvariants, by combining potent SARS-CoV-2-specific neutralizing antibodies with broader antibodies that also neutralize SARS-CoV. We demonstrated that the parental antibodies rely on avidity for neutralization using bsAbs containing one irrelevant Fab arm. Using mass photometry to measure the formation of antibody:spike complexes, we determined that bsAbs increase binding stoichiometry compared to corresponding cocktails, without a loss of binding affinity. The heterogeneous binding pattern of bsAbs to spike, observed by negative-stain electron microscopy and mass photometry provided evidence for both intra- and inter-spike crosslinking. This study highlights the utility of cross-neutralizing antibodies for designing bivalent agents to combat circulating and future SARS-like coronaviruses.
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Affiliation(s)
- Laura Radić
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Kwinten Sliepen
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Victor Yin
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands
- Netherlands Proteomics Center, 3584 CH Utrecht, the Netherlands
| | - Mitch Brinkkemper
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Joan Capella-Pujol
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Angela I. Schriek
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Jonathan L. Torres
- Department of Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sandhya Bangaru
- Department of Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Judith A. Burger
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Meliawati Poniman
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Ilja Bontjer
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Joey H. Bouhuijs
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - David Gideonse
- Center for Infectious Disease Control, WHO COVID-19 reference laboratory, National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, the Netherlands
| | - Dirk Eggink
- Center for Infectious Disease Control, WHO COVID-19 reference laboratory, National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, the Netherlands
| | - Andrew B. Ward
- Department of Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands
- Netherlands Proteomics Center, 3584 CH Utrecht, the Netherlands
| | - Marit J. Van Gils
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Rogier W. Sanders
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Janke Schinkel
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
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14
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O'Brien RE, Bravo JPK, Ramos D, Hibshman GN, Wright JT, Taylor DW. Structural snapshots of R-loop formation by a type I-C CRISPR Cascade. Mol Cell 2023; 83:746-758.e5. [PMID: 36805026 PMCID: PMC10026943 DOI: 10.1016/j.molcel.2023.01.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/12/2022] [Accepted: 01/26/2023] [Indexed: 02/18/2023]
Abstract
Type I CRISPR-Cas systems employ multi-subunit Cascade effector complexes to target foreign nucleic acids for destruction. Here, we present structures of D. vulgaris type I-C Cascade at various stages of double-stranded (ds)DNA target capture, revealing mechanisms that underpin PAM recognition and Cascade allosteric activation. We uncover an interesting mechanism of non-target strand (NTS) DNA stabilization via stacking interactions with the "belly" subunits, securing the NTS in place. This "molecular seatbelt" mechanism facilitates efficient R-loop formation and prevents dsDNA reannealing. Additionally, we provide structural insights into how two anti-CRISPR (Acr) proteins utilize distinct strategies to achieve a shared mechanism of type I-C Cascade inhibition by blocking PAM scanning. These observations form a structural basis for directional R-loop formation and reveal how different Acr proteins have converged upon common molecular mechanisms to efficiently shut down CRISPR immunity.
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Affiliation(s)
- Roisin E O'Brien
- Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX 78712, USA
| | - Jack P K Bravo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Delisa Ramos
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Grace N Hibshman
- Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX 78712, USA
| | - Jacquelyn T Wright
- Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX 78712, USA
| | - David W Taylor
- Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; LIVESTRONG Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA.
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15
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Brinkkemper M, Veth TS, Brouwer PJ, Turner H, Poniman M, Burger JA, Bouhuijs JH, Olijhoek W, Bontjer I, Snitselaar JL, Caniels TG, van der Linden CA, Ravichandran R, Villaudy J, van der Velden YU, Sliepen K, van Gils MJ, Ward AB, King NP, Heck AJ, Sanders RW. Co-display of diverse spike proteins on nanoparticles broadens sarbecovirus neutralizing antibody responses. iScience 2022; 25:105649. [PMID: 36439375 PMCID: PMC9678814 DOI: 10.1016/j.isci.2022.105649] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/07/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants poses continuous challenges in combating the virus. Here, we describe vaccination strategies to broaden SARS-CoV-2 and sarbecovirus immunity by combining spike proteins based on different viruses or viral strains displayed on two-component protein nanoparticles. First, we combined spike proteins based on ancestral and Beta SARS-CoV-2 strains to broaden SARS-CoV-2 immune responses. Inclusion of Beta spike improved neutralizing antibody responses against SARS-CoV-2 Beta, Gamma, and Omicron BA.1 and BA.4/5. A third vaccination with ancestral SARS-CoV-2 spike also improved cross-neutralizing antibody responses against SARS-CoV-2 variants, in particular against the Omicron sublineages. Second, we combined SARS-CoV and SARS-CoV-2 spike proteins to broaden sarbecovirus immune responses. Adding SARS-CoV spike to a SARS-CoV-2 spike vaccine improved neutralizing responses against SARS-CoV and SARS-like bat sarbecoviruses SHC014 and WIV1. These results should inform the development of broadly active SARS-CoV-2 and pan-sarbecovirus vaccines and highlight the versatility of two-component nanoparticles for displaying diverse antigens.
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Affiliation(s)
- Mitch Brinkkemper
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Tim S. Veth
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, the Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Philip J.M. Brouwer
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hannah Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meliawati Poniman
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Judith A. Burger
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Joey H. Bouhuijs
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Wouter Olijhoek
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Ilja Bontjer
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Jonne L. Snitselaar
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Tom G. Caniels
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Cynthia A. van der Linden
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Julien Villaudy
- J&S Preclinical Solutions, 5345 RR, OSS, the Netherlands
- AIMM Therapeutics BV, 1105 BA Amsterdam, the Netherlands
| | - Yme U. van der Velden
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Kwinten Sliepen
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Marit J. van Gils
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, the Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Rogier W. Sanders
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA
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16
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Antibodies targeting the neuraminidase active site inhibit influenza H3N2 viruses with an S245N glycosylation site. Nat Commun 2022; 13:7864. [PMID: 36543789 PMCID: PMC9772378 DOI: 10.1038/s41467-022-35586-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Contemporary influenza A H3N2 viruses circulating since 2016 have acquired a glycosylation site in the neuraminidase in close proximity to the enzymatic active site. Here, we investigate if this S245N glycosylation site, as a result of antigenic evolution, can impact binding and function of human monoclonal antibodies that target the conserved active site. While we find that a reduction in the inhibitory ability of neuraminidase active site binders is measurable, this class of broadly reactive monoclonal antibodies maintains protective efficacy in vivo.
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17
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Peng R, Fu X, Mendez JH, Randolph PS, Bammes BE, Stagg SM. Characterizing the resolution and throughput of the Apollo direct electron detector. J Struct Biol X 2022; 7:100080. [PMID: 36578473 PMCID: PMC9791170 DOI: 10.1016/j.yjsbx.2022.100080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Advances in electron detection have been essential to the success of high-resolution cryo-EM structure determination. A new generation of direct electron detector called the Apollo, has been developed by Direct Electron. The Apollo uses a novel event-based MAPS detector custom designed for ultra-fast electron counting. We have evaluated this new camera, finding that it delivers high detective quantum efficiency (DQE) and low coincidence loss, enabling high-quality electron counting data acquisition at up to nearly 80 input electrons per pixel per second. We further characterized the performance of Apollo for single particle cryo-EM on real biological samples. Using mouse apoferritin, Apollo yielded better than 1.9 Å resolution reconstructions at all three tested dose rates from a half-day data collection session each. With longer collection time and improved specimen preparation, mouse apoferritin was reconstructed to 1.66 Å resolution. Applied to a more challenging small protein aldolase, we obtained a 2.24 Å resolution reconstruction. The high quality of the map indicates that the Apollo has sufficiently high DQE to reconstruct smaller proteins and complexes with high-fidelity. Our results demonstrate that the Apollo camera performs well across a broad range of dose rates and is capable of capturing high quality data that produce high-resolution reconstructions for large and small single particle samples.
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Affiliation(s)
- Ruizhi Peng
- Institute of Molecular Biophysics, 91 Chieftain Way, Florida State University, Tallahassee, FL 32306, United States
| | - Xiaofeng Fu
- Department of Biological Sciences, 319 Stadium Drive, Tallahassee, FL 32306, United States
| | - Joshua H. Mendez
- Simons Electron Microscopy Center, 89 Convent Avenue, New York, NY 10027, United States
| | - Peter S. Randolph
- Institute of Molecular Biophysics, 91 Chieftain Way, Florida State University, Tallahassee, FL 32306, United States
| | - Benjamin E. Bammes
- Direct Electron LP, 13240 Evening Creek Drive South, Suite 311, San Diego, CA 92128, United States
| | - Scott M. Stagg
- Institute of Molecular Biophysics, 91 Chieftain Way, Florida State University, Tallahassee, FL 32306, United States,Department of Biological Sciences, 319 Stadium Drive, Tallahassee, FL 32306, United States,Corresponding author at: Institute of Molecular Biophysics, 91 Chieftain Way, Florida State University, Tallahassee, FL 32306, United States
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18
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Burley SK, Berman HM, Chiu W, Dai W, Flatt JW, Hudson BP, Kaelber JT, Khare SD, Kulczyk AW, Lawson CL, Pintilie GD, Sali A, Vallat B, Westbrook JD, Young JY, Zardecki C. Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future. Biophys Rev 2022; 14:1281-1301. [PMID: 36474933 PMCID: PMC9715422 DOI: 10.1007/s12551-022-01013-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/06/2022] [Indexed: 12/04/2022] Open
Abstract
As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) "Resolution Revolution" made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.
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Affiliation(s)
- Stephen K. Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093 USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Helen M. Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA USA
| | - Wei Dai
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Justin W. Flatt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Brian P. Hudson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Jason T. Kaelber
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Sagar D. Khare
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Arkadiusz W. Kulczyk
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08901 USA
| | - Catherine L. Lawson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | | | - Andrej Sali
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158 USA
| | - Brinda Vallat
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
| | - John D. Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
| | - Jasmine Y. Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
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19
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Brown ZP, Abaeva IS, De S, Hellen CUT, Pestova TV, Frank J. Molecular architecture of 40S translation initiation complexes on the hepatitis C virus IRES. EMBO J 2022; 41:e110581. [PMID: 35822879 DOI: 10.15252/embj.2022110581] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/01/2022] [Accepted: 06/14/2022] [Indexed: 02/05/2023] Open
Abstract
Hepatitis C virus mRNA contains an internal ribosome entry site (IRES) that mediates end-independent translation initiation, requiring a subset of eukaryotic initiation factors (eIFs). Biochemical studies revealed that direct binding of the IRES to the 40S ribosomal subunit places the initiation codon into the P site, where it base pairs with eIF2-bound Met-tRNAiMet forming a 48S initiation complex. Subsequently, eIF5 and eIF5B mediate subunit joining, yielding an elongation-competent 80S ribosome. Initiation can also proceed without eIF2, in which case Met-tRNAiMet is recruited directly by eIF5B. However, the structures of initiation complexes assembled on the HCV IRES, the transitions between different states, and the accompanying conformational changes have remained unknown. To fill these gaps, we now obtained cryo-EM structures of IRES initiation complexes, at resolutions up to 3.5 Å, that cover all major stages from the initial ribosomal association, through eIF2-containing 48S initiation complexes, to eIF5B-containing complexes immediately prior to subunit joining. These structures provide insights into the dynamic network of 40S/IRES contacts, highlight the role of IRES domain II, and reveal conformational changes that occur during the transition from eIF2- to eIF5B-containing 48S complexes and prepare them for subunit joining.
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Affiliation(s)
- Zuben P Brown
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Irina S Abaeva
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Swastik De
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Christopher U T Hellen
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Tatyana V Pestova
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.,Department of Biological Sciences, Columbia University, New York, NY, USA
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20
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Zhou Y, Moscovich A, Bartesaghi A. Data-driven determination of number of discrete conformations in single-particle cryo-EM. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2022; 221:106892. [PMID: 35597206 PMCID: PMC10131080 DOI: 10.1016/j.cmpb.2022.106892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND OBJECTIVE One of the strengths of single-particle cryo-EM compared to other structural determination techniques is its ability to image heterogeneous samples containing multiple molecular species, different oligomeric states or distinct conformations. This is achieved using routines for in-silico 3D classification that are now well established in the field and have successfully been used to characterize the structural heterogeneity of important biomolecules. These techniques, however, rely on expert-user knowledge and trial-and-error experimentation to determine the correct number of conformations, making it a labor intensive, subjective, and difficult to reproduce procedure. METHODS We propose an approach to address the problem of automatically determining the number of discrete conformations present in heterogeneous single-particle cryo-EM datasets. We do this by systematically evaluating all possible partitions of the data and selecting the result that maximizes the average variance of similarities measured between particle images and the corresponding 3D reconstructions. RESULTS Using this strategy, we successfully analyzed datasets of heterogeneous protein complexes, including: 1) in-silico mixtures obtained by combining closely related antibody-bound HIV-1 Env trimers and other important membrane channels, and 2) naturally occurring mixtures from diverse and dynamic protein complexes representing varying degrees of structural heterogeneity and conformational plasticity. CONCLUSIONS The availability of unsupervised strategies for 3D classification combined with existing approaches for fully automatic pre-processing and 3D refinement, represents an important step towards converting single-particle cryo-EM into a high-throughput technique.
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Affiliation(s)
- Ye Zhou
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Amit Moscovich
- Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv, Israel
| | - Alberto Bartesaghi
- Department of Computer Science, Duke University, Durham, NC 27708, USA; Department of Biochemistry, Duke University School of Medicine, Durham, NC 27708, USA; Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA.
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21
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Zhang S, Wang K, Wang WL, Nguyen HT, Chen S, Lu M, Go EP, Ding H, Steinbock RT, Desaire H, Kappes JC, Sodroski J, Mao Y. Asymmetric Structures and Conformational Plasticity of the Uncleaved Full-Length Human Immunodeficiency Virus Envelope Glycoprotein Trimer. J Virol 2021; 95:e0052921. [PMID: 34549974 PMCID: PMC8610584 DOI: 10.1128/jvi.00529-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/06/2021] [Indexed: 11/20/2022] Open
Abstract
The functional human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer [(gp120/gp41)3] is produced by cleavage of a conformationally flexible gp160 precursor. gp160 cleavage or the binding of BMS-806, an entry inhibitor, stabilizes the pretriggered, "closed" (state 1) conformation recognized by rarely elicited broadly neutralizing antibodies. Poorly neutralizing antibodies (pNAbs) elicited at high titers during natural infection recognize more "open" Env conformations (states 2 and 3) induced by binding the receptor, CD4. We found that BMS-806 treatment and cross-linking decreased the exposure of pNAb epitopes on cell surface gp160; however, after detergent solubilization, cross-linked and BMS-806-treated gp160 sampled non-state-1 conformations that could be recognized by pNAbs. Cryo-electron microscopy of the purified BMS-806-bound gp160 revealed two hitherto unknown asymmetric trimer conformations, providing insights into the allosteric coupling between trimer opening and structural variation in the gp41 HR1N region. The individual protomer structures in the asymmetric gp160 trimers resemble those of other genetically modified or antibody-bound cleaved HIV-1 Env trimers, which have been suggested to assume state-2-like conformations. Asymmetry of the uncleaved Env potentially exposes surfaces of the trimer to pNAbs. To evaluate the effect of stabilizing a state-1-like conformation of the membrane Env precursor, we treated cells expressing wild-type HIV-1 Env with BMS-806. BMS-806 treatment decreased both gp160 cleavage and the addition of complex glycans, implying that gp160 conformational flexibility contributes to the efficiency of these processes. Selective pressure to maintain flexibility in the precursor of functional Env allows the uncleaved Env to sample asymmetric conformations that potentially skew host antibody responses toward pNAbs. IMPORTANCE The envelope glycoprotein (Env) trimers on the surface of human immunodeficiency virus (HIV-1) mediate the entry of the virus into host cells and serve as targets for neutralizing antibodies. The functional Env trimer is produced by cleavage of the gp160 precursor in the infected cell. We found that the HIV-1 Env precursor is highly plastic, allowing it to assume different asymmetric shapes. This conformational plasticity is potentially important for Env cleavage and proper modification by sugars. Having a flexible, asymmetric Env precursor that can misdirect host antibody responses without compromising virus infectivity would be an advantage for a persistent virus like HIV-1.
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Affiliation(s)
- Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Kunyu Wang
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
| | - Wei Li Wang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
- Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Hanh T. Nguyen
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Shuobing Chen
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
| | - Maolin Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Eden P. Go
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Haitao Ding
- Department of Medicine, University of Alabama at Birmingham, Alabama, USA
| | - Robert T. Steinbock
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - John C. Kappes
- Department of Medicine, University of Alabama at Birmingham, Alabama, USA
- Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, Alabama, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
- Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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22
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Brouwer PJM, Brinkkemper M, Maisonnasse P, Dereuddre-Bosquet N, Grobben M, Claireaux M, de Gast M, Marlin R, Chesnais V, Diry S, Allen JD, Watanabe Y, Giezen JM, Kerster G, Turner HL, van der Straten K, van der Linden CA, Aldon Y, Naninck T, Bontjer I, Burger JA, Poniman M, Mykytyn AZ, Okba NMA, Schermer EE, van Breemen MJ, Ravichandran R, Caniels TG, van Schooten J, Kahlaoui N, Contreras V, Lemaître J, Chapon C, Fang RHT, Villaudy J, Sliepen K, van der Velden YU, Haagmans BL, de Bree GJ, Ginoux E, Ward AB, Crispin M, King NP, van der Werf S, van Gils MJ, Le Grand R, Sanders RW. Two-component spike nanoparticle vaccine protects macaques from SARS-CoV-2 infection. Cell 2021; 184:1188-1200.e19. [PMID: 33577765 PMCID: PMC7834972 DOI: 10.1016/j.cell.2021.01.035] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/23/2020] [Accepted: 01/21/2021] [Indexed: 02/08/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is continuing to disrupt personal lives, global healthcare systems, and economies. Hence, there is an urgent need for a vaccine that prevents viral infection, transmission, and disease. Here, we present a two-component protein-based nanoparticle vaccine that displays multiple copies of the SARS-CoV-2 spike protein. Immunization studies show that this vaccine induces potent neutralizing antibody responses in mice, rabbits, and cynomolgus macaques. The vaccine-induced immunity protects macaques against a high-dose challenge, resulting in strongly reduced viral infection and replication in the upper and lower airways. These nanoparticles are a promising vaccine candidate to curtail the SARS-CoV-2 pandemic.
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Affiliation(s)
- Philip J M Brouwer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Mitch Brinkkemper
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Pauline Maisonnasse
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Nathalie Dereuddre-Bosquet
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Marloes Grobben
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Mathieu Claireaux
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Marlon de Gast
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Romain Marlin
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | | | | | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Julia M Giezen
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Gius Kerster
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Karlijn van der Straten
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Cynthia A van der Linden
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Yoann Aldon
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Thibaut Naninck
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Ilja Bontjer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Judith A Burger
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Meliawati Poniman
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Anna Z Mykytyn
- Department of Viroscience, Erasmus Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Nisreen M A Okba
- Department of Viroscience, Erasmus Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Edith E Schermer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Marielle J van Breemen
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Tom G Caniels
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Jelle van Schooten
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Nidhal Kahlaoui
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Vanessa Contreras
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Julien Lemaître
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Catherine Chapon
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Raphaël Ho Tsong Fang
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | | | - Kwinten Sliepen
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Yme U van der Velden
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Godelieve J de Bree
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105 AZ Amsterdam, the Netherlands
| | - Eric Ginoux
- Life and Soft, 92350 Le Plessis-Robinson, France
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Sylvie van der Werf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, CNRS UMR 3569, Université de Paris, Paris, France; National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Roger Le Grand
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France.
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands.
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23
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Bouwman KM, Tomris I, Turner HL, van der Woude R, Shamorkina TM, Bosman GP, Rockx B, Herfst S, Snijder J, Haagmans BL, Ward AB, Boons GJ, de Vries RP. Multimerization- and glycosylation-dependent receptor binding of SARS-CoV-2 spike proteins. PLoS Pathog 2021; 17:e1009282. [PMID: 33556147 PMCID: PMC7895411 DOI: 10.1371/journal.ppat.1009282] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/19/2021] [Accepted: 01/06/2021] [Indexed: 01/16/2023] Open
Abstract
Receptor binding studies on sarbecoviruses would benefit from an available toolkit of recombinant spike proteins, or domains thereof, that recapitulate receptor binding properties of native viruses. We hypothesized that trimeric Receptor Binding Domain (RBD) proteins would be suitable candidates to study receptor binding properties of SARS-CoV-1 and -2. Here we created monomeric and trimeric fluorescent RBD proteins, derived from adherent HEK293T, as well as in GnTI-/- mutant cells, to analyze the effect of complex vs high mannose glycosylation on receptor binding. The results demonstrate that trimeric, complex glycosylated proteins are superior in receptor binding compared to monomeric and immaturely glycosylated variants. Although differences in binding to commonly used cell lines were minimal between the different RBD preparations, substantial differences were observed when respiratory tissues of experimental animals were stained. The RBD trimers demonstrated distinct ACE2 expression profiles in bronchiolar ducts and confirmed the higher binding affinity of SARS-CoV-2 over SARS-CoV-1. Our results show that complex glycosylated trimeric RBD proteins are attractive to analyze sarbecovirus receptor binding and explore ACE2 expression profiles in tissues.
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Affiliation(s)
- Kim M Bouwman
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Ilhan Tomris
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Roosmarijn van der Woude
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Tatiana M Shamorkina
- Biomolecular Mass Spectrometry and Proteomics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Gerlof P Bosman
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Barry Rockx
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sander Herfst
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Geert-Jan Boons
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
- Department of Chemistry, University of Georgia, Athens, Georgia, United States of America
| | - Robert P de Vries
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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24
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Cheng A, Negro C, Bruhn JF, Rice WJ, Dallakyan S, Eng ET, Waterman DG, Potter CS, Carragher B. Leginon: New features and applications. Protein Sci 2021; 30:136-150. [PMID: 33030237 PMCID: PMC7737759 DOI: 10.1002/pro.3967] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 01/21/2023]
Abstract
Leginon is a system for automated data acquisition from a transmission electron microscope. Here we provide an updated summary of the overall Leginon architecture and an update of the current state of the package. We also highlight a few recent developments to provide some concrete examples and use cases.
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Affiliation(s)
- Anchi Cheng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy CenterNew York Structural Biology CenterNew YorkNew YorkUSA
| | - Carl Negro
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy CenterNew York Structural Biology CenterNew YorkNew YorkUSA
| | | | - William J. Rice
- Cryo‐Electron Microscopy CoreNew York University School of MedicineNew YorkNew YorkUSA
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
| | - Sargis Dallakyan
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy CenterNew York Structural Biology CenterNew YorkNew YorkUSA
| | - Edward T. Eng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy CenterNew York Structural Biology CenterNew YorkNew YorkUSA
| | - David G. Waterman
- STFCRutherford Appleton LaboratoryDidcotUK
- CCP4, Research Complex at HarwellRutherford Appleton LaboratoryDidcotUK
| | - Clinton S. Potter
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy CenterNew York Structural Biology CenterNew YorkNew YorkUSA
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy CenterNew York Structural Biology CenterNew YorkNew YorkUSA
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
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25
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Bangaru S, Ozorowski G, Turner HL, Antanasijevic A, Huang D, Wang X, Torres JL, Diedrich JK, Tian JH, Portnoff AD, Patel N, Massare MJ, Yates JR, Nemazee D, Paulson JC, Glenn G, Smith G, Ward AB. Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate. Science 2020; 370:1089-1094. [PMID: 33082295 PMCID: PMC7857404 DOI: 10.1126/science.abe1502] [Citation(s) in RCA: 235] [Impact Index Per Article: 58.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/13/2020] [Indexed: 12/25/2022]
Abstract
Vaccine efforts to combat the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is responsible for the current coronavirus disease 2019 (COVID-19) pandemic, are focused on SARS-CoV-2 spike glycoprotein, the primary target for neutralizing antibodies. We performed cryo-election microscopy and site-specific glycan analysis of one of the leading subunit vaccine candidates from Novavax, which is based on a full-length spike protein formulated in polysorbate 80 detergent. Our studies reveal a stable prefusion conformation of the spike immunogen with slight differences in the S1 subunit compared with published spike ectodomain structures. We also observed interactions between the spike trimers, allowing formation of higher-order spike complexes. This study confirms the structural integrity of the full-length spike protein immunogen and provides a basis for interpreting immune responses to this multivalent nanoparticle immunogen.
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Affiliation(s)
- Sandhya Bangaru
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaoning Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jing-Hui Tian
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | | | - Nita Patel
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | | | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James C Paulson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Greg Glenn
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | - Gale Smith
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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26
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O'Brien RE, Santos IC, Wrapp D, Bravo JPK, Schwartz EA, Brodbelt JS, Taylor DW. Structural basis for assembly of non-canonical small subunits into type I-C Cascade. Nat Commun 2020; 11:5931. [PMID: 33230133 PMCID: PMC7684278 DOI: 10.1038/s41467-020-19785-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/30/2020] [Indexed: 01/07/2023] Open
Abstract
Bacteria and archaea employ CRISPR (clustered, regularly, interspaced, short palindromic repeats)-Cas (CRISPR-associated) systems as a type of adaptive immunity to target and degrade foreign nucleic acids. While a myriad of CRISPR-Cas systems have been identified to date, type I-C is one of the most commonly found subtypes in nature. Interestingly, the type I-C system employs a minimal Cascade effector complex, which encodes only three unique subunits in its operon. Here, we present a 3.1 Å resolution cryo-EM structure of the Desulfovibrio vulgaris type I-C Cascade, revealing the molecular mechanisms that underlie RNA-directed complex assembly. We demonstrate how this minimal Cascade utilizes previously overlooked, non-canonical small subunits to stabilize R-loop formation. Furthermore, we describe putative PAM and Cas3 binding sites. These findings provide the structural basis for harnessing the type I-C Cascade as a genome-engineering tool.
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Affiliation(s)
- Roisin E O'Brien
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Inês C Santos
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Daniel Wrapp
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jack P K Bravo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Evan A Schwartz
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - David W Taylor
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA.
- Livestrong Cancer Institutes, Dell Medical School, Austin, TX, 78712, USA.
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27
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Wang N, Rosen O, Wang L, Turner HL, Stevens LJ, Corbett KS, Bowman CA, Pallesen J, Shi W, Zhang Y, Leung K, Kirchdoerfer RN, Becker MM, Denison MR, Chappell JD, Ward AB, Graham BS, McLellan JS. Structural Definition of a Neutralization-Sensitive Epitope on the MERS-CoV S1-NTD. Cell Rep 2020; 28:3395-3405.e6. [PMID: 31553909 PMCID: PMC6935267 DOI: 10.1016/j.celrep.2019.08.052] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/06/2019] [Accepted: 08/16/2019] [Indexed: 12/13/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) emerged into the human population in 2012 and has caused substantial morbidity and mortality. Potently neutralizing antibodies targeting the receptor-binding domain (RBD) on MERS-CoV spike (S) protein have been characterized, but much less is known about antibodies targeting non-RBD epitopes. Here, we report the structural and functional characterization of G2, a neutralizing antibody targeting the MERS-CoV S1 N-terminal domain (S1-NTD). Structures of G2 alone and in complex with the MERS-CoV S1-NTD define a site of vulnerability comprising two loops, each of which contain a residue mutated in G2-escape variants. Cell-surface binding studies and in vitro competition experiments demonstrate that G2 strongly disrupts the attachment of MERS-CoV S to its receptor, dipeptidyl peptidase-4 (DPP4), with the inhibition requiring the native trimeric S conformation. These results advance our understanding of antibody-mediated neutralization of coronaviruses and should facilitate the development of immunotherapeutics and vaccines against MERS-CoV. The epitope for the neutralizing antibody G2 is confined to the apex of the MERS-CoV S1-NTD G2 epitope is relatively well conserved G2 IgG and Fab both neutralize pseudotyped and authentic MERS-CoV G2 neutralizes by preventing the binding of DPP4 to trimeric S protein
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Affiliation(s)
- Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Osnat Rosen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Laura J Stevens
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Charles A Bowman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jesper Pallesen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Robert N Kirchdoerfer
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michelle M Becker
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Mark R Denison
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - James D Chappell
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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28
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van der Woude R, Turner HL, Tomris I, Bouwman KM, Ward AB, de Vries RP. Drivers of recombinant soluble influenza A virus hemagglutinin and neuraminidase expression in mammalian cells. Protein Sci 2020; 29:1975-1982. [PMID: 32710576 PMCID: PMC7454420 DOI: 10.1002/pro.3918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/13/2020] [Accepted: 07/20/2020] [Indexed: 11/11/2022]
Abstract
Recombinant soluble trimeric influenza A virus hemagglutinins (HA) and tetrameric neuraminidases (NAs) have proven to be excellent tools to decipher biological properties. Receptor binding and sialic acid cleavage by recombinant proteins correlate satisfactorily compared to whole viruses. Expression of HA and NA can be achieved in a plethora of different laboratory hosts. For immunological and receptor interaction studies however, insect and mammalian cell expressed proteins are preferred due to the presence of N-linked glycosylation and disulfide bond formation. Because mammalian-cell expression is widely applied, an increased expression yield is an important goal. Here we report that using codon-optimized genes and sfGFP fusions, the expression yield of HA can be significantly improved. sfGFP also significantly increased expression yields when fused to the N-terminus of NA. In this study, a suite of different hemagglutinin and neuraminidase constructs are described, which can be valuable tools to study a wide array of different HAs, NAs and their mutants.
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Affiliation(s)
- Roosmarijn van der Woude
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Ilhan Tomris
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Kim M Bouwman
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Robert P de Vries
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
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29
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Brouwer PJM, Caniels TG, van der Straten K, Snitselaar JL, Aldon Y, Bangaru S, Torres JL, Okba NMA, Claireaux M, Kerster G, Bentlage AEH, van Haaren MM, Guerra D, Burger JA, Schermer EE, Verheul KD, van der Velde N, van der Kooi A, van Schooten J, van Breemen MJ, Bijl TPL, Sliepen K, Aartse A, Derking R, Bontjer I, Kootstra NA, Wiersinga WJ, Vidarsson G, Haagmans BL, Ward AB, de Bree GJ, Sanders RW, van Gils MJ. Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability. Science 2020; 369:643-650. [PMID: 32540902 PMCID: PMC7299281 DOI: 10.1126/science.abc5902] [Citation(s) in RCA: 880] [Impact Index Per Article: 220.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/10/2020] [Indexed: 12/14/2022]
Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a large impact on global health, travel, and economy. Therefore, preventative and therapeutic measures are urgently needed. Here, we isolated monoclonal antibodies from three convalescent coronavirus disease 2019 (COVID-19) patients using a SARS-CoV-2 stabilized prefusion spike protein. These antibodies had low levels of somatic hypermutation and showed a strong enrichment in VH1-69, VH3-30-3, and VH1-24 gene usage. A subset of the antibodies was able to potently inhibit authentic SARS-CoV-2 infection at a concentration as low as 0.007 micrograms per milliliter. Competition and electron microscopy studies illustrate that the SARS-CoV-2 spike protein contains multiple distinct antigenic sites, including several receptor-binding domain (RBD) epitopes as well as non-RBD epitopes. In addition to providing guidance for vaccine design, the antibodies described here are promising candidates for COVID-19 treatment and prevention.
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MESH Headings
- Adult
- Aged
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Antibody Affinity
- Antigens, Viral/immunology
- B-Lymphocyte Subsets/immunology
- Betacoronavirus/immunology
- Broadly Neutralizing Antibodies/immunology
- COVID-19
- Cell Line, Tumor
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/therapy
- Epitopes/immunology
- Female
- Humans
- Immunologic Memory
- Immunophenotyping
- Male
- Middle Aged
- Pandemics/prevention & control
- Pneumonia, Viral/immunology
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/therapy
- Protein Domains
- Protein Interaction Domains and Motifs/immunology
- Receptors, Coronavirus
- Receptors, Virus/metabolism
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- Philip J M Brouwer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Tom G Caniels
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Karlijn van der Straten
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Jonne L Snitselaar
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Yoann Aldon
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Sandhya Bangaru
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nisreen M A Okba
- Department of Viroscience, Erasmus Medical Center, Rotterdam, 3015GD, Netherlands
| | - Mathieu Claireaux
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Gius Kerster
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Arthur E H Bentlage
- Sanquin Research, Department of Experimental Immunohematology, Amsterdam, Netherlands and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, 1006AD Amsterdam, Netherlands
| | - Marlies M van Haaren
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Denise Guerra
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Judith A Burger
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Edith E Schermer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Kirsten D Verheul
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | | | | | - Jelle van Schooten
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Mariëlle J van Breemen
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Tom P L Bijl
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Kwinten Sliepen
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Aafke Aartse
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
- Department of Virology, Biomedical Primate Research Centre, 2288GJ Rijswijk, Netherlands
| | - Ronald Derking
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Ilja Bontjer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Neeltje A Kootstra
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - W Joost Wiersinga
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Gestur Vidarsson
- Sanquin Research, Department of Experimental Immunohematology, Amsterdam, Netherlands and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, 1006AD Amsterdam, Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, 3015GD, Netherlands
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Godelieve J de Bree
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands.
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands.
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands.
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30
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Bangaru S, Ozorowski G, Turner HL, Antanasijevic A, Huang D, Wang X, Torres JL, Diedrich JK, Tian JH, Portnoff AD, Patel N, Massare MJ, Yates JR, Nemazee D, Paulson JC, Glenn G, Smith G, Ward AB. Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.08.06.234674. [PMID: 32793901 PMCID: PMC7418715 DOI: 10.1101/2020.08.06.234674] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Vaccine efforts against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the current COVID-19 pandemic are focused on SARS-CoV-2 spike glycoprotein, the primary target for neutralizing antibodies. Here, we performed cryo-EM and site-specific glycan analysis of one of the leading subunit vaccine candidates from Novavax based on a full-length spike protein formulated in polysorbate 80 (PS 80) detergent. Our studies reveal a stable prefusion conformation of the spike immunogen with slight differences in the S1 subunit compared to published spike ectodomain structures. Interestingly, we also observed novel interactions between the spike trimers allowing formation of higher order spike complexes. This study confirms the structural integrity of the full-length spike protein immunogen and provides a basis for interpreting immune responses to this multivalent nanoparticle immunogen.
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Affiliation(s)
- Sandhya Bangaru
- Dept. of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Gabriel Ozorowski
- Dept. of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Hannah L. Turner
- Dept. of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Aleksandar Antanasijevic
- Dept. of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Deli Huang
- Dept. of Immunology and Microbiology, The Scripps Research Institute, La Jolla CA, 92037, USA
| | - Xiaoning Wang
- Dept. of Molecular Medicine, The Scripps Research Institute, La Jolla CA, 92037, USA
| | - Jonathan L. Torres
- Dept. of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jolene K. Diedrich
- Dept. of Molecular Medicine, The Scripps Research Institute, La Jolla CA, 92037, USA
| | - Jing-Hui Tian
- Novavax, Inc. 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | | | - Nita Patel
- Novavax, Inc. 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | | | - John R. Yates
- Dept. of Molecular Medicine, The Scripps Research Institute, La Jolla CA, 92037, USA
| | - David Nemazee
- Dept. of Immunology and Microbiology, The Scripps Research Institute, La Jolla CA, 92037, USA
| | - James C. Paulson
- Dept. of Immunology and Microbiology, The Scripps Research Institute, La Jolla CA, 92037, USA
- Dept. of Molecular Medicine, The Scripps Research Institute, La Jolla CA, 92037, USA
| | - Greg Glenn
- Novavax, Inc. 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | - Gale Smith
- Novavax, Inc. 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | - Andrew B. Ward
- Dept. of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
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31
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Rantalainen K, Berndsen ZT, Antanasijevic A, Schiffner T, Zhang X, Lee WH, Torres JL, Zhang L, Irimia A, Copps J, Zhou KH, Kwon YD, Law WH, Schramm CA, Verardi R, Krebs SJ, Kwong PD, Doria-Rose NA, Wilson IA, Zwick MB, Yates JR, Schief WR, Ward AB. HIV-1 Envelope and MPER Antibody Structures in Lipid Assemblies. Cell Rep 2020; 31:107583. [PMID: 32348769 PMCID: PMC7196886 DOI: 10.1016/j.celrep.2020.107583] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 03/05/2020] [Accepted: 04/07/2020] [Indexed: 11/25/2022] Open
Abstract
Structural and functional studies of HIV envelope glycoprotein (Env) as a transmembrane protein have long been complicated by challenges associated with inherent flexibility of the molecule and the membrane-embedded hydrophobic regions. Here, we present approaches for incorporating full-length, wild-type HIV-1 Env, as well as C-terminally truncated and stabilized versions, into lipid assemblies, providing a modular platform for Env structural studies by single particle electron microscopy. We reconstitute a full-length Env clone into a nanodisc, complex it with a membrane-proximal external region (MPER) targeting antibody 10E8, and structurally define the full quaternary epitope of 10E8 consisting of lipid, MPER, and ectodomain contacts. By aligning this and other Env-MPER antibody complex reconstructions with the lipid bilayer, we observe evidence of Env tilting as part of the neutralization mechanism for MPER-targeting antibodies. We also adapt the platform toward vaccine design purposes by introducing stabilizing mutations that allow purification of unliganded Env with a peptidisc scaffold.
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Affiliation(s)
- Kimmo Rantalainen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Zachary T Berndsen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Torben Schiffner
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xi Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lei Zhang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Adriana Irimia
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kenneth H Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Young D Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - William H Law
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Shelly J Krebs
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael B Zwick
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - William R Schief
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA.
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32
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Molecular dysregulation of ciliary polycystin-2 channels caused by variants in the TOP domain. Proc Natl Acad Sci U S A 2020; 117:10329-10338. [PMID: 32332171 PMCID: PMC7229662 DOI: 10.1073/pnas.1920777117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Genetic variants in PKD2 which encodes for the polycystin-2 ion channel are responsible for many clinical cases of autosomal dominant polycystic kidney disease (ADPKD). Despite our strong understanding of the genetic basis of ADPKD, we do not know how most variants impact channel function. Polycystin-2 is found in organelle membranes, including the primary cilium-an antennae-like structure on the luminal side of the collecting duct. In this study, we focus on the structural and mechanistic regulation of polycystin-2 by its TOP domain-a site with unknown function that is commonly altered by missense variants. We use direct cilia electrophysiology, cryogenic electron microscopy, and superresolution imaging to determine that variants of the TOP domain finger 1 motif destabilizes the channel structure and impairs channel opening without altering cilia localization and channel assembly. Our findings support the channelopathy classification of PKD2 variants associated with ADPKD, where polycystin-2 channel dysregulation in the primary cilia may contribute to cystogenesis.
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33
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Gilchuk P, Murin CD, Milligan JC, Cross RW, Mire CE, Ilinykh PA, Huang K, Kuzmina N, Altman PX, Hui S, Gunn BM, Bryan AL, Davidson E, Doranz BJ, Turner HL, Alkutkar T, Flinko R, Orlandi C, Carnahan R, Nargi R, Bombardi RG, Vodzak ME, Li S, Okoli A, Ibeawuchi M, Ohiaeri B, Lewis GK, Alter G, Bukreyev A, Saphire EO, Geisbert TW, Ward AB, Crowe JE. Analysis of a Therapeutic Antibody Cocktail Reveals Determinants for Cooperative and Broad Ebolavirus Neutralization. Immunity 2020; 52:388-403.e12. [PMID: 32023489 PMCID: PMC7111202 DOI: 10.1016/j.immuni.2020.01.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/14/2019] [Accepted: 01/08/2020] [Indexed: 01/14/2023]
Abstract
Structural principles underlying the composition of protective antiviral monoclonal antibody (mAb) cocktails are poorly defined. Here, we exploited antibody cooperativity to develop a therapeutic mAb cocktail against Ebola virus. We systematically analyzed the antibody repertoire in human survivors and identified a pair of potently neutralizing mAbs that cooperatively bound to the ebolavirus glycoprotein (GP). High-resolution structures revealed that in a two-antibody cocktail, molecular mimicry was a major feature of mAb-GP interactions. Broadly neutralizing mAb rEBOV-520 targeted a conserved epitope on the GP base region. mAb rEBOV-548 bound to a glycan cap epitope, possessed neutralizing and Fc-mediated effector function activities, and potentiated neutralization by rEBOV-520. Remodeling of the glycan cap structures by the cocktail enabled enhanced GP binding and virus neutralization. The cocktail demonstrated resistance to virus escape and protected non-human primates (NHPs) against Ebola virus disease. These data illuminate structural principles of antibody cooperativity with implications for development of antiviral immunotherapeutics.
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Affiliation(s)
- Pavlo Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Charles D. Murin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jacob C. Milligan
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robert W. Cross
- Galveston National Laboratory, Galveston, TX 77550, USA,Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Chad E. Mire
- Galveston National Laboratory, Galveston, TX 77550, USA,Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Philipp A. Ilinykh
- Galveston National Laboratory, Galveston, TX 77550, USA,Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Kai Huang
- Galveston National Laboratory, Galveston, TX 77550, USA,Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Natalia Kuzmina
- Galveston National Laboratory, Galveston, TX 77550, USA,Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Pilar X. Altman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sean Hui
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bronwyn M. Gunn
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | | | | | | | - Hannah L. Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tanwee Alkutkar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robin Flinko
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Chiara Orlandi
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Robert Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rachel Nargi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robin G. Bombardi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Megan E. Vodzak
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sheng Li
- Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Adaora Okoli
- First Consultants Medical Center, Lagos, Nigeria
| | | | | | - George K. Lewis
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Alexander Bukreyev
- Galveston National Laboratory, Galveston, TX 77550, USA,Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA,Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Erica Ollmann Saphire
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Thomas W. Geisbert
- Galveston National Laboratory, Galveston, TX 77550, USA,Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Corresponding author
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34
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Engineered immunogen binding to alum adjuvant enhances humoral immunity. Nat Med 2020; 26:430-440. [PMID: 32066977 PMCID: PMC7069805 DOI: 10.1038/s41591-020-0753-3] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 01/06/2020] [Indexed: 01/07/2023]
Abstract
Adjuvants are central to the efficacy of subunit vaccines. Aluminum hydroxide (alum) is the most commonly used vaccine adjuvant, yet its adjuvanticity is often weak and mechanisms of triggering antibody responses remain poorly understood. We demonstrate that site-specific modification of immunogens with short peptides composed of repeating phosphoserine (pSer) residues enhances binding to alum and prolongs immunogen bioavailability. The pSer-modified immunogens formulated in alum elicited greatly increased germinal center, antibody, neutralizing antibody, memory and long-lived plasma cell responses compared to conventional alum-adsorbed immunogens. Mechanistically, pSer-immunogen:alum complexes form nanoparticles that traffic to lymph nodes and trigger B cell activation through multivalent and oriented antigen display. Direct uptake of antigen-decorated alum particles by B cells upregulated antigen processing and presentation pathways, further enhancing B cell activation. These data provide insights into mechanisms of action of alum and introduce a readily translatable approach to significantly improve humoral immunity to subunit vaccines using a clinical adjuvant. Alum coupled to protein immunogens via site-specific phosphoserine-containing linkers enhances long-lived B cell responses and can selectively direct antibodies toward protective neutralizing epitopes.
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35
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Tan TY, Fibriansah G, Kostyuchenko VA, Ng TS, Lim XX, Zhang S, Lim XN, Wang J, Shi J, Morais MC, Corti D, Lok SM. Capsid protein structure in Zika virus reveals the flavivirus assembly process. Nat Commun 2020; 11:895. [PMID: 32060358 PMCID: PMC7021721 DOI: 10.1038/s41467-020-14647-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 01/18/2020] [Indexed: 01/22/2023] Open
Abstract
Structures of flavivirus (dengue virus and Zika virus) particles are known to near-atomic resolution and show detailed structure and arrangement of their surface proteins (E and prM in immature virus or M in mature virus). By contrast, the arrangement of the capsid proteins:RNA complex, which forms the core of the particle, is poorly understood, likely due to inherent dynamics. Here, we stabilize immature Zika virus via an antibody that binds across the E and prM proteins, resulting in a subnanometer resolution structure of capsid proteins within the virus particle. Fitting of the capsid protein into densities shows the presence of a helix previously thought to be removed via proteolysis. This structure illuminates capsid protein quaternary organization, including its orientation relative to the lipid membrane and the genomic RNA, and its interactions with the transmembrane regions of the surface proteins. Results show the capsid protein plays a central role in the flavivirus assembly process.
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Affiliation(s)
- Ter Yong Tan
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, 169857, Singapore
- Centre for BioImaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore
| | - Guntur Fibriansah
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, 169857, Singapore
- Centre for BioImaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore
| | - Victor A Kostyuchenko
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, 169857, Singapore
- Centre for BioImaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore
| | - Thiam-Seng Ng
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, 169857, Singapore
- Centre for BioImaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore
| | - Xin-Xiang Lim
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Shuijun Zhang
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, 169857, Singapore
- Centre for BioImaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore
| | - Xin-Ni Lim
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, 169857, Singapore
- Centre for BioImaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore
| | - Jiaqi Wang
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, 169857, Singapore
- Centre for BioImaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore
| | - Jian Shi
- CryoEM Unit, Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore
| | - Marc C Morais
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, 77555-0647, USA
| | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Inc., CH-6500, Bellinzona, Switzerland
| | - Shee-Mei Lok
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, 169857, Singapore.
- Centre for BioImaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore.
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36
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Bangaru S, Lang S, Schotsaert M, Vanderven HA, Zhu X, Kose N, Bombardi R, Finn JA, Kent SJ, Gilchuk P, Gilchuk I, Turner HL, García-Sastre A, Li S, Ward AB, Wilson IA, Crowe JE. A Site of Vulnerability on the Influenza Virus Hemagglutinin Head Domain Trimer Interface. Cell 2020; 177:1136-1152.e18. [PMID: 31100268 DOI: 10.1016/j.cell.2019.04.011] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 02/25/2019] [Accepted: 04/04/2019] [Indexed: 12/17/2022]
Abstract
Here, we describe the discovery of a naturally occurring human antibody (Ab), FluA-20, that recognizes a new site of vulnerability on the hemagglutinin (HA) head domain and reacts with most influenza A viruses. Structural characterization of FluA-20 with H1 and H3 head domains revealed a novel epitope in the HA trimer interface, suggesting previously unrecognized dynamic features of the trimeric HA protein. The critical HA residues recognized by FluA-20 remain conserved across most subtypes of influenza A viruses, which explains the Ab's extraordinary breadth. The Ab rapidly disrupted the integrity of HA protein trimers, inhibited cell-to-cell spread of virus in culture, and protected mice against challenge with viruses of H1N1, H3N2, H5N1, or H7N9 subtypes when used as prophylaxis or therapy. The FluA-20 Ab has uncovered an exceedingly conserved protective determinant in the influenza HA head domain trimer interface that is an unexpected new target for anti-influenza therapeutics and vaccines.
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Affiliation(s)
- Sandhya Bangaru
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Shanshan Lang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hillary A Vanderven
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nurgun Kose
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robin Bombardi
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jessica A Finn
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Stephen J Kent
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Pavlo Gilchuk
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Iuliia Gilchuk
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sheng Li
- Department of Medicine and Biomedical Sciences, School of Medicine, University of California, San Diego, CA 92093, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - James E Crowe
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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37
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Shigematsu H. Electron cryo-microscopy for elucidating the dynamic nature of live-protein complexes. Biochim Biophys Acta Gen Subj 2020; 1864:129436. [DOI: 10.1016/j.bbagen.2019.129436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 08/31/2019] [Accepted: 09/11/2019] [Indexed: 12/30/2022]
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38
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Zhang L, Irimia A, He L, Landais E, Rantalainen K, Leaman DP, Vollbrecht T, Stano A, Sands DI, Kim AS, Poignard P, Burton DR, Murrell B, Ward AB, Zhu J, Wilson IA, Zwick MB. An MPER antibody neutralizes HIV-1 using germline features shared among donors. Nat Commun 2019; 10:5389. [PMID: 31772165 PMCID: PMC6879610 DOI: 10.1038/s41467-019-12973-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 10/11/2019] [Indexed: 11/09/2022] Open
Abstract
The membrane-proximal external region (MPER) of HIV-1 envelope glycoprotein (Env) can be targeted by neutralizing antibodies of exceptional breadth. MPER antibodies usually have long, hydrophobic CDRH3s, lack activity as inferred germline precursors, are often from the minor IgG3 subclass, and some are polyreactive, such as 4E10. Here we describe an MPER broadly neutralizing antibody from the major IgG1 subclass, PGZL1, which shares germline V/D-region genes with 4E10, has a shorter CDRH3, and is less polyreactive. A recombinant sublineage variant pan-neutralizes a 130-isolate panel at 1.4 μg/ml (IC50). Notably, a germline revertant with mature CDR3s neutralizes 12% of viruses and still binds MPER after DJ reversion. Crystal structures of lipid-bound PGZL1 variants and cryo-EM reconstruction of an Env-PGZL1 complex reveal how these antibodies recognize MPER and viral membrane. Discovery of common genetic and structural elements among MPER antibodies from different patients suggests that such antibodies could be elicited using carefully designed immunogens.
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Affiliation(s)
- Lei Zhang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- CTK Biotech, Inc., 3855 Stowe Drive, Poway, California, 92064, USA
| | - Adriana Irimia
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Lingling He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Elise Landais
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative, New York, New York, 10004, USA
| | - Kimmo Rantalainen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Daniel P Leaman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Thomas Vollbrecht
- Department of Medicine, University of California, San Diego, California, 92093, USA
| | - Armando Stano
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Daniel I Sands
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Arthur S Kim
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- Departments of Medicine, Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
| | - Pascal Poignard
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative, New York, New York, 10004, USA
- Institut de Biologie Structurale, Université Grenoble Alpes, Commissariat a l'Energie Atomique, Centre National de Recherche Scientifique and Centre Hospitalier Universitaire Grenoble Alpes, 38044, Grenoble, France
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, 92037, USA
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, Massachussetts, 02114, USA
| | - Ben Murrell
- Department of Medicine, University of California, San Diego, California, 92093, USA
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Jiang Zhu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA.
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA.
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA.
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, 92037, USA.
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, 92037, USA.
| | - Michael B Zwick
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA.
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39
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Gilchuk IM, Bangaru S, Gilchuk P, Irving RP, Kose N, Bombardi RG, Thornburg NJ, Creech CB, Edwards KM, Li S, Turner HL, Yu W, Zhu X, Wilson IA, Ward AB, Crowe JE. Influenza H7N9 Virus Neuraminidase-Specific Human Monoclonal Antibodies Inhibit Viral Egress and Protect from Lethal Influenza Infection in Mice. Cell Host Microbe 2019; 26:715-728.e8. [PMID: 31757769 DOI: 10.1016/j.chom.2019.10.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/20/2019] [Accepted: 10/07/2019] [Indexed: 02/05/2023]
Abstract
H7N9 avian influenza virus causes severe infections and might have the potential to trigger a major pandemic. Molecular determinants of human humoral immune response to N9 neuraminidase (NA) proteins, which exhibit unusual features compared with seasonal influenza virus NA proteins, are ill-defined. We isolated 35 human monoclonal antibodies (mAbs) from two H7N9 survivors and two vaccinees. These mAbs react to NA in a subtype-specific manner and recognize diverse antigenic sites on the surface of N9 NA, including epitopes overlapping with, or distinct from, the enzyme active site. Despite recognizing multiple antigenic sites, the mAbs use a common mechanism of action by blocking egress of nascent virions from infected cells, thereby providing an antiviral prophylactic and therapeutic protection in vivo in mice. Studies of breadth, potency, and diversity of antigenic recognition from four subjects suggest that vaccination with inactivated adjuvanted vaccine induce NA-reactive responses comparable to that of H7N9 natural infection.
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Affiliation(s)
- Iuliia M Gilchuk
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sandhya Bangaru
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Pavlo Gilchuk
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ryan P Irving
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nurgun Kose
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robin G Bombardi
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Natalie J Thornburg
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - C Buddy Creech
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kathryn M Edwards
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sheng Li
- Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wenli Yu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James E Crowe
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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40
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Rantalainen K, Berndsen ZT, Murrell S, Cao L, Omorodion O, Torres JL, Wu M, Umotoy J, Copps J, Poignard P, Landais E, Paulson JC, Wilson IA, Ward AB. Co-evolution of HIV Envelope and Apex-Targeting Neutralizing Antibody Lineage Provides Benchmarks for Vaccine Design. Cell Rep 2019; 23:3249-3261. [PMID: 29898396 PMCID: PMC6019700 DOI: 10.1016/j.celrep.2018.05.046] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/09/2018] [Accepted: 05/14/2018] [Indexed: 11/28/2022] Open
Abstract
Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at serial time points during infection provide a basis for understanding the co-evolutionary contest between HIV and the humoral immune system. Here, we describe the structural characterization of an apex-targeting antibody lineage and autologous clade A viral Env from a donor in the Protocol C cohort. Comparison of Ab-Env complexes at early and late time points reveals that, within the antibody lineage, the CDRH3 loop rigidifies, the bnAb angle of approach steepens, and surface charges are mutated to accommodate glycan changes. Additionally, we observed differences in site-specific glycosylation between soluble and full-length Env constructs, which may be important for tuning optimal immunogenicity in soluble Env trimers. These studies therefore provide important guideposts for design of immunogens that prime and mature nAb responses to the Env V2-apex. HIV Env-antibody structural co-evolution in PC64 donor involves five key mechanisms Antibody binding angle, CDRH3 loop, surface charges, and glycan contacts are affected Membrane-bound recombinant Env glycan shield differs from the soluble, SOSIP Env
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Affiliation(s)
- Kimmo Rantalainen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and Collaboration of AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Zachary T Berndsen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and Collaboration of AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sasha Murrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and Collaboration of AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Liwei Cao
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oluwarotimi Omorodion
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and Collaboration of AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mengyu Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffrey Umotoy
- IAVI Neutralizing Antibody Center and Collaboration of AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and Collaboration of AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pascal Poignard
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and Collaboration of AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Elise Landais
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and Collaboration of AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James C Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and Collaboration of AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and Collaboration of AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.
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41
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Brouwer PJM, Antanasijevic A, Berndsen Z, Yasmeen A, Fiala B, Bijl TPL, Bontjer I, Bale JB, Sheffler W, Allen JD, Schorcht A, Burger JA, Camacho M, Ellis D, Cottrell CA, Behrens AJ, Catalano M, Del Moral-Sánchez I, Ketas TJ, LaBranche C, van Gils MJ, Sliepen K, Stewart LJ, Crispin M, Montefiori DC, Baker D, Moore JP, Klasse PJ, Ward AB, King NP, Sanders RW. Enhancing and shaping the immunogenicity of native-like HIV-1 envelope trimers with a two-component protein nanoparticle. Nat Commun 2019; 10:4272. [PMID: 31537780 PMCID: PMC6753213 DOI: 10.1038/s41467-019-12080-1] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 08/16/2019] [Indexed: 12/26/2022] Open
Abstract
The development of native-like HIV-1 envelope (Env) trimer antigens has enabled the induction of neutralizing antibody (NAb) responses against neutralization-resistant HIV-1 strains in animal models. However, NAb responses are relatively weak and narrow in specificity. Displaying antigens in a multivalent fashion on nanoparticles (NPs) is an established strategy to increase their immunogenicity. Here we present the design and characterization of two-component protein NPs displaying 20 stabilized SOSIP trimers from various HIV-1 strains. The two-component nature permits the incorporation of exclusively well-folded, native-like Env trimers into NPs that self-assemble in vitro with high efficiency. Immunization studies show that the NPs are particularly efficacious as priming immunogens, improve the quality of the Ab response over a conventional one-component nanoparticle system, and are most effective when SOSIP trimers with an apex-proximate neutralizing epitope are displayed. Their ability to enhance and shape the immunogenicity of SOSIP trimers make these NPs a promising immunogen platform.
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Affiliation(s)
- Philip J M Brouwer
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Zachary Berndsen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, 10065, USA
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA
| | - Tom P L Bijl
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Ilja Bontjer
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Jacob B Bale
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA.,Arzeda Corporation, Seattle, Washington, 98119, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA
| | - Joel D Allen
- Biological Sciences and Institute of Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK
| | - Anna Schorcht
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Judith A Burger
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Miguel Camacho
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Daniel Ellis
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA
| | - Christopher A Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Anna-Janina Behrens
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, OX1 3QU, Oxford, UK.,New England Biolabs, Inc., Ipswich, Massachussetts, 01938, USA
| | - Marco Catalano
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Iván Del Moral-Sánchez
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Thomas J Ketas
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, 10065, USA
| | - Celia LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - Marit J van Gils
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Kwinten Sliepen
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Lance J Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA
| | - Max Crispin
- Biological Sciences and Institute of Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK.,Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, OX1 3QU, Oxford, UK
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington, 98105, USA
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, 10065, USA
| | - Per Johan Klasse
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, 10065, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA. .,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA.
| | - Rogier W Sanders
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands.
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42
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von Bredow B, Andrabi R, Grunst M, Grandea AG, Le K, Song G, Berndsen ZT, Porter K, Pallesen J, Ward AB, Burton DR, Evans DT. Differences in the Binding Affinity of an HIV-1 V2 Apex-Specific Antibody for the SIV smm/mac Envelope Glycoprotein Uncouple Antibody-Dependent Cellular Cytotoxicity from Neutralization. mBio 2019; 10:e01255-19. [PMID: 31266872 PMCID: PMC6606807 DOI: 10.1128/mbio.01255-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 05/29/2019] [Indexed: 11/20/2022] Open
Abstract
As a consequence of their independent evolutionary origins in apes and Old World monkeys, human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency viruses of the SIVsmm/mac lineage express phylogenetically and antigenically distinct envelope glycoproteins. Thus, HIV-1 Env-specific antibodies do not typically cross-react with the Env proteins of SIVsmm/mac isolates. Here we show that PGT145, a broadly neutralizing antibody to a quaternary epitope at the V2 apex of HIV-1 Env, directs the lysis of SIVsmm/mac-infected cells by antibody-dependent cellular cytotoxicity (ADCC) but does not neutralize SIVsmm/mac infectivity. Amino acid substitutions in the V2 loop of SIVmac239 corresponding to the epitope for PGT145 in HIV-1 Env modulate sensitivity to this antibody. Whereas a substitution in a conserved N-linked glycosylation site (N171Q) eliminates sensitivity to ADCC, a lysine-to-serine substitution in this region (K180S) increases ADCC and renders the virus susceptible to neutralization. These differences in function correlate with an increase in the affinity of PGT145 binding to Env on the surface of virus-infected cells and to soluble Env trimers. To our knowledge, this represents the first instance of an HIV-1 Env-specific antibody that cross-reacts with SIVsmm/mac Env and illustrates how differences in antibody binding affinity for Env can differentiate sensitivity to ADCC from neutralization.IMPORTANCE Here we show that PGT145, a potent broadly neutralizing antibody to HIV-1, directs the lysis of SIV-infected cells by antibody-dependent cellular cytotoxicity but does not neutralize SIV infectivity. This represents the first instance of cross-reactivity of an HIV-1 Env-specific antibody with SIVsmm/mac Env and reveals that antibody binding affinity can differentiate sensitivity to ADCC from neutralization.
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Affiliation(s)
- Benjamin von Bredow
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, California, USA
| | - Michael Grunst
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Andres G Grandea
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Khoa Le
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, California, USA
| | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, California, USA
| | - Zachary T Berndsen
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, California, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Katelyn Porter
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, California, USA
| | - Jesper Pallesen
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, California, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Andrew B Ward
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, California, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, California, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
| | - David T Evans
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, Wisconsin, USA
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43
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Cirelli KM, Carnathan DG, Nogal B, Martin JT, Rodriguez OL, Upadhyay AA, Enemuo CA, Gebru EH, Choe Y, Viviano F, Nakao C, Pauthner MG, Reiss S, Cottrell CA, Smith ML, Bastidas R, Gibson W, Wolabaugh AN, Melo MB, Cossette B, Kumar V, Patel NB, Tokatlian T, Menis S, Kulp DW, Burton DR, Murrell B, Schief WR, Bosinger SE, Ward AB, Watson CT, Silvestri G, Irvine DJ, Crotty S. Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance. Cell 2019; 177:1153-1171.e28. [PMID: 31080066 PMCID: PMC6619430 DOI: 10.1016/j.cell.2019.04.012] [Citation(s) in RCA: 233] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 02/26/2019] [Accepted: 04/05/2019] [Indexed: 12/14/2022]
Abstract
Conventional immunization strategies will likely be insufficient for the development of a broadly neutralizing antibody (bnAb) vaccine for HIV or other difficult pathogens because of the immunological hurdles posed, including B cell immunodominance and germinal center (GC) quantity and quality. We found that two independent methods of slow delivery immunization of rhesus monkeys (RMs) resulted in more robust T follicular helper (TFH) cell responses and GC B cells with improved Env-binding, tracked by longitudinal fine needle aspirates. Improved GCs correlated with the development of >20-fold higher titers of autologous nAbs. Using a new RM genomic immunoglobulin locus reference, we identified differential IgV gene use between immunization modalities. Ab mapping demonstrated targeting of immunodominant non-neutralizing epitopes by conventional bolus-immunized animals, whereas slow delivery-immunized animals targeted a more diverse set of epitopes. Thus, alternative immunization strategies can enhance nAb development by altering GCs and modulating the immunodominance of non-neutralizing epitopes.
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Affiliation(s)
- Kimberly M Cirelli
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Diane G Carnathan
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Bartek Nogal
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jacob T Martin
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Oscar L Rodriguez
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Amit A Upadhyay
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA
| | - Chiamaka A Enemuo
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Etse H Gebru
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yury Choe
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Federico Viviano
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Catherine Nakao
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Matthias G Pauthner
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Samantha Reiss
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher A Cottrell
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Melissa L Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Raiza Bastidas
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - William Gibson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Amber N Wolabaugh
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA
| | - Mariane B Melo
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Benjamin Cossette
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Venkatesh Kumar
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Nirav B Patel
- Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Talar Tokatlian
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sergey Menis
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel W Kulp
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA
| | - Dennis R Burton
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Ben Murrell
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - William R Schief
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Steven E Bosinger
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Andrew B Ward
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Guido Silvestri
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Darrell J Irvine
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA; Departments of Biological Engineering and Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
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44
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Abstract
Cryogenic electron microscopy (cryo-EM) enables structure determination of macromolecular objects and their assemblies. Although the techniques have been developing for nearly four decades, they have gained widespread attention in recent years due to technical advances on numerous fronts, enabling traditional microscopists to break into the world of molecular structural biology. Many samples can now be routinely analyzed at near-atomic resolution using standard imaging and image analysis techniques. However, numerous challenges to conventional workflows remain, and continued technical advances open entirely novel opportunities for discovery and exploration. Here, I will review some of the main methods surrounding cryo-EM with an emphasis specifically on single-particle analysis, and I will highlight challenges, open questions, and opportunities for methodology development.
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Affiliation(s)
- Dmitry Lyumkis
- From the Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, La Jolla, California 92037
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45
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Jesaitis AJ, Riesselman M, Taylor RM, Brumfield S. Enhanced Immunoaffinity Purification of Human Neutrophil Flavocytochrome B for Structure Determination by Electron Microscopy. Methods Mol Biol 2019; 1982:39-59. [PMID: 31172465 DOI: 10.1007/978-1-4939-9424-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Determination of the structure of human neutrophil (PMN) flavocytochrome b (Cytb) is a necessary step for the understanding of the structure-function essentials of NADPH oxidase activity. This understanding is crucial for structure-driven therapeutic approaches addressing control of inflammation and infection. Our work on purification and sample preparation of Cytb has facilitated progress toward the goal of structure determination. Here we describe exploiting immunoaffinity purification of Cytb for initial examination of its size and shape by a combination of classical and cryoelectron microscopic (EM) methods. For these evaluations, we used conventional negative-stain transmission electron microscopy (TEM) to examine both detergent-solubilized Cytb as single particles and Cytb in phosphatidylcholine reconstituted membrane vesicles as densely packed random, partially ordered, and subcrystalline arrays. In preliminary trials, we also examined single particles by cryoelectron microscopy (cryoEM) methods. We conclude that Cytb in detergent and reconstituted in membrane is a relatively compact, symmetrical protein of about 100 Å in maximum dimension. The negative stain, preliminary cryoEM, and crude molecular models suggest that the protein is probably a heterotetramer of two p22phox and gp91phox subunits in both detergent micelles and membrane vesicles. This exploratory study also suggests that high-resolution 2D electron microscopic approaches may be accessible to human material collected from single donors.
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Affiliation(s)
- Algirdas J Jesaitis
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA.
| | - Marcia Riesselman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Ross M Taylor
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
- Universal Cells , Seattle, WA, USA
| | - Susan Brumfield
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
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46
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Nemanichvili N, Tomris I, Turner HL, McBride R, Grant OC, van der Woude R, Aldosari MH, Pieters RJ, Woods RJ, Paulson JC, Boons GJ, Ward AB, Verheije MH, de Vries RP. Fluorescent Trimeric Hemagglutinins Reveal Multivalent Receptor Binding Properties. J Mol Biol 2018; 431:842-856. [PMID: 30597163 DOI: 10.1016/j.jmb.2018.12.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/17/2018] [Accepted: 12/21/2018] [Indexed: 01/04/2023]
Abstract
Influenza A virus carries hundreds of trimeric hemagglutinin (HA) proteins on its viral envelope that interact with various sialylated glycans on a host cell. This interaction represents a multivalent binding event that is present in all the current receptor binding assays, including those employing viruses or precomplexed HA trimers. To study the nature of such multivalent binding events, we fused a superfolder green fluorescent protein (sfGFP) to the C-terminus of trimeric HA to allow for direct visualization of HA-receptor interactions without the need for additional fluorescent antibodies. The multivalent binding of the HA-sfGFP proteins was studied using glycan arrays and tissue staining. The HA-sfGFP with human-type receptor specificity was able to bind to a glycan array as the free trimer. In contrast, the HA-sfGFP with avian-type receptor specificity required multimerization by antibodies before binding to glycans on the glycan array could be observed. Interestingly, multimerization was not required for binding to tissues. The array data may be explained by the possible bivalent binding mode of a single human-specific HA trimer to complex branched N-glycans, which is not possible for the avian-specific HA due to geometrical constrains of the binding sites. The fact that this specificity pattern changes upon interaction with a cell surface probably represents the enhanced amount of glycan orientations and variable densities versus those on the glycan array.
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Affiliation(s)
- Nikoloz Nemanichvili
- Pathology Division, Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, 3584, CL, Utrecht, the Netherlands
| | - Ilhan Tomris
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584, CG, Utrecht, the Netherlands
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ryan McBride
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Immunology & Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Roosmarijn van der Woude
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584, CG, Utrecht, the Netherlands
| | - Mohammed H Aldosari
- Department of Pharmaceutical Sciences, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584, CG, Utrecht, the Netherlands; Drug sector, Saudi Food and Drug Authority, Riyadh, Saudi Arabia
| | - Roland J Pieters
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584, CG, Utrecht, the Netherlands
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
| | - James C Paulson
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Immunology & Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Geert-Jan Boons
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584, CG, Utrecht, the Netherlands; Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Monique H Verheije
- Pathology Division, Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, 3584, CL, Utrecht, the Netherlands.
| | - Robert P de Vries
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584, CG, Utrecht, the Netherlands.
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47
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Hughes TET, Pumroy RA, Yazici AT, Kasimova MA, Fluck EC, Huynh KW, Samanta A, Molugu SK, Zhou ZH, Carnevale V, Rohacs T, Moiseenkova-Bell VY. Structural insights on TRPV5 gating by endogenous modulators. Nat Commun 2018; 9:4198. [PMID: 30305626 PMCID: PMC6179994 DOI: 10.1038/s41467-018-06753-6] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/14/2018] [Indexed: 11/10/2022] Open
Abstract
TRPV5 is a transient receptor potential channel involved in calcium reabsorption. Here we investigate the interaction of two endogenous modulators with TRPV5. Both phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) and calmodulin (CaM) have been shown to directly bind to TRPV5 and activate or inactivate the channel, respectively. Using cryo-electron microscopy (cryo-EM), we determined TRPV5 structures in the presence of dioctanoyl PI(4,5)P2 and CaM. The PI(4,5)P2 structure reveals a binding site between the N-linker, S4-S5 linker and S6 helix of TRPV5. These interactions with PI(4,5)P2 induce conformational rearrangements in the lower gate, opening the channel. The CaM structure reveals two TRPV5 C-terminal peptides anchoring a single CaM molecule and that calcium inhibition is mediated through a cation-π interaction between Lys116 on the C-lobe of calcium-activated CaM and Trp583 at the intracellular gate of TRPV5. Overall, this investigation provides insight into the endogenous modulation of TRPV5, which has the potential to guide drug discovery.
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Affiliation(s)
- Taylor E T Hughes
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ruth A Pumroy
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Aysenur Torun Yazici
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Marina A Kasimova
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Edwin C Fluck
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kevin W Huynh
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Amrita Samanta
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sudheer K Molugu
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Z Hong Zhou
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Tibor Rohacs
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Vera Y Moiseenkova-Bell
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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48
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Gilchuk P, Kuzmina N, Ilinykh PA, Huang K, Gunn BM, Bryan A, Davidson E, Doranz BJ, Turner HL, Fusco ML, Bramble MS, Hoff NA, Binshtein E, Kose N, Flyak AI, Flinko R, Orlandi C, Carnahan R, Parrish EH, Sevy AM, Bombardi RG, Singh PK, Mukadi P, Muyembe-Tamfum JJ, Ohi MD, Saphire EO, Lewis GK, Alter G, Ward AB, Rimoin AW, Bukreyev A, Crowe JE. Multifunctional Pan-ebolavirus Antibody Recognizes a Site of Broad Vulnerability on the Ebolavirus Glycoprotein. Immunity 2018; 49:363-374.e10. [PMID: 30029854 PMCID: PMC6104738 DOI: 10.1016/j.immuni.2018.06.018] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 05/19/2018] [Accepted: 06/28/2018] [Indexed: 01/14/2023]
Abstract
Ebolaviruses cause severe disease in humans, and identification of monoclonal antibodies (mAbs) that are effective against multiple ebolaviruses are important for therapeutics development. Here we describe a distinct class of broadly neutralizing human mAbs with protective capacity against three ebolaviruses infectious for humans: Ebola (EBOV), Sudan (SUDV), and Bundibugyo (BDBV) viruses. We isolated mAbs from human survivors of ebolavirus disease and identified a potent mAb, EBOV-520, which bound to an epitope in the glycoprotein (GP) base region. EBOV-520 efficiently neutralized EBOV, BDBV, and SUDV and also showed protective capacity in relevant animal models of these infections. EBOV-520 mediated protection principally by direct virus neutralization and exhibited multifunctional properties. This study identified a potent naturally occurring mAb and defined key features of the human antibody response that may contribute to broad protection. This multifunctional mAb and related clones are promising candidates for development as broadly protective pan-ebolavirus therapeutic molecules.
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Affiliation(s)
- Pavlo Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Natalia Kuzmina
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA,Galveston National Laboratory, Galveston, TX 77550, USA
| | - Philipp A. Ilinykh
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA,Galveston National Laboratory, Galveston, TX 77550, USA
| | - Kai Huang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA,Galveston National Laboratory, Galveston, TX 77550, USA
| | - Bronwyn M. Gunn
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Aubrey Bryan
- Integral Molecular, Inc., Philadelphia, PA 19104, USA
| | | | | | - Hannah L. Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marnie L. Fusco
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Matthew S. Bramble
- Department of Epidemiology, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095, USA,Department of Genetic Medicine Research, Children’s Research Institute, Children’s National Medical Center, Washington, DC 20010, USA
| | - Nicole A. Hoff
- Department of Epidemiology, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Elad Binshtein
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Nurgun Kose
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andrew I. Flyak
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robin Flinko
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Chiara Orlandi
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Robert Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Erica H. Parrish
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Alexander M. Sevy
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN 37232, USA
| | - Robin G. Bombardi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Prashant K. Singh
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Patrick Mukadi
- Institut Nationale de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | | | - Melanie D. Ohi
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Erica Ollmann Saphire
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - George K. Lewis
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Anne W. Rimoin
- Department of Epidemiology, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA,Galveston National Laboratory, Galveston, TX 77550, USA,Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA,Corresponding author
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN 37232, USA,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Corresponding author
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49
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Wilkinson ME, Lin PC, Plaschka C, Nagai K. Cryo-EM Studies of Pre-mRNA Splicing: From Sample Preparation to Model Visualization. Annu Rev Biophys 2018; 47:175-199. [PMID: 29494253 DOI: 10.1146/annurev-biophys-070317-033410] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The removal of noncoding introns from pre-messenger RNA (pre-mRNA) is an essential step in eukaryotic gene expression and is catalyzed by a dynamic multi-megadalton ribonucleoprotein complex called the spliceosome. The spliceosome assembles on pre-mRNA substrates by the stepwise addition of small nuclear ribonucleoprotein particles and numerous protein factors. Extensive remodeling is required to form the RNA-based active site and to mediate the pre-mRNA branching and ligation reactions. In the past two years, cryo-electron microscopy (cryo-EM) structures of spliceosomes captured in different assembly and catalytic states have greatly advanced our understanding of its mechanism. This was made possible by long-standing efforts in the purification of spliceosome intermediates as well as recent developments in cryo-EM imaging and computational methodology. The resulting high-resolution densities allow for de novo model building in core regions of the complexes. In peripheral and less ordered regions, the combination of cross-linking, bioinformatics, biochemical, and genetic data is essential for accurate modeling. Here, we summarize these achievements and highlight the critical steps in obtaining near-atomic resolution structures of the spliceosome.
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Affiliation(s)
- Max E Wilkinson
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; , , ,
| | - Pei-Chun Lin
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; , , ,
| | - Clemens Plaschka
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; , , ,
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; , , ,
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50
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Steinhardt JJ, Guenaga J, Turner HL, McKee K, Louder MK, O'Dell S, Chiang CI, Lei L, Galkin A, Andrianov AK, A Doria-Rose N, Bailer RT, Ward AB, Mascola JR, Li Y. Rational design of a trispecific antibody targeting the HIV-1 Env with elevated anti-viral activity. Nat Commun 2018; 9:877. [PMID: 29491415 PMCID: PMC5830440 DOI: 10.1038/s41467-018-03335-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 02/05/2018] [Indexed: 11/09/2022] Open
Abstract
HIV-1 broadly neutralizing antibodies (bNAbs) are being explored as passively administered therapeutic and preventative agents. However, the extensively diversified HIV-1 envelope glycoproteins (Env) rapidly acquire mutations to evade individual bNAbs in monotherapy regimens. The use of a "single" agent to simultaneously target distinct Env epitopes is desirable to overcome viral diversity. Here, we report the use of tandem single-chain variable fragment (ScFv) domains of two bNAbs, specific for the CD4-binding site and V3 glycan patch, to form anti-HIV-1 bispecific ScFvs (Bi-ScFvs). The optimal Bi-ScFv crosslinks adjacent protomers within one HIV-1 Env spike and has greater neutralization breadth than its parental bNAbs. Furthermore, the combination of this Bi-ScFv with a third bNAb recognizing the Env membrane proximal external region (MPER) results in a trispecific bNAb, which has nearly pan-isolate neutralization breadth and high potency. Thus, multispecific antibodies combining functional moieties of bNAbs could achieve outstanding neutralization capacity with augmented avidity.
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Affiliation(s)
- James J Steinhardt
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA.,Virology Program at the University of Maryland, College Park, MD, 20740, USA
| | - Javier Guenaga
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Chi-I Chiang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA
| | - Lin Lei
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA
| | - Andrey Galkin
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Alexander K Andrianov
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yuxing Li
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA. .,Virology Program at the University of Maryland, College Park, MD, 20740, USA. .,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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