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Wu D, Prem A, Xiao J, Salsbury FR. Thrombin - A Molecular Dynamics Perspective. Mini Rev Med Chem 2024; 24:1112-1124. [PMID: 37605420 DOI: 10.2174/1389557523666230821102655] [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: 03/13/2023] [Revised: 07/08/2023] [Accepted: 07/15/2023] [Indexed: 08/23/2023]
Abstract
Thrombin is a crucial enzyme involved in blood coagulation, essential for maintaining circulatory system integrity and preventing excessive bleeding. However, thrombin is also implicated in pathological conditions such as thrombosis and cancer. Despite the application of various experimental techniques, including X-ray crystallography, NMR spectroscopy, and HDXMS, none of these methods can precisely detect thrombin's dynamics and conformational ensembles at high spatial and temporal resolution. Fortunately, molecular dynamics (MD) simulation, a computational technique that allows the investigation of molecular functions and dynamics in atomic detail, can be used to explore thrombin behavior. This review summarizes recent MD simulation studies on thrombin and its interactions with other biomolecules. Specifically, the 17 studies discussed here provide insights into thrombin's switch between 'slow' and 'fast' forms, active and inactive forms, the role of Na+ binding, the effects of light chain mutation, and thrombin's interactions with other biomolecules. The findings of these studies have significant implications for developing new therapies for thrombosis and cancer. By understanding thrombin's complex behavior, researchers can design more effective drugs and treatments that target thrombin.
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Affiliation(s)
- Dizhou Wu
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27106, USA
| | - Athul Prem
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27106, USA
| | - Jiajie Xiao
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27106, USA
- Freenome, South San Francisco, CA, 94080, USA
| | - Freddie R Salsbury
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27106, USA
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2
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Guseman AJ, Rennick LJ, Nambulli S, Roy CN, Martinez DR, Yang DT, Bhinderwhala F, Vergara S, Baric RS, Ambrose Z, Duprex WP, Gronenborn AM. Targeting Spike Glycans to Inhibit SARS-CoV2 Viral Entry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.22.521642. [PMID: 36597530 PMCID: PMC9810211 DOI: 10.1101/2022.12.22.521642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 Spike harbors glycans which function as ligands for lectins. Therefore, it should be possible to exploit lectins to target SARS-CoV-2 and inhibit cellular entry by binding glycans on the Spike protein. Burkholderia oklahomensis agglutinin (BOA) is an antiviral lectin that interacts with viral glycoproteins via N-linked high mannose glycans. Here, we show that BOA binds to the Spike protein and is a potent inhibitor of SARS-CoV-2 viral entry at nanomolar concentrations. Using a variety of biophysical tools, we demonstrate that the interaction is avidity driven and that BOA crosslinks the Spike protein into soluble aggregates. Furthermore, using virus neutralization assays, we demonstrate that BOA effectively inhibits all tested variants of concern as well as SARS-CoV 2003, establishing that glycan-targeting molecules have the potential to be pan-coronavirus inhibitors.
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Affiliation(s)
- Alex J Guseman
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA, USA
| | - Linda J Rennick
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA, USA
| | - Sham Nambulli
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA, USA
| | - Chandra N Roy
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Darian T Yang
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA, USA
| | - Fatema Bhinderwhala
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA, USA
| | - Sandra Vergara
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zandrea Ambrose
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA, USA
| | - W Paul Duprex
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA, USA
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA, USA
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3
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Phetsouphanh C, Khoo WH, Jackson K, Klemm V, Howe A, Aggarwal A, Akerman A, Milogiannakis V, Stella AO, Rouet R, Schofield P, Faulks ML, Law H, Danwilai T, Starr M, Munier CML, Christ D, Singh M, Croucher PI, Brilot-Turville F, Turville S, Phan TG, Dore GJ, Darley D, Cunningham P, Matthews GV, Kelleher AD, Zaunders JJ. High titre neutralizing antibodies in response to SARS-CoV-2 infection require RBD-specific CD4 T cells that include proliferative memory cells. Front Immunol 2022; 13:1032911. [PMID: 36544780 PMCID: PMC9762180 DOI: 10.3389/fimmu.2022.1032911] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/31/2022] [Indexed: 12/12/2022] Open
Abstract
Background Long-term immunity to SARS-CoV-2 infection, including neutralizing antibodies and T cell-mediated immunity, is required in a very large majority of the population in order to reduce ongoing disease burden. Methods We have investigated the association between memory CD4 and CD8 T cells and levels of neutralizing antibodies in convalescent COVID-19 subjects. Findings Higher titres of convalescent neutralizing antibodies were associated with significantly higher levels of RBD-specific CD4 T cells, including specific memory cells that proliferated vigorously in vitro. Conversely, up to half of convalescent individuals had low neutralizing antibody titres together with a lack of receptor binding domain (RBD)-specific memory CD4 T cells. These low antibody subjects had other, non-RBD, spike-specific CD4 T cells, but with more of an inhibitory Foxp3+ and CTLA-4+ cell phenotype, in contrast to the effector T-bet+, cytotoxic granzymes+ and perforin+ cells seen in RBD-specific memory CD4 T cells from high antibody subjects. Single cell transcriptomics of antigen-specific CD4+ T cells from high antibody subjects similarly revealed heterogenous RBD-specific CD4+ T cells that comprised central memory, transitional memory and Tregs, as well as cytotoxic clusters containing diverse TCR repertoires, in individuals with high antibody levels. However, vaccination of low antibody convalescent individuals led to a slight but significant improvement in RBD-specific memory CD4 T cells and increased neutralizing antibody titres. Interpretation Our results suggest that targeting CD4 T cell epitopes proximal to and within the RBD-region should be prioritized in booster vaccines.
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Affiliation(s)
| | - Weng Hua Khoo
- Garvan Institute of Medical Research, Sydney, NSW, Australia,St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Sydney, NSW, Australia
| | | | - Vera Klemm
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Annett Howe
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Anupriya Aggarwal
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Anouschka Akerman
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | | | | | - Romain Rouet
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Megan L. Faulks
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Hannah Law
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Thidarat Danwilai
- NSW State Reference Laboratory for HIV, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia
| | - Mitchell Starr
- NSW State Reference Laboratory for HIV, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia
| | - C. Mee Ling Munier
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Mandeep Singh
- Garvan Institute of Medical Research, Sydney, NSW, Australia,St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Sydney, NSW, Australia
| | | | - Fabienne Brilot-Turville
- Brain and Mind Centre, Children’s Hospital at Westmead, University of Sydney, Sydney, NSW, Australia,Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
| | - Stuart Turville
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Tri Giang Phan
- Garvan Institute of Medical Research, Sydney, NSW, Australia,St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Sydney, NSW, Australia
| | - Gregory J. Dore
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia,Department of Infectious Diseases, St. Vincent's Hospital, Sydney, NSW, Australia
| | - David Darley
- Department of Infectious Diseases, St. Vincent's Hospital, Sydney, NSW, Australia
| | - Philip Cunningham
- NSW State Reference Laboratory for HIV, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia
| | - Gail V. Matthews
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia,Department of Infectious Diseases, St. Vincent's Hospital, Sydney, NSW, Australia
| | - Anthony D. Kelleher
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia,Department of Immunology, St Vincent's Hospital, Sydney, NSW, Australia
| | - John J. Zaunders
- NSW State Reference Laboratory for HIV, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia,*Correspondence: John J. Zaunders,
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4
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Gong Y, Qin S, Dai L, Tian Z. The glycosylation in SARS-CoV-2 and its receptor ACE2. Signal Transduct Target Ther 2021; 6:396. [PMID: 34782609 PMCID: PMC8591162 DOI: 10.1038/s41392-021-00809-8] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/10/2021] [Accepted: 10/24/2021] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), a highly infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected more than 235 million individuals and led to more than 4.8 million deaths worldwide as of October 5 2021. Cryo-electron microscopy and topology show that the SARS-CoV-2 genome encodes lots of highly glycosylated proteins, such as spike (S), envelope (E), membrane (M), and ORF3a proteins, which are responsible for host recognition, penetration, binding, recycling and pathogenesis. Here we reviewed the detections, substrates, biological functions of the glycosylation in SARS-CoV-2 proteins as well as the human receptor ACE2, and also summarized the approved and undergoing SARS-CoV-2 therapeutics associated with glycosylation. This review may not only broad the understanding of viral glycobiology, but also provide key clues for the development of new preventive and therapeutic methodologies against SARS-CoV-2 and its variants.
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Affiliation(s)
- Yanqiu Gong
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China
| | - Suideng Qin
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China.
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5
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Schwestka J, König-Beihammer J, Shin YJ, Vavra U, Kienzl NF, Grünwald-Gruber C, Maresch D, Klausberger M, Laurent E, Stadler M, Manhart G, Huber J, Hofner M, Vierlinger K, Weinhäusel A, Swoboda I, Binder CJ, Gerner W, Grebien F, Altmann F, Mach L, Stöger E, Strasser R. Impact of Specific N-Glycan Modifications on the Use of Plant-Produced SARS-CoV-2 Antigens in Serological Assays. FRONTIERS IN PLANT SCIENCE 2021; 12:747500. [PMID: 34646292 PMCID: PMC8503525 DOI: 10.3389/fpls.2021.747500] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/08/2021] [Indexed: 05/04/2023]
Abstract
The receptor binding domain (RBD) of the SARS-CoV-2 spike protein plays a key role in the virus-host cell interaction, and viral infection. The RBD is a major target for neutralizing antibodies, whilst recombinant RBD is commonly used as an antigen in serological assays. Such assays are essential tools to gain control over the pandemic and detect the extent and durability of an immune response in infected or vaccinated populations. Transient expression in plants can contribute to the fast production of viral antigens, which are required by industry in high amounts. Whilst plant-produced RBDs are glycosylated, N-glycan modifications in plants differ from humans. This can give rise to the formation of carbohydrate epitopes that can be recognized by anti-carbohydrate antibodies present in human sera. For the performance of serological tests using plant-produced recombinant viral antigens, such cross-reactive carbohydrate determinants (CCDs) could result in false positives. Here, we transiently expressed an RBD variant in wild-type and glycoengineered Nicotiana benthamiana leaves and characterized the impact of different plant-specific N-glycans on RBD reactivity in serological assays. While the overall performance of the different RBD glycoforms was comparable to each other and to a human cell line produced RBD, there was a higher tendency toward false positive results with sera containing allergy-related CCD-antibodies when an RBD carrying β1,2-xylose and core α1,3-fucose was used. These rare events could be further minimized by pre-incubating sera from allergic individuals with a CCD-inhibitor. Thereby, false positive signals obtained from anti-CCD antibodies, could be reduced by 90%, on average.
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Affiliation(s)
- Jennifer Schwestka
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Julia König-Beihammer
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Yun-Ji Shin
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Ulrike Vavra
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nikolaus F. Kienzl
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens Grünwald-Gruber
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Daniel Maresch
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Miriam Klausberger
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Elisabeth Laurent
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Core Facility Biomolecular & Cellular Analysis, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Maria Stadler
- Institute of Immunology, University of Veterinary Medicine, Vienna, Austria
| | - Gabriele Manhart
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Jasmin Huber
- Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Manuela Hofner
- Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Klemens Vierlinger
- Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Andreas Weinhäusel
- Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Ines Swoboda
- Biotechnology Section, FH Campus Wien, University of Applied Sciences, Vienna, Austria
| | - Christoph J. Binder
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Wilhelm Gerner
- Institute of Immunology, University of Veterinary Medicine, Vienna, Austria
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Friedrich Altmann
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Lukas Mach
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Eva Stöger
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
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6
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Liu Z, Xu W, Chen Z, Fu W, Zhan W, Gao Y, Zhou J, Zhou Y, Wu J, Wang Q, Zhang X, Hao A, Wu W, Zhang Q, Li Y, Fan K, Chen R, Jiang Q, Mayer CT, Schoofs T, Xie Y, Jiang S, Wen Y, Yuan Z, Wang K, Lu L, Sun L, Wang Q. An ultrapotent pan-β-coronavirus lineage B (β-CoV-B) neutralizing antibody locks the receptor-binding domain in closed conformation by targeting its conserved epitope. Protein Cell 2021; 13:655-675. [PMID: 34554412 PMCID: PMC8458794 DOI: 10.1007/s13238-021-00871-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/02/2021] [Indexed: 01/09/2023] Open
Abstract
New threats posed by the emerging circulating variants of SARS-CoV-2 highlight the need to find conserved neutralizing epitopes for therapeutic antibodies and efficient vaccine design. Here, we identified a receptor-binding domain (RBD)-binding antibody, XG014, which potently neutralizes β-coronavirus lineage B (β-CoV-B), including SARS-CoV-2, its circulating variants, SARS-CoV and bat SARSr-CoV WIV1. Interestingly, antibody family members competing with XG014 binding show reduced levels of cross-reactivity and induce antibody-dependent SARS-CoV-2 spike (S) protein-mediated cell-cell fusion, suggesting a unique mode of recognition by XG014. Structural analyses reveal that XG014 recognizes a conserved epitope outside the ACE2 binding site and completely locks RBD in the non-functional "down" conformation, while its family member XG005 directly competes with ACE2 binding and position the RBD "up". Single administration of XG014 is effective in protection against and therapy of SARS-CoV-2 infection in vivo. Our findings suggest the potential to develop XG014 as pan-β-CoV-B therapeutics and the importance of the XG014 conserved antigenic epitope for designing broadly protective vaccines against β-CoV-B and newly emerging SARS-CoV-2 variants of concern.
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Affiliation(s)
- Zezhong Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhenguo Chen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wangjun Fu
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wuqiang Zhan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yidan Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jie Zhou
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yunjiao Zhou
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jianbo Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Qian Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xiang Zhang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Aihua Hao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wei Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Qianqian Zhang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yaming Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Kaiyue Fan
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ruihong Chen
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qiaochu Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Christian T Mayer
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Youhua Xie
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yumei Wen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Kang Wang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Lei Sun
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences; Shanghai Institute of Infectious Disease and Biosecurity; the Fifth People's Hospital of Shanghai; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology); Institutes of Biomedical Sciences; Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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7
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Wang J, Maschietto F, Guberman-Pfeffer MJ, Reiss K, Allen B, Xiong Y, Lolis E, Batista VS. Computational insights into the membrane fusion mechanism of SARS-CoV-2 at the cellular level. Comput Struct Biotechnol J 2021; 19:5019-5028. [PMID: 34540146 PMCID: PMC8442599 DOI: 10.1016/j.csbj.2021.08.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 08/14/2021] [Accepted: 08/31/2021] [Indexed: 12/25/2022] Open
Abstract
The membrane fusion mechanism of SARS-CoV-2 offers an attractive target for the development of small molecule antiviral inhibitors. Fusion involves an initial binding of the crown-like trimeric spike glycoproteins of SARS-CoV-2 to the receptor angiotensin II-converting enzyme 2 (ACE2) on the permissive host cellular membrane and a prefusion to post-fusion conversion of the spike trimer. During this conversion, the fusion peptides of the spike trimer are inserted into the host membrane to bring together the host and viral membranes for membrane fusion in highly choreographic events. However, geometric constraints due to interactions with the membranes remain poorly understood. In this study, we build structural models of super-complexes of spike trimer/ACE2 dimers based on the molecular structures of the ACE2/neutral amino acid transporter B(0)AT heterodimer. We determine the conformational constraints due to the membrane geometry on the enzymatic activity of ACE2 and on the viral fusion process. Furthermore, we find that binding three ACE2 dimers per spike trimer is essential to open the central pore as necessary for triggering productive membrane fusion through an elongation of the central stalk. The reported findings thus provide valuable insights for targeting the membrane fusion mechanism for drug design at the molecular level.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, United States
| | - Federica Maschietto
- Department of Chemistry, Yale University, New Haven, CT 06511-8499, United States
| | | | - Krystle Reiss
- Department of Chemistry, Yale University, New Haven, CT 06511-8499, United States
| | - Brandon Allen
- Department of Chemistry, Yale University, New Haven, CT 06511-8499, United States
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, United States
| | - Elias Lolis
- Department of Pharmacology, Yale University, New Haven, CT 06520-8066, United States
| | - Victor S. Batista
- Department of Chemistry, Yale University, New Haven, CT 06511-8499, United States
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8
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Weiß RG, Losfeld ME, Aebi M, Riniker S. N-Glycosylation Enhances Conformational Flexibility of Protein Disulfide Isomerase Revealed by Microsecond Molecular Dynamics and Markov State Modeling. J Phys Chem B 2021; 125:9467-9479. [PMID: 34379416 DOI: 10.1021/acs.jpcb.1c04279] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Secreted proteins of eukaryotes are decorated with branched carbohydrate oligomers called glycans. This fact is only starting to be considered for in silico investigations of protein dynamics. Using all-atom molecular dynamics (MD) simulations and Markov state modeling (MSM), we unveil the influence of glycans on the conformational flexibility of the multidomain protein disulfide isomerase (PDI), which is a ubiquitous chaperone in the endoplasmic reticulum (ER). Yeast PDI (yPDI) from Saccharomyces cerevisiae is glycosylated at asparagine side chains and the knowledge of its five modified sites enables a realistic computational modeling. We compare simulations of glycosylated and unglycosylated yPDI and find that the presence of glycan-glycan and glycan-protein interactions influences the flexibility of PDI in different ways. For example, glycosylation reduces interdomain interactions, shifting the conformational ensemble toward more open, extended structures. In addition, we compare our results on yPDI with structural information of homologous proteins such as human PDI (hPDI), which is natively unglycosylated. Interestingly, hPDI lacks a surface recess that is present in yPDI. We find that glycosylation of yPDI facilitates its catalytic site to reach close to this surface recess. Hence, this might point to a possible functional relevance of glycosylation in yeast to act on substrates, while glycosylation seems redundant for the human homologous protein. We conclude that glycosylation is fundamental for protein dynamics, making it a necessity for a truthful representation of the flexibility and function in in silico studies of glycoproteins.
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Affiliation(s)
- R Gregor Weiß
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, ETH Zürich, 8093 Zürich, Switzerland
| | - Marie-Estelle Losfeld
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, 8093 Zürich, Switzerland
| | - Markus Aebi
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, 8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, ETH Zürich, 8093 Zürich, Switzerland
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9
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Gobeil SMC, Janowska K, McDowell S, Mansouri K, Parks R, Stalls V, Kopp MF, Manne K, Li D, Wiehe K, Saunders KO, Edwards RJ, Korber B, Haynes BF, Henderson R, Acharya P. Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity. Science 2021; 373:eabi6226. [PMID: 34168071 PMCID: PMC8611377 DOI: 10.1126/science.abi6226] [Citation(s) in RCA: 257] [Impact Index Per Article: 85.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 06/16/2021] [Indexed: 01/04/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with multiple spike mutations enable increased transmission and antibody resistance. We combined cryo-electron microscopy (cryo-EM), binding, and computational analyses to study variant spikes, including one that was involved in transmission between minks and humans, and others that originated and spread in human populations. All variants showed increased angiotensin-converting enzyme 2 (ACE2) receptor binding and increased propensity for receptor binding domain (RBD)-up states. While adaptation to mink resulted in spike destabilization, the B.1.1.7 (UK) spike balanced stabilizing and destabilizing mutations. A local destabilizing effect of the RBD E484K mutation was implicated in resistance of the B.1.1.28/P.1 (Brazil) and B.1.351 (South Africa) variants to neutralizing antibodies. Our studies revealed allosteric effects of mutations and mechanistic differences that drive either interspecies transmission or escape from antibody neutralization.
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MESH Headings
- Amino Acid Substitution
- Angiotensin-Converting Enzyme 2/metabolism
- Animals
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Antigens, Viral/immunology
- COVID-19/transmission
- COVID-19/veterinary
- COVID-19/virology
- Cryoelectron Microscopy
- Host Adaptation
- Humans
- Immune Evasion
- Mink/virology
- Models, Molecular
- Mutation
- Protein Binding
- Protein Conformation
- Protein Interaction Domains and Motifs
- Protein Structure, Quaternary
- Protein Subunits/chemistry
- Receptors, Coronavirus/metabolism
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
| | | | | | | | - Robert Parks
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | - Megan F Kopp
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Kartik Manne
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Dapeng Li
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Durham, NC 27710, USA
- Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Durham, NC 27710, USA
- Department of Surgery, Duke University, Durham, NC 27710, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
- Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Robert J Edwards
- Duke Human Vaccine Institute, Durham, NC 27710, USA
- Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Durham, NC 27710, USA
- Department of Medicine, Duke University, Durham, NC 27710, USA
- Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Rory Henderson
- Duke Human Vaccine Institute, Durham, NC 27710, USA.
- Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC 27710, USA.
- Department of Surgery, Duke University, Durham, NC 27710, USA
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
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10
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Kondo Y, Larabee JL, Gao L, Shi H, Shao B, Hoover CM, McDaniel JM, Ho YC, Silasi-Mansat R, Archer-Hartmann SA, Azadi P, Srinivasan RS, Rezaie AR, Borczuk A, Laurence JC, Lupu F, Ahamed J, McEver RP, Papin JF, Yu Z, Xia L. L-SIGN is a receptor on liver sinusoidal endothelial cells for SARS-CoV-2 virus. JCI Insight 2021; 6:e148999. [PMID: 34291736 PMCID: PMC8410055 DOI: 10.1172/jci.insight.148999] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a pandemic. Severe disease is associated with dysfunction of multiple organs, but some infected cells do not express ACE2, the canonical entry receptor for SARS-CoV-2. Here, we report that the C-type lectin receptor L-SIGN interacted in a Ca2+-dependent manner with high-mannose–type N-glycans on the SARS-CoV-2 spike protein. We found that L-SIGN was highly expressed on human liver sinusoidal endothelial cells (LSECs) and lymph node lymphatic endothelial cells but not on blood endothelial cells. Using high-resolution confocal microscopy imaging, we detected SARS-CoV-2 viral proteins within the LSECs from liver autopsy samples from patients with COVID-19. We found that both pseudo-typed virus enveloped with SARS-CoV-2 spike protein and authentic SARS-CoV-2 virus infected L-SIGN–expressing cells relative to control cells. Moreover, blocking L-SIGN function reduced CoV-2–type infection. These results indicate that L-SIGN is a receptor for SARS-CoV-2 infection. LSECs are major sources of the clotting factors vWF and factor VIII (FVIII). LSECs from liver autopsy samples from patients with COVID-19 expressed substantially higher levels of vWF and FVIII than LSECs from uninfected liver samples. Our data demonstrate that L-SIGN is an endothelial cell receptor for SARS-CoV-2 that may contribute to COVID-19–associated coagulopathy.
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Affiliation(s)
- Yuji Kondo
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | | | - Liang Gao
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Huiping Shi
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Bojing Shao
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Christopher M Hoover
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA.,Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - J Michael McDaniel
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Yen-Chun Ho
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Robert Silasi-Mansat
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | | | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - R Sathish Srinivasan
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Alireza R Rezaie
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA.,Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | | | - Jeffrey C Laurence
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York, USA
| | - Florea Lupu
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA.,Department of Pathology and
| | - Jasimuddin Ahamed
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA.,Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Rodger P McEver
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA.,Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | | | | | - Lijun Xia
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA.,Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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11
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Rey F. Structure-function relations of the SARS-CoV-2 spike protein and impact of mutations in the variants of concern. C R Biol 2021; 344:77-110. [PMID: 34213849 DOI: 10.5802/crbiol.53] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This review covers the main features of the severe acquired respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein, its interaction with the main entry receptor, the human angiotensin converting enzyme 2 (ACE2), and the subsequent membrane fusion step. The focus is on the structural organization of these proteins and mechanistic aspects of their interactions that lead to cytoplasmic release of the viral genome. The most potently neutralizing antibodies against SARS-CoV-2 were shown to interfere with the spike/ACE2 interaction. I thus also review the location and the potential impact of mutations in the spike protein observed in the variants of concern that emerged concomitantly with acquired immunity in the population after one year of virus circulation. Understanding how these interactions affect the spike/ACE2 interactions and the subsequent spike-protein-induced membrane fusion reaction is important to stay one step ahead of the virus evolution and develop efficient countermeasures.
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Affiliation(s)
- Félix Rey
- Unité de Virologie Structurale, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75015 Paris, France
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12
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Shin YJ, König-Beihammer J, Vavra U, Schwestka J, Kienzl NF, Klausberger M, Laurent E, Grünwald-Gruber C, Vierlinger K, Hofner M, Margolin E, Weinhäusel A, Stöger E, Mach L, Strasser R. N-Glycosylation of the SARS-CoV-2 Receptor Binding Domain Is Important for Functional Expression in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:689104. [PMID: 34211491 PMCID: PMC8239413 DOI: 10.3389/fpls.2021.689104] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/20/2021] [Indexed: 05/17/2023]
Abstract
Nicotiana benthamiana is used worldwide as production host for recombinant proteins. Many recombinant proteins such as monoclonal antibodies, growth factors or viral antigens require posttranslational modifications like glycosylation for their function. Here, we transiently expressed different variants of the glycosylated receptor binding domain (RBD) from the SARS-CoV-2 spike protein in N. benthamiana. We characterized the impact of variations in RBD-length and posttranslational modifications on protein expression, yield and functionality. We found that a truncated RBD variant (RBD-215) consisting of amino acids Arg319-Leu533 can be efficiently expressed as a secreted soluble protein. Purified RBD-215 was mainly present as a monomer and showed binding to the conformation-dependent antibody CR3022, the cellular receptor angiotensin converting enzyme 2 (ACE2) and to antibodies present in convalescent sera. Expression of RBD-215 in glycoengineered ΔXT/FT plants resulted in the generation of complex N-glycans on both N-glycosylation sites. While site-directed mutagenesis showed that the N-glycans are important for proper RBD folding, differences in N-glycan processing had no effect on protein expression and function.
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Affiliation(s)
- Yun-Ji Shin
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Julia König-Beihammer
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Ulrike Vavra
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Jennifer Schwestka
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Nikolaus F. Kienzl
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Miriam Klausberger
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Elisabeth Laurent
- Department of Biotechnology, Core Facility Biomolecular and Cellular Analysis, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Clemens Grünwald-Gruber
- Department of Chemistry, Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Klemens Vierlinger
- Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Manuela Hofner
- Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Emmanuel Margolin
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Andreas Weinhäusel
- Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Eva Stöger
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Lukas Mach
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
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13
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Nguyen K, Chakraborty S, Mansbach RA, Korber B, Gnanakaran S. Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. Viruses 2021; 13:927. [PMID: 34067878 PMCID: PMC8156887 DOI: 10.3390/v13050927] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/03/2021] [Accepted: 05/07/2021] [Indexed: 01/01/2023] Open
Abstract
COVID-19 is a highly infectious respiratory disease caused by the novel coronavirus SARS-CoV-2. It has become a global pandemic and its frequent mutations may pose new challenges for vaccine design. During viral infection, the Spike RBD of SARS-CoV-2 binds the human host cell receptor ACE2, enabling the virus to enter the host cell. Both the Spike and ACE2 are densely glycosylated, and it is unclear how distinctive glycan types may modulate the interaction of RBD and ACE2. Detailed understanding of these determinants is key for the development of novel therapeutic strategies. To this end, we perform extensive all-atom simulations of the (i) RBD-ACE2 complex without glycans, (ii) RBD-ACE2 with oligomannose MAN9 glycans in ACE2, and (iii) RBD-ACE2 with complex FA2 glycans in ACE2. These simulations identify the key residues at the RBD-ACE2 interface that form contacts with higher probabilities, thus providing a quantitative evaluation that complements recent structural studies. Notably, we find that this RBD-ACE2 contact signature is not altered by the presence of different glycoforms, suggesting that RBD-ACE2 interaction is robust. Applying our simulated results, we illustrate how the recently prevalent N501Y mutation may alter specific interactions with host ACE2 that facilitate the virus-host binding. Furthermore, our simulations reveal how the glycan on Asn90 of ACE2 can play a distinct role in the binding and unbinding of RBD. Finally, an energetics analysis shows that MAN9 glycans on ACE2 decrease RBD-ACE2 affinity, while FA2 glycans lead to enhanced binding of the complex. Together, our results provide a more comprehensive picture of the detailed interplay between virus and human receptor, which is much needed for the discovery of effective treatments that aim at modulating the physical-chemical properties of this virus.
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Affiliation(s)
- Kien Nguyen
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (K.N.); (S.C.); (B.K.)
| | - Srirupa Chakraborty
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (K.N.); (S.C.); (B.K.)
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (K.N.); (S.C.); (B.K.)
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (K.N.); (S.C.); (B.K.)
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14
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Sun D, Sang Z, Kim YJ, Xiang Y, Cohen T, Belford AK, Huet A, Conway JF, Sun J, Taylor DJ, Schneidman-Duhovny D, Zhang C, Huang W, Shi Y. Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.09.434592. [PMID: 33758850 PMCID: PMC7987009 DOI: 10.1101/2021.03.09.434592] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There is an urgent need to develop effective interventions resistant to the evolving variants of SARS-CoV-2. Nanobodies (Nbs) are stable and cost-effective agents that can be delivered by novel aerosolization route to treat SARS-CoV-2 infections efficiently. However, it remains unknown if they possess broadly neutralizing activities against the prevalent circulating strains. We found that potent neutralizing Nbs are highly resistant to the convergent variants of concern that evade a large panel of neutralizing antibodies (Abs) and significantly reduce the activities of convalescent or vaccine-elicited sera. Subsequent determination of 9 high-resolution structures involving 6 potent neutralizing Nbs by cryoelectron microscopy reveals conserved and novel epitopes on virus spike inaccessible to Abs. Systematic structural comparison of neutralizing Abs and Nbs provides critical insights into how Nbs uniquely target the spike to achieve high-affinity and broadly neutralizing activity against the evolving virus. Our study will inform the rational design of novel pan-coronavirus vaccines and therapeutics.
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Affiliation(s)
- Dapeng Sun
- Department of Pharmacology and Chemical Biology, University of Pittsburgh
| | - Zhe Sang
- The University of Pittsburgh and Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA, USA
- Department of Cell Biology, University of Pittsburgh, PA, USA
| | - Yong Joon Kim
- Department of Cell Biology, University of Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine and Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yufei Xiang
- Department of Cell Biology, University of Pittsburgh, PA, USA
| | - Tomer Cohen
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | | | - Alexis Huet
- Department of Structural Biology, University of Pittsburgh
| | | | - Ji Sun
- Department of Structure Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Derek J. Taylor
- Department of Pharmacology, Case Western Reserve University, Clevaland, OH, USA
- Department of Biochemistry, Case Western Reserve University, Clevaland, OH, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Cheng Zhang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University, Clevaland, OH, USA
| | - Yi Shi
- The University of Pittsburgh and Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA, USA
- Department of Cell Biology, University of Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine and Carnegie Mellon University, Pittsburgh, PA, USA
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