401
|
Serapian SA, Colombo G. Bow to the enemy: How flexibility of host protein receptors can favor SARS-CoV-2. Biophys J 2021; 120:977-979. [PMID: 33577761 PMCID: PMC7857073 DOI: 10.1016/j.bpj.2021.01.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/10/2021] [Accepted: 01/28/2021] [Indexed: 01/10/2023] Open
|
402
|
Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells. Nat Methods 2021; 18:186-193. [PMID: 33542511 PMCID: PMC7611018 DOI: 10.1038/s41592-020-01054-7] [Citation(s) in RCA: 237] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023]
Abstract
Cryo-electron microscopy (cryo-EM) enables macromolecular structure determination in vitro and inside cells. In addition to aligning individual particles, accurate registration of sample motion and three-dimensional deformation during exposures are crucial for achieving high-resolution reconstructions. Here we describe M, a software tool that establishes a reference-based, multi-particle refinement framework for cryo-EM data and couples a comprehensive spatial deformation model to in silico correction of electron-optical aberrations. M provides a unified optimization framework for both frame-series and tomographic tilt-series data. We show that tilt-series data can provide the same resolution as frame-series data on a purified protein specimen, indicating that the alignment step no longer limits the resolution obtainable from tomographic data. In combination with Warp and RELION, M resolves to residue level a 70S ribosome bound to an antibiotic inside intact bacterial cells. Our work provides a computational tool that facilitates structural biology in cells.
Collapse
|
403
|
Jackson CB, Zhang L, Farzan M, Choe H. Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Biochem Biophys Res Commun 2021; 538:108-115. [PMID: 33220921 PMCID: PMC7664360 DOI: 10.1016/j.bbrc.2020.11.026] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped virus which binds its cellular receptor angiotensin-converting enzyme 2 (ACE2) and enters hosts cells through the action of its spike (S) glycoprotein displayed on the surface of the virion. Compared to the reference strain of SARS-CoV-2, the majority of currently circulating isolates possess an S protein variant characterized by an aspartic acid-to-glycine substitution at amino acid position 614 (D614G). Residue 614 lies outside the receptor binding domain (RBD) and the mutation does not alter the affinity of monomeric S protein for ACE2. However, S(G614), compared to S(D614), mediates more efficient ACE2-mediated transduction of cells by S-pseudotyped vectors and more efficient infection of cells and animals by live SARS-CoV-2. This review summarizes and synthesizes the epidemiological and functional observations of the D614G spike mutation, with focus on the biochemical and cell-biological impact of this mutation and its consequences for S protein function. We further discuss the significance of these recent findings in the context of the current global pandemic.
Collapse
Affiliation(s)
- Cody B Jackson
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA.
| | - Lizhou Zhang
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Hyeryun Choe
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| |
Collapse
|
404
|
Yuan M, Liu H, Wu NC, Wilson IA. Recognition of the SARS-CoV-2 receptor binding domain by neutralizing antibodies. Biochem Biophys Res Commun 2021; 538:192-203. [PMID: 33069360 PMCID: PMC7547570 DOI: 10.1016/j.bbrc.2020.10.012] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 10/07/2020] [Indexed: 12/21/2022]
Abstract
Immediately from the outset of the COVID-19 pandemic, researchers from diverse biomedical and biological disciplines have united to study the novel pandemic virus, SARS-CoV-2. The antibody response to SARS-CoV-2 has been a major focus of COVID-19 research due to its clinical relevance and importance in vaccine and therapeutic development. Isolation and characterization of antibodies to SARS-CoV-2 have been accumulating at an unprecedented pace. Most of the SARS-CoV-2 neutralizing antibodies to date target the spike (S) protein receptor binding domain (RBD), which engages the host receptor ACE2 for viral entry. Here we review the binding sites and molecular features of monoclonal antibodies that target the SARS-CoV-2 RBD, including a few that also cross-neutralize SARS-CoV.
Collapse
Affiliation(s)
- Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, 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 the Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
| |
Collapse
|
405
|
Multiscale Electron Microscopy for the Study of Viral Replication Organelles. Viruses 2021; 13:v13020197. [PMID: 33525547 PMCID: PMC7912242 DOI: 10.3390/v13020197] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 11/17/2022] Open
Abstract
During infection with positive-strand RNA viruses, viral RNA synthesis associates with modified intracellular membranes that form unique and captivating structures in the cytoplasm of the infected cell. These viral replication organelles (ROs) play a key role in the replicative cycle of important human pathogens like coronaviruses, enteroviruses, or flaviviruses. From their discovery to date, progress in our understanding of viral ROs has closely followed new developments in electron microscopy (EM). This review gives a chronological account of this progress and an introduction to the different EM techniques that enabled it. With an ample repertoire of imaging modalities, EM is nowadays a versatile technique that provides structural and functional information at a wide range of scales. Together with well-established approaches like electron tomography or labeling methods, we examine more recent developments, such as volume scanning electron microscopy (SEM) and in situ cryotomography, which are only beginning to be applied to the study of viral ROs. We also highlight the first cryotomography analyses of viral ROs, which have led to the discovery of macromolecular complexes that may serve as RO channels that control the export of newly-made viral RNA. These studies are key first steps towards elucidating the macromolecular complexity of viral ROs.
Collapse
|
406
|
Verkhivker GM, Di Paola L. Dynamic Network Modeling of Allosteric Interactions and Communication Pathways in the SARS-CoV-2 Spike Trimer Mutants: Differential Modulation of Conformational Landscapes and Signal Transmission via Cascades of Regulatory Switches. J Phys Chem B 2021; 125:850-873. [PMID: 33448856 PMCID: PMC7839160 DOI: 10.1021/acs.jpcb.0c10637] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/08/2021] [Indexed: 12/13/2022]
Abstract
The rapidly growing body of structural and biochemical studies of the SARS-CoV-2 spike glycoprotein has revealed a variety of distinct functional states with radically different arrangements of the receptor-binding domain, highlighting a remarkable function-driven conformational plasticity and adaptability of the spike proteins. In this study, we examined molecular mechanisms underlying conformational and dynamic changes in the SARS-CoV-2 spike mutant trimers through the lens of dynamic analysis of allosteric interaction networks and atomistic modeling of signal transmission. Using an integrated approach that combined coarse-grained molecular simulations, protein stability analysis, and perturbation-based modeling of residue interaction networks, we examined how mutations in the regulatory regions of the SARS-CoV-2 spike protein can differentially affect dynamics and allosteric signaling in distinct functional states. The results of this study revealed key functional regions and regulatory centers that govern collective dynamics, allosteric interactions, and control signal transmission in the SARS-CoV-2 spike proteins. We found that the experimentally confirmed regulatory hotspots that dictate dynamic switching between conformational states of the SARS-CoV-2 spike protein correspond to the key hinge sites and global mediating centers of the allosteric interaction networks. The results of this study provide a novel insight into allosteric regulatory mechanisms of SARS-CoV-2 spike proteins showing that mutations at the key regulatory positions can differentially modulate distribution of states and determine topography of signal communication pathways operating through state-specific cascades of control switch points. This analysis provides a plausible strategy for allosteric probing of the conformational equilibrium and therapeutic intervention by targeting specific hotspots of allosteric interactions and communications in the SARS-CoV-2 spike proteins.
Collapse
Affiliation(s)
- Gennady M. Verkhivker
- Keck
Center for Science and Engineering, Schmid College of Science and
Technology, Chapman University, One University Drive, Orange, California 92866, United States
- Department
of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
| | - Luisa Di Paola
- Unit
of Chemical-Physics Fundamentals in Chemical Engineering, Department
of Engineering, Università Campus
Bio-Medico di Roma, via
Álvaro del Portillo 21, 00128 Rome, Italy
| |
Collapse
|
407
|
Powell A, Zhang K, Sanyal M, Tang S, Weidenbacher PA, Li S, Pham TD, Pak JE, Chiu W, Kim PS. A Single Immunization with Spike-Functionalized Ferritin Vaccines Elicits Neutralizing Antibody Responses against SARS-CoV-2 in Mice. ACS CENTRAL SCIENCE 2021; 7:183-199. [PMID: 33527087 PMCID: PMC7805605 DOI: 10.1021/acscentsci.0c01405] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Indexed: 05/05/2023]
Abstract
The development of a safe and effective SARS-CoV-2 vaccine is a public health priority. We designed subunit vaccine candidates using self-assembling ferritin nanoparticles displaying one of two multimerized SARS-CoV-2 spikes: full-length ectodomain (S-Fer) or a C-terminal 70 amino-acid deletion (SΔC-Fer). Ferritin is an attractive nanoparticle platform for production of vaccines, and ferritin-based vaccines have been investigated in humans in two separate clinical trials. We confirmed proper folding and antigenicity of spike on the surface of ferritin by cryo-EM and binding to conformation-specific monoclonal antibodies. After a single immunization of mice with either of the two spike ferritin particles, a lentiviral SARS-CoV-2 pseudovirus assay revealed mean neutralizing antibody titers at least 2-fold greater than those in convalescent plasma from COVID-19 patients. Additionally, a single dose of SΔC-Fer elicited significantly higher neutralizing responses as compared to immunization with the spike receptor binding domain (RBD) monomer or spike ectodomain trimer alone. After a second dose, mice immunized with SΔC-Fer exhibited higher neutralizing titers than all other groups. Taken together, these results demonstrate that multivalent presentation of SARS-CoV-2 spike on ferritin can notably enhance elicitation of neutralizing antibodies, thus constituting a viable strategy for single-dose vaccination against COVID-19.
Collapse
Affiliation(s)
- Abigail
E. Powell
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Kaiming Zhang
- Department
of Bioengineering & James H. Clark Center, Stanford University, Stanford, California 94305, United States
| | - Mrinmoy Sanyal
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Shaogeng Tang
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Payton A. Weidenbacher
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Shanshan Li
- Department
of Bioengineering & James H. Clark Center, Stanford University, Stanford, California 94305, United States
| | - Tho D. Pham
- Department
of Pathology, Stanford University, Stanford, California 94305, United States
- Stanford
Blood Center, Palo Alto, California 94304, United States
| | - John E. Pak
- Chan Zuckerberg
Biohub, San Francisco, California 94158, United States
| | - Wah Chiu
- Department
of Bioengineering & James H. Clark Center, Stanford University, Stanford, California 94305, United States
- Chan Zuckerberg
Biohub, San Francisco, California 94158, United States
- Division
of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Peter S. Kim
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
- Chan Zuckerberg
Biohub, San Francisco, California 94158, United States
| |
Collapse
|
408
|
Mori T, Jung J, Kobayashi C, Dokainish HM, Re S, Sugita Y. Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein. Biophys J 2021; 120:1060-1071. [PMID: 33484712 PMCID: PMC7825899 DOI: 10.1016/j.bpj.2021.01.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/31/2020] [Accepted: 01/13/2021] [Indexed: 12/23/2022] Open
Abstract
The ongoing COVID-19 pandemic caused by the new coronavirus, SARS-CoV-2, calls for urgent developments of vaccines and antiviral drugs. The spike protein of SARS-CoV-2 (S-protein), which consists of trimeric polypeptide chains with glycosylated residues on the surface, triggers the virus entry into a host cell. Extensive structural and functional studies on this protein have rapidly advanced our understanding of the S-protein structure at atomic resolutions, although most of these structural studies overlook the effect of glycans attached to the S-protein on the conformational stability and functional motions between the inactive down and active up forms. Here, we performed all-atom molecular dynamics simulations of both down and up forms of a fully glycosylated S-protein in solution as well as targeted molecular dynamics simulations between them to elucidate key interdomain interactions for stabilizing each form and inducing the large-scale conformational transitions. The residue-level interaction analysis of the simulation trajectories detects distinct amino acid residues and N-glycans as determinants on conformational stability of each form. During the conformational transitions between them, interdomain interactions mediated by glycosylated residues are switched to play key roles on the stabilization of another form. Electrostatic interactions, as well as hydrogen bonds between the three receptor binding domains, work as driving forces to initiate the conformational transitions toward the active form. This study sheds light on the mechanisms underlying conformational stability and functional motions of the S-protein, which are relevant for vaccine and antiviral drug developments.
Collapse
Affiliation(s)
- Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Jaewoon Jung
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan; Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan
| | - Chigusa Kobayashi
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan
| | - Hisham M Dokainish
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Suyong Re
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan; Center for Drug Design Research, National Institutes of Biomedical Innovation, Health, and Nutrition, Osaka, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan; Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan; Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
| |
Collapse
|
409
|
Biological and Clinical Consequences of Integrin Binding via a Rogue RGD Motif in the SARS CoV-2 Spike Protein. Viruses 2021; 13:v13020146. [PMID: 33498225 PMCID: PMC7909284 DOI: 10.3390/v13020146] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/12/2022] Open
Abstract
Although ACE2 (angiotensin converting enzyme 2) is considered the primary receptor for CoV-2 cell entry, recent reports suggest that alternative pathways may contribute. This paper considers the hypothesis that viral binding to cell-surface integrins may contribute to the high infectivity and widespread extra-pulmonary impacts of the SARS-CoV-2 virus. This potential is suggested on the basis of the emergence of an RGD (arginine-glycine-aspartate) sequence in the receptor-binding domain of the spike protein. RGD is a motif commonly used by viruses to bind cell-surface integrins. Numerous signaling pathways are mediated by integrins and virion binding could lead to dysregulation of these pathways, with consequent tissue damage. Integrins on the surfaces of pneumocytes, endothelial cells and platelets may be vulnerable to CoV-2 virion binding. For instance, binding of intact virions to integrins on alveolar cells could enhance viral entry. Binding of virions to integrins on endothelial cells could activate angiogenic cell signaling pathways; dysregulate integrin-mediated signaling pathways controlling developmental processes; and precipitate endothelial activation to initiate blood clotting. Such a procoagulant state, perhaps together with enhancement of platelet aggregation through virions binding to integrins on platelets, could amplify the production of microthrombi that pose the threat of pulmonary thrombosis and embolism, strokes and other thrombotic consequences. The susceptibility of different tissues to virion–integrin interactions may be modulated by a host of factors, including the conformation of relevant integrins and the impact of the tissue microenvironment on spike protein conformation. Patient-specific differences in these factors may contribute to the high variability of clinical presentation. There is danger that the emergence of receptor-binding domain mutations that increase infectivity may also enhance access of the RGD motif for integrin binding, resulting in viral strains with ACE2 independent routes of cell entry and novel integrin-mediated biological and clinical impacts. The highly infectious variant, B.1.1.7 (or VUI 202012/01), includes a receptor-binding domain amino acid replacement, N501Y, that could potentially provide the RGD motif with enhanced access to cell-surface integrins, with consequent clinical impacts.
Collapse
|
410
|
Zhang P, Mendonca L, Howe A, Gilchrist J, Sun D, Knight M, Zanetti-Domingues L, Bateman B, Krebs AS, Chen L, Radecke J, Sheng Y, Li V, Ni T, Kounatidis I, Koronfel M, Szynkiewicz M, Harkiolaki M, Martin-Fernandez M, James W. Correlative Multi-scale Cryo-imaging Unveils SARS-CoV-2 Assembly and Egress. RESEARCH SQUARE 2021. [PMID: 33501431 PMCID: PMC7836121 DOI: 10.21203/rs.3.rs-134794/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Since the outbreak of the SARS-CoV-2 pandemic, there have been intense structural studies on purified recombinant viral components and inactivated viruses. However, structural and ultrastructural evidence on how the SARS-CoV-2 infection progresses in the frozen-hydrated native cellular context is scarce, and there is a lack of comprehensive knowledge on the SARS-CoV-2 replicative cycle. To correlate the cytopathic events induced by SARS-CoV-2 with virus replication process under the frozen-hydrated condition, here we established a unique multi-modal, multi-scale cryo-correlative platform to image SARS-CoV-2 infection in Vero cells. This platform combines serial cryoFIB/SEM volume imaging and soft X-ray cryo-tomography with cell lamellae-based cryo-electron tomography (cryoET) and subtomogram averaging. The results place critical SARS-CoV-2 structural events – e.g. viral RNA transport portals on double membrane vesicles, virus assembly and budding intermediates, virus egress pathways, and native virus spike structures from intracellular assembled and extracellular released virus - in the context of whole-cell images. The latter revealed numerous heterogeneous cytoplasmic vesicles, the formation of membrane tunnels through which viruses exit, and the drastic cytoplasm invasion into the nucleus. This integrated approach allows a holistic view of SARS-CoV-2 infection, from the whole cell to individual molecules.
Collapse
|
411
|
Yuan Y, Jacobs CA, Llorente Garcia I, Pereira PM, Lawrence SP, Laine RF, Marsh M, Henriques R. Single-Molecule Super-Resolution Imaging of T-Cell Plasma Membrane CD4 Redistribution upon HIV-1 Binding. Viruses 2021; 13:142. [PMID: 33478139 PMCID: PMC7835772 DOI: 10.3390/v13010142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/21/2022] Open
Abstract
The first step of cellular entry for the human immunodeficiency virus type-1 (HIV-1) occurs through the binding of its envelope protein (Env) with the plasma membrane receptor CD4 and co-receptor CCR5 or CXCR4 on susceptible cells, primarily CD4+ T cells and macrophages. Although there is considerable knowledge of the molecular interactions between Env and host cell receptors that lead to successful fusion, the precise way in which HIV-1 receptors redistribute to sites of virus binding at the nanoscale remains unknown. Here, we quantitatively examine changes in the nanoscale organisation of CD4 on the surface of CD4+ T cells following HIV-1 binding. Using single-molecule super-resolution imaging, we show that CD4 molecules are distributed mostly as either individual molecules or small clusters of up to 4 molecules. Following virus binding, we observe a local 3-to-10-fold increase in cluster diameter and molecule number for virus-associated CD4 clusters. Moreover, a similar but smaller magnitude reorganisation of CD4 was also observed with recombinant gp120. For one of the first times, our results quantify the nanoscale CD4 reorganisation triggered by HIV-1 on host CD4+ T cells. Our quantitative approach provides a robust methodology for characterising the nanoscale organisation of plasma membrane receptors in general with the potential to link spatial organisation to function.
Collapse
Affiliation(s)
- Yue Yuan
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (Y.Y.); (C.A.J.); (P.M.P.); (S.P.L.)
| | - Caron A. Jacobs
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (Y.Y.); (C.A.J.); (P.M.P.); (S.P.L.)
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town 7925, South Africa
| | | | - Pedro M. Pereira
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (Y.Y.); (C.A.J.); (P.M.P.); (S.P.L.)
- Bacterial Cell Biology, MOSTMICRO, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Scott P. Lawrence
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (Y.Y.); (C.A.J.); (P.M.P.); (S.P.L.)
| | - Romain F. Laine
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (Y.Y.); (C.A.J.); (P.M.P.); (S.P.L.)
- The Francis Crick Institute, London NW1 1AT, UK
| | - Mark Marsh
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (Y.Y.); (C.A.J.); (P.M.P.); (S.P.L.)
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (Y.Y.); (C.A.J.); (P.M.P.); (S.P.L.)
- The Francis Crick Institute, London NW1 1AT, UK
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| |
Collapse
|
412
|
Gobeil SMC, Janowska K, McDowell S, Mansouri K, Parks R, Manne K, Stalls V, Kopp MF, Henderson R, Edwards RJ, Haynes BF, Acharya P. D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Cell Rep 2021; 34:108630. [PMID: 33417835 PMCID: PMC7762703 DOI: 10.1016/j.celrep.2020.108630] [Citation(s) in RCA: 213] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/12/2020] [Accepted: 12/18/2020] [Indexed: 12/29/2022] Open
Abstract
The severe acute respiratory coronavirus 2 (SARS-CoV-2) spike (S) protein is the target of vaccine design efforts to end the coronavirus disease 2019 (COVID-19) pandemic. Despite a low mutation rate, isolates with the D614G substitution in the S protein appeared early during the pandemic and are now the dominant form worldwide. Here, we explore S conformational changes and the effects of the D614G mutation on a soluble S ectodomain construct. Cryoelectron microscopy (cryo-EM) structures reveal altered receptor binding domain (RBD) disposition; antigenicity and proteolysis experiments reveal structural changes and enhanced furin cleavage efficiency of the G614 variant. Furthermore, furin cleavage alters the up/down ratio of the RBDs in the G614 S ectodomain, demonstrating an allosteric effect on RBD positioning triggered by changes in the SD2 region, which harbors residue 614 and the furin cleavage site. Our results elucidate SARS-CoV-2 S conformational landscape and allostery and have implications for vaccine design.
Collapse
Affiliation(s)
| | | | | | | | - Robert Parks
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Kartik Manne
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | - Megan F Kopp
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Rory Henderson
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, 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
| | - 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
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham NC 27710, USA.
| |
Collapse
|
413
|
Sauer MM, Tortorici MA, Park YJ, Walls AC, Homad L, Acton O, Bowen J, Wang C, Xiong X, de van der Schueren W, Quispe J, Hoffstrom BG, Bosch BJ, McGuire AT, Veesler D. Structural basis for broad coronavirus neutralization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.12.29.424482. [PMID: 33398277 PMCID: PMC7781312 DOI: 10.1101/2020.12.29.424482] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Three highly pathogenic β-coronaviruses crossed the animal-to-human species barrier in the past two decades: SARS-CoV, MERS-CoV and SARS-CoV-2. SARS-CoV-2 has infected more than 64 million people worldwide, claimed over 1.4 million lives and is responsible for the ongoing COVID-19 pandemic. We isolated a monoclonal antibody, termed B6, cross-reacting with eight β-coronavirus spike glycoproteins, including all five human-infecting β-coronaviruses, and broadly inhibiting entry of pseudotyped viruses from two coronavirus lineages. Cryo-electron microscopy and X-ray crystallography characterization reveal that B6 binds to a conserved cryptic epitope located in the fusion machinery and indicate that antibody binding sterically interferes with spike conformational changes leading to membrane fusion. Our data provide a structural framework explaining B6 cross-reactivity with β-coronaviruses from three lineages along with proof-of-concept for antibody-mediated broad coronavirus neutralization elicited through vaccination. This study unveils an unexpected target for next-generation structure-guided design of a pan-coronavirus vaccine.
Collapse
Affiliation(s)
- Maximilian M. Sauer
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - M. Alexandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institut Pasteur, Unité de Virologie Structurale, Paris, France; CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Leah Homad
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Oliver Acton
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - John Bowen
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Chunyan Wang
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Xiaoli Xiong
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | | | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Benjamin G. Hoffstrom
- Antibody Technology Resource, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Berend-Jan Bosch
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Andrew T. McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| |
Collapse
|
414
|
Wilson IA, Stanfield RL. 50 Years of structural immunology. J Biol Chem 2021; 296:100745. [PMID: 33957119 PMCID: PMC8163984 DOI: 10.1016/j.jbc.2021.100745] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/24/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
Fifty years ago, the first landmark structures of antibodies heralded the dawn of structural immunology. Momentum then started to build toward understanding how antibodies could recognize the vast universe of potential antigens and how antibody-combining sites could be tailored to engage antigens with high specificity and affinity through recombination of germline genes (V, D, J) and somatic mutation. Equivalent groundbreaking structures in the cellular immune system appeared some 15 to 20 years later and illustrated how processed protein antigens in the form of peptides are presented by MHC molecules to T cell receptors. Structures of antigen receptors in the innate immune system then explained their inherent specificity for particular microbial antigens including lipids, carbohydrates, nucleic acids, small molecules, and specific proteins. These two sides of the immune system act immediately (innate) to particular microbial antigens or evolve (adaptive) to attain high specificity and affinity to a much wider range of antigens. We also include examples of other key receptors in the immune system (cytokine receptors) that regulate immunity and inflammation. Furthermore, these antigen receptors use a limited set of protein folds to accomplish their various immunological roles. The other main players are the antigens themselves. We focus on surface glycoproteins in enveloped viruses including SARS-CoV-2 that enable entry and egress into host cells and are targets for the antibody response. This review covers what we have learned over the past half century about the structural basis of the immune response to microbial pathogens and how that information can be utilized to design vaccines and therapeutics.
Collapse
MESH Headings
- Adaptive Immunity
- Allergy and Immunology/history
- Animals
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibody Specificity
- Antigen Presentation
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- COVID-19/immunology
- COVID-19/virology
- Crystallography/history
- Crystallography/methods
- History, 20th Century
- History, 21st Century
- Humans
- Immunity, Innate
- Protein Folding
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Cytokine/chemistry
- Receptors, Cytokine/genetics
- Receptors, Cytokine/immunology
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- V(D)J Recombination
Collapse
Affiliation(s)
- Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| |
Collapse
|
415
|
Srivastava S, Banu S, Singh P, Sowpati DT, Mishra RK. SARS-CoV-2 genomics: An Indian perspective on sequencing viral variants. J Biosci 2021; 46:22. [PMID: 33737495 PMCID: PMC7895735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 01/25/2021] [Indexed: 04/01/2024]
Abstract
Since its emergence as a pneumonia-like outbreak in the Chinese city of Wuhan in late 2019, the novel coronavirus disease COVID-19 has spread widely to become a global pandemic. The first case of COVID-19 in India was reported on 30 January 2020 and since then it has affected more than ten million people and resulted in around 150,000 deaths in the country. Over time, the viral genome has accumulated mutations as it passes through its human hosts, a common evolutionary mechanism found in all microorganisms. This has implications for disease surveillance and management, vaccines and therapeutics, and the emergence of reinfections. Sequencing the viral genome can help monitor these changes and provides an extraordinary opportunity to understand the genetic epidemiology and evolution of the virus as well as tracking its spread in a population. Here we review the past year in the context of the phylogenetic analysis of variants isolated over the course of the pandemic in India and highlight the importance of continued sequencing-based surveillance in the country.
Collapse
Affiliation(s)
- Surabhi Srivastava
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
| | - Sofia Banu
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
| | - Priya Singh
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
| | - Divya Tej Sowpati
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
| | - Rakesh K. Mishra
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
| |
Collapse
|
416
|
Mukherjee R, Satardekar R. Why are some coronavirus variants more infectious? J Biosci 2021; 46:101. [PMID: 34785628 PMCID: PMC8594289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/28/2021] [Indexed: 09/22/2023]
Abstract
Since the start of the pandemic, SARS-CoV-2 has infected almost 200 million human hosts and is set to encounter and gain entry in many more in the coming months. As the coronavirus flourish, the evolutionary pressure selects those variants that can complete the infection cycle faster and reproduce in large numbers compared to others. This increase in infectivity and transmissibility coupled with the immune response from high viral load may cause moderate to severe disease. Whether this leads to enhanced virulence in the prevalent Alpha and Delta variants is still not clear. This review describes the different types of SARS-CoV-2 variants that are now prevalent, their emergence, the mutations responsible for their growth advantages, and how they affect vaccine efficacy and increase chances of reinfection. Finally, we have also summarized the efforts made to recognize and predict the mutations, which can cause immune escape and track their emergence through impactful genomic surveillance.
Collapse
MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/immunology
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Binding Sites
- COVID-19/epidemiology
- COVID-19/pathology
- COVID-19/transmission
- COVID-19/virology
- COVID-19 Vaccines
- Genome, Viral
- Humans
- Immune Evasion/genetics
- Models, Molecular
- Mutation
- Phylogeny
- Protein Binding
- Protein Interaction Domains and Motifs
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/immunology
- SARS-CoV-2/classification
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Serine Endopeptidases/chemistry
- Serine Endopeptidases/genetics
- Serine Endopeptidases/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Virulence
Collapse
Affiliation(s)
- Raju Mukherjee
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
| | - Rohit Satardekar
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
| |
Collapse
|
417
|
Ngo ST, Nguyen TH, Pham DH, Tung NT, Nam PC. Thermodynamics and kinetics in antibody resistance of the 501Y.V2 SARS-CoV-2 variant. RSC Adv 2021; 11:33438-33446. [PMID: 35497518 PMCID: PMC9042284 DOI: 10.1039/d1ra04134g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/06/2021] [Indexed: 02/01/2023] Open
Abstract
Understanding the thermodynamics and kinetics of the binding process of an antibody to the SARS-CoV-2 receptor-binding domain (RBD) of the spike protein is very important for the development of COVID-19 vaccines. In particular, it is essential to understand how the binding mechanism may change under the effects of RBD mutations. In this context, we have demonstrated that the South African variant (B1.351 or 501Y.V2) can resist the neutralizing antibody (NAb). Three substitutions in the RBD including K417N, E484K, and N501Y alter the free energy landscape, binding pose, binding free energy, binding kinetics, hydrogen bonding, nonbonded contacts, and unbinding pathway of RBD + NAb complexes. The low binding affinity of NAb to 501Y.V2 RBD confirms the antibody resistance of the South African variant. Moreover, the fragment of NAb + RBD can be used as an affordable model to investigate changes in the binding process between the mutated RBD and antibodies. Increasing FEL minima of 501Y.V2 RBD + antibody in comparison with the WT RBD systems imply that the complex 501Y.V2 RBD + antibody is more unstable than the WT one.![]()
Collapse
Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Duc-Hung Pham
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati 45229, OH, USA
| | - Nguyen Thanh Tung
- Institute of Materials Science, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Pham Cam Nam
- Department of Chemical Engineering, The University of Da Nang, University of Science and Technology, Da Nang City, Vietnam
| |
Collapse
|
418
|
Updated insight into COVID-19 disease and health management to combat the pandemic. ENVIRONMENTAL AND HEALTH MANAGEMENT OF NOVEL CORONAVIRUS DISEASE (COVID-19 ) 2021. [PMCID: PMC8237642 DOI: 10.1016/b978-0-323-85780-2.00017-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19 disease in humans and is the responsible viral agent for the currently ongoing pandemic. Early cases of COVID-19 were reported from Wuhan, Hubei province of China, the likely birthplace of this outbreak. Currently, over 92 million people in the globe are actively battling this virus, and over 2 million individuals have already succumbed to the disease. The high human-to-human transmission capacity of the virus is among the primary causes for such a rapid global spread of COVID-19. In humans, it causes acute to severe respiratory distress in the form of pneumonia. The presentation of clinical features of the disease ranges from mild in healthy adults to severe among individuals with weakened or immunocompromised immune systems and the elderly. Thus, increasing patient cases of COVID-19 warrants a growing demand for medical attention that is eventually overburdening our health care systems. Rapid detection of COVID-19 in suspected individuals and isolation are among the crucial intervention norms in health management strategies to control the COVID-19 pandemic, in addition to strict observance of public hygienic practices such as reduced public gathering, use of facial masks, and practicing of social distancing. This chapter provides an overview of the epidemiology of COVID-19 and the current classical health management strategies and issues to tackle this pandemic. It particularly highlights the role of standard as well as novel biomolecular diagnostic techniques as a tool for successful implementation of such public safety measures issued by medical policy makers and the governing bodies.
Collapse
|
419
|
Abstract
Spurred into action by the COVID-19 pandemic, the global scientific community has, in a short of period of time, made astonishing progress in understanding and combating COVID-19. Given the known human protein machinery for (a) SARS-CoV-2 entry, (b) the host innate immune response, and (c) virus-host interactions (protein-protein and RNA-protein), the potential effects of human genetic variation in this machinery, which may contribute to clinical differences in SARS-CoV-2 pathogenesis and help determine individual risk for COVID-19 infection, are explored. The Genome Aggregation Database (gnomAD) was used to show that several rare germline exome variants of proteins in these pathways occur in the human population, suggesting that carriers of these rare variants (especially for proteins of innate immunity pathways) are at risk for severe symptoms (like the severe symptoms in patients who are known to be rare variant carriers), whereas carriers of other variants could have a protective advantage against infection. The occurrence of genetic variation is thus expected to motivate the experimental probing of natural variants to understand the mechanistic differences in SARS-CoV-2 pathogenesis from one individual to another.
Collapse
Affiliation(s)
- Suvobrata Chakravarty
- Chemistry & Biochemistry, South
Dakota State University, Brookings, South Dakota 57007, United
States
- BioSNTR, Brookings, South
Dakota 57007, United States
| |
Collapse
|
420
|
Aguirre García MM, Mancilla-Galindo J, Paredes-Paredes M, Tiburcio ÁZ, Ávila-Vanzzini N. Mechanisms of infection by SARS-CoV-2, inflammation and potential links with the microbiome. Future Virol 2021. [PMCID: PMC7876557 DOI: 10.2217/fvl-2020-0310] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The pandemic SARS coronavirus 2 utilizes efficient mechanisms to establish infection and evade the immune system. Established infection leads to severe inflammation in susceptible patients, the main hallmark of progression to severe coronavirus disease (COVID-19). Knowledge of the mechanisms of disease has expanded rapidly. As inflammation emerges as the central pathophysiological feature in COVID-19, elucidating how the immune system, lungs and gut communicate and interact with microbial components of the ecological niches that conform the human microbiome will shed light on how inflammation and disease progression are promoted. Studying the microbiome in COVID-19 could allow scientists to identify novel approaches to prevent severe inflammation by targeting components of the human microbiome. Innovation in the aforementioned is needed to combat this pandemic.
Collapse
Affiliation(s)
- María Magdalena Aguirre García
- División de Investigación, Facultad de Medicina, Unidad de Investigación UNAM-INC, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano No. 1, Col. Sección XVI, Tlalpan C.P. 14080, Ciudad de México, Mexico
| | - Javier Mancilla-Galindo
- División de Investigación, Facultad de Medicina, Unidad de Investigación UNAM-INC, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano No. 1, Col. Sección XVI, Tlalpan C.P. 14080, Ciudad de México, Mexico
| | - Mercedes Paredes-Paredes
- División de Investigación, Facultad de Medicina, Unidad de Investigación UNAM-INC, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano No. 1, Col. Sección XVI, Tlalpan C.P. 14080, Ciudad de México, Mexico
| | - Álvaro Zamudio Tiburcio
- Departamento de Gastroenterología, Unidad de Trasplante de Microbiota Intestinal, Especialidades Médicas Nápoles, Oficina 12, Pennsylvania No. 209 Esq. Kansas, Col. Nápoles, Benito Juárez C.P 03810, Ciudad de México, Mexico
| | - Nydia Ávila-Vanzzini
- Departamento de Consulta Externa, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano No. 1, Col. Sección XVI, Tlalpan C.P. 14080, Ciudad de México, Mexico
| |
Collapse
|
421
|
Akisawa K, Hatada R, Okuwaki K, Mochizuki Y, Fukuzawa K, Komeiji Y, Tanaka S. Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations. RSC Adv 2021; 11:3272-3279. [PMID: 35424290 PMCID: PMC8694004 DOI: 10.1039/d0ra09555a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022] Open
Abstract
At the stage of SARS-CoV-2 infection in human cells, the spike protein consisting of three chains, A, B, and C, with a total of 3300 residues plays a key role, and thus its structural properties and the binding nature of receptor proteins to host human cells or neutralizing antibodies has attracted considerable interest. Here, we report on interaction analyses of the spike protein in both closed (PDB-ID: 6VXX) and open (6VYB) structures, based on large-scale fragment molecular orbital (FMO) calculations at the level of up to the fourth-order Møller–Plesset perturbation with singles, doubles, and quadruples (MP4(SDQ)). Inter-chain interaction energies were evaluated for both structures, and a mutual comparison indicated considerable losses of stabilization energies in the open structure, especially in the receptor binding domain (RBD) of chain-B. The role of charged residues in inter-chain interactions was illuminated as well. By two separate calculations for the RBD complexes with angiotensin-converting enzyme 2 (ACE2) (6M0J) and B38 Fab antibody (7BZ5), it was found that the binding with ACE2 or antibody partially compensated for this stabilization loss of RBD. Visualized IFIE results seen from chain-B of spike protein.![]()
Collapse
Affiliation(s)
- Kazuki Akisawa
- Department of Chemistry and Research Center for Smart Molecules
- Faculty of Science
- Rikkyo University
- Toshima-ku
- Japan
| | - Ryo Hatada
- Department of Chemistry and Research Center for Smart Molecules
- Faculty of Science
- Rikkyo University
- Toshima-ku
- Japan
| | - Koji Okuwaki
- Department of Chemistry and Research Center for Smart Molecules
- Faculty of Science
- Rikkyo University
- Toshima-ku
- Japan
| | - Yuji Mochizuki
- Department of Chemistry and Research Center for Smart Molecules
- Faculty of Science
- Rikkyo University
- Toshima-ku
- Japan
| | - Kaori Fukuzawa
- Institute of Industrial Science
- The University of Tokyo
- Meguro-ku
- Japan
- School of Pharmacy and Pharmaceutical Sciences
| | - Yuto Komeiji
- Health and Medical Research Institute
- AIST
- Tsukuba
- Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics
- Department of Computational Science
- Kobe University
- Kobe 657-8501
- Japan
| |
Collapse
|
422
|
Abstract
In this issue of Cell Host & Microbe, Lu et al. utilize single-molecule FRET to reveal the conformation dynamics of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein, showing transitions from a closed ground state to the open receptor-accessible conformation via an on-path intermediate. These insights into spike conformations will facilitate rational immunogen design.
Collapse
Affiliation(s)
- Vitor Hugo B Serrão
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Jeffrey E Lee
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
| |
Collapse
|
423
|
Affiliation(s)
- Adrian J Mulholland
- School of Chemistry, Cantock's Close, Bristol BS8 1TS, United Kingdom of Great Britain and Northern Ireland
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, 3234 Urey Hall, no. 0340 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| |
Collapse
|
424
|
Bernard I, Limonta D, Mahal LK, Hobman TC. Endothelium Infection and Dysregulation by SARS-CoV-2: Evidence and Caveats in COVID-19. Viruses 2020; 13:E29. [PMID: 33375371 PMCID: PMC7823949 DOI: 10.3390/v13010029] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/16/2020] [Accepted: 12/25/2020] [Indexed: 02/06/2023] Open
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by the acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) poses a persistent threat to global public health. Although primarily a respiratory illness, extrapulmonary manifestations of COVID-19 include gastrointestinal, cardiovascular, renal and neurological diseases. Recent studies suggest that dysfunction of the endothelium during COVID-19 may exacerbate these deleterious events by inciting inflammatory and microvascular thrombotic processes. Although controversial, there is evidence that SARS-CoV-2 may infect endothelial cells by binding to the angiotensin-converting enzyme 2 (ACE2) cellular receptor using the viral Spike protein. In this review, we explore current insights into the relationship between SARS-CoV-2 infection, endothelial dysfunction due to ACE2 downregulation, and deleterious pulmonary and extra-pulmonary immunothrombotic complications in severe COVID-19. We also discuss preclinical and clinical development of therapeutic agents targeting SARS-CoV-2-mediated endothelial dysfunction. Finally, we present evidence of SARS-CoV-2 replication in primary human lung and cardiac microvascular endothelial cells. Accordingly, in striving to understand the parameters that lead to severe disease in COVID-19 patients, it is important to consider how direct infection of endothelial cells by SARS-CoV-2 may contribute to this process.
Collapse
Affiliation(s)
- Isabelle Bernard
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada;
| | - Daniel Limonta
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada;
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Lara K. Mahal
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada;
| | - Tom C. Hobman
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada;
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada;
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Women & Children’s Health Research Institute, University of Alberta, Edmonton, AB T6G 1C9, Canada
| |
Collapse
|
425
|
Zuo YY, Uspal WE, Wei T. Airborne Transmission of COVID-19: Aerosol Dispersion, Lung Deposition, and Virus-Receptor Interactions. ACS NANO 2020; 14:16502-16524. [PMID: 33236896 PMCID: PMC7724984 DOI: 10.1021/acsnano.0c08484] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 11/19/2020] [Indexed: 05/02/2023]
Abstract
Coronavirus disease 2019 (COVID-19), due to infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is now causing a global pandemic. Aerosol transmission of COVID-19, although plausible, has not been confirmed by the World Health Organization (WHO) as a general transmission route. Considering the rapid spread of SARS-CoV-2, especially nosocomial outbreaks and other superspreading events, there is an urgent need to study the possibility of airborne transmission and its impact on the lung, the primary body organ attacked by the virus. Here, we review the complete pathway of airborne transmission of SARS-CoV-2 from aerosol dispersion in air to subsequent biological uptake after inhalation. In particular, we first review the aerodynamic and colloidal mechanisms by which aerosols disperse and transmit in air and deposit onto surfaces. We then review the fundamental mechanisms that govern regional deposition of micro- and nanoparticles in the lung. Focus is given to biophysical interactions between particles and the pulmonary surfactant film, the initial alveolar-capillary barrier and first-line host defense system against inhaled particles and pathogens. Finally, we summarize the current understanding about the structural dynamics of the SARS-CoV-2 spike protein and its interactions with receptors at the atomistic and molecular scales, primarily as revealed by molecular dynamics simulations. This review provides urgent and multidisciplinary knowledge toward understanding the airborne transmission of SARS-CoV-2 and its health impact on the respiratory system.
Collapse
Affiliation(s)
- Yi Y. Zuo
- Department of Mechanical Engineering,
University of Hawaii at Manoa,
Honolulu, Hawaii 96822, United States
- Department of Pediatrics, John A.
Burns School of Medicine, University of
Hawaii, Honolulu, Hawaii 96826, United
States
| | - William E. Uspal
- Department of Mechanical Engineering,
University of Hawaii at Manoa,
Honolulu, Hawaii 96822, United States
| | - Tao Wei
- Chemical Engineering Department,
Howard University, Washington, DC
20059, United States
| |
Collapse
|
426
|
Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbølle CB, Puchades C, Azumaya CM, Kratochvil HT, Zimanyi M, Deshpande I, Liang J, Dickinson S, Nguyen HC, Chio CM, Merz GE, Thompson MC, Diwanji D, Schaefer K, Anand AA, Dobzinski N, Zha BS, Simoneau CR, Leon K, White KM, Chio US, Gupta M, Jin M, Li F, Liu Y, Zhang K, Bulkley D, Sun M, Smith AM, Rizo AN, Moss F, Brilot AF, Pourmal S, Trenker R, Pospiech T, Gupta S, Barsi-Rhyne B, Belyy V, Barile-Hill AW, Nock S, Liu Y, Krogan NJ, Ralston CY, Swaney DL, García-Sastre A, Ott M, Vignuzzi M, Walter P, Manglik A. An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike. Science 2020; 370:1473-1479. [PMID: 33154106 PMCID: PMC7857409 DOI: 10.1126/science.abe3255] [Citation(s) in RCA: 284] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 10/30/2020] [Indexed: 01/12/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus enters host cells via an interaction between its Spike protein and the host cell receptor angiotensin-converting enzyme 2 (ACE2). By screening a yeast surface-displayed library of synthetic nanobody sequences, we developed nanobodies that disrupt the interaction between Spike and ACE2. Cryo-electron microscopy (cryo-EM) revealed that one nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains locked into their inaccessible down state, incapable of binding ACE2. Affinity maturation and structure-guided design of multivalency yielded a trivalent nanobody, mNb6-tri, with femtomolar affinity for Spike and picomolar neutralization of SARS-CoV-2 infection. mNb6-tri retains function after aerosolization, lyophilization, and heat treatment, which enables aerosol-mediated delivery of this potent neutralizer directly to the airway epithelia.
Collapse
Affiliation(s)
- Michael Schoof
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Corresponding author. (M.S.); (P.W.); (A.M.)
| | - Bryan Faust
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Reuben A. Saunders
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA
| | - Smriti Sangwan
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Veronica Rezelj
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris Cedex 15, France
| | - Nick Hoppe
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Morgane Boone
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Christian B. Billesbølle
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Cristina Puchades
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Caleigh M. Azumaya
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Huong T. Kratochvil
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Marcell Zimanyi
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Ishan Deshpande
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Jiahao Liang
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Sasha Dickinson
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Henry C. Nguyen
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Cynthia M. Chio
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Gregory E. Merz
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Michael C. Thompson
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Devan Diwanji
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Kaitlin Schaefer
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Aditya A. Anand
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Niv Dobzinski
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Beth Shoshana Zha
- Department of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Camille R. Simoneau
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kristoffer Leon
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kris M. White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Un Seng Chio
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Meghna Gupta
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Mingliang Jin
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Fei Li
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Yanxin Liu
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Kaihua Zhang
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - David Bulkley
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Ming Sun
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Amber M. Smith
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Alexandrea N. Rizo
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Frank Moss
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Axel F. Brilot
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Sergei Pourmal
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Raphael Trenker
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Thomas Pospiech
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA
| | - Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging and the Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Benjamin Barsi-Rhyne
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Vladislav Belyy
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | | | - Silke Nock
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Yuwei Liu
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Nevan J. Krogan
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA
| | - Corie Y. Ralston
- Molecular Biophysics and Integrated Bioimaging and the Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Danielle L. Swaney
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melanie Ott
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris Cedex 15, France
| | | | - Peter Walter
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Corresponding author. (M.S.); (P.W.); (A.M.)
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Anesthesia and Perioperative Care, University of California at San Francisco, San Francisco, CA, USA.,Corresponding author. (M.S.); (P.W.); (A.M.)
| |
Collapse
|
427
|
Mariano G, Farthing RJ, Lale-Farjat SLM, Bergeron JRC. Structural Characterization of SARS-CoV-2: Where We Are, and Where We Need to Be. Front Mol Biosci 2020; 7:605236. [PMID: 33392262 PMCID: PMC7773825 DOI: 10.3389/fmolb.2020.605236] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/22/2020] [Indexed: 01/18/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread in humans in almost every country, causing the disease COVID-19. Since the start of the COVID-19 pandemic, research efforts have been strongly directed towards obtaining a full understanding of the biology of the viral infection, in order to develop a vaccine and therapeutic approaches. In particular, structural studies have allowed to comprehend the molecular basis underlying the role of many of the SARS-CoV-2 proteins, and to make rapid progress towards treatment and preventive therapeutics. Despite the great advances that have been provided by these studies, many knowledge gaps on the biology and molecular basis of SARS-CoV-2 infection still remain. Filling these gaps will be the key to tackle this pandemic, through development of effective treatments and specific vaccination strategies.
Collapse
Affiliation(s)
- Giuseppina Mariano
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Rebecca J. Farthing
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | | | - Julien R. C. Bergeron
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| |
Collapse
|
428
|
Ng KW, Faulkner N, Cornish GH, Rosa A, Harvey R, Hussain S, Ulferts R, Earl C, Wrobel AG, Benton DJ, Roustan C, Bolland W, Thompson R, Agua-Doce A, Hobson P, Heaney J, Rickman H, Paraskevopoulou S, Houlihan CF, Thomson K, Sanchez E, Shin GY, Spyer MJ, Joshi D, O'Reilly N, Walker PA, Kjaer S, Riddell A, Moore C, Jebson BR, Wilkinson M, Marshall LR, Rosser EC, Radziszewska A, Peckham H, Ciurtin C, Wedderburn LR, Beale R, Swanton C, Gandhi S, Stockinger B, McCauley J, Gamblin SJ, McCoy LE, Cherepanov P, Nastouli E, Kassiotis G. Preexisting and de novo humoral immunity to SARS-CoV-2 in humans. Science 2020; 370:1339-1343. [PMID: 33159009 DOI: 10.1101/2020.05.14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/29/2020] [Indexed: 05/20/2023]
Abstract
Zoonotic introduction of novel coronaviruses may encounter preexisting immunity in humans. Using diverse assays for antibodies recognizing SARS-CoV-2 proteins, we detected preexisting humoral immunity. SARS-CoV-2 spike glycoprotein (S)-reactive antibodies were detectable using a flow cytometry-based method in SARS-CoV-2-uninfected individuals and were particularly prevalent in children and adolescents. They were predominantly of the immunoglobulin G (IgG) class and targeted the S2 subunit. By contrast, SARS-CoV-2 infection induced higher titers of SARS-CoV-2 S-reactive IgG antibodies targeting both the S1 and S2 subunits, and concomitant IgM and IgA antibodies, lasting throughout the observation period. SARS-CoV-2-uninfected donor sera exhibited specific neutralizing activity against SARS-CoV-2 and SARS-CoV-2 S pseudotypes. Distinguishing preexisting and de novo immunity will be critical for our understanding of susceptibility to and the natural course of SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Kevin W Ng
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Nikhil Faulkner
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | | | - Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Saira Hussain
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachel Ulferts
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Christopher Earl
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Donald J Benton
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Chloe Roustan
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - William Bolland
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachael Thompson
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Ana Agua-Doce
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Philip Hobson
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Judith Heaney
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Hannah Rickman
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | | | - Catherine F Houlihan
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK
| | - Kirsty Thomson
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Emilie Sanchez
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Gee Yen Shin
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Moira J Spyer
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
- Department of Population, Policy and Practice, Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Dhira Joshi
- Peptide Chemistry, The Francis Crick Institute, London NW1 1AT, UK
| | - Nicola O'Reilly
- Peptide Chemistry, The Francis Crick Institute, London NW1 1AT, UK
| | - Philip A Walker
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Svend Kjaer
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Andrew Riddell
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Catherine Moore
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Bethany R Jebson
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Meredyth Wilkinson
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Lucy R Marshall
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Elizabeth C Rosser
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Anna Radziszewska
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Hannah Peckham
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Coziana Ciurtin
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Lucy R Wedderburn
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Sonia Gandhi
- Neurodegeneration Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | | | - John McCauley
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Steve J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Laura E McCoy
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK.
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
| | - Eleni Nastouli
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK.
- Department of Population, Policy and Practice, Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK.
- Department of Medicine, Faculty of Medicine, Imperial College London, London W2 1PG, UK
| |
Collapse
|
429
|
Ng KW, Faulkner N, Cornish GH, Rosa A, Harvey R, Hussain S, Ulferts R, Earl C, Wrobel AG, Benton DJ, Roustan C, Bolland W, Thompson R, Agua-Doce A, Hobson P, Heaney J, Rickman H, Paraskevopoulou S, Houlihan CF, Thomson K, Sanchez E, Shin GY, Spyer MJ, Joshi D, O'Reilly N, Walker PA, Kjaer S, Riddell A, Moore C, Jebson BR, Wilkinson M, Marshall LR, Rosser EC, Radziszewska A, Peckham H, Ciurtin C, Wedderburn LR, Beale R, Swanton C, Gandhi S, Stockinger B, McCauley J, Gamblin SJ, McCoy LE, Cherepanov P, Nastouli E, Kassiotis G. Preexisting and de novo humoral immunity to SARS-CoV-2 in humans. Science 2020; 370:1339-1343. [PMID: 33159009 PMCID: PMC7857411 DOI: 10.1126/science.abe1107] [Citation(s) in RCA: 607] [Impact Index Per Article: 151.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022]
Abstract
Zoonotic introduction of novel coronaviruses may encounter preexisting immunity in humans. Using diverse assays for antibodies recognizing SARS-CoV-2 proteins, we detected preexisting humoral immunity. SARS-CoV-2 spike glycoprotein (S)-reactive antibodies were detectable using a flow cytometry-based method in SARS-CoV-2-uninfected individuals and were particularly prevalent in children and adolescents. They were predominantly of the immunoglobulin G (IgG) class and targeted the S2 subunit. By contrast, SARS-CoV-2 infection induced higher titers of SARS-CoV-2 S-reactive IgG antibodies targeting both the S1 and S2 subunits, and concomitant IgM and IgA antibodies, lasting throughout the observation period. SARS-CoV-2-uninfected donor sera exhibited specific neutralizing activity against SARS-CoV-2 and SARS-CoV-2 S pseudotypes. Distinguishing preexisting and de novo immunity will be critical for our understanding of susceptibility to and the natural course of SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Kevin W Ng
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Nikhil Faulkner
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | | | - Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Saira Hussain
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachel Ulferts
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Christopher Earl
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Donald J Benton
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Chloe Roustan
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - William Bolland
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachael Thompson
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Ana Agua-Doce
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Philip Hobson
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Judith Heaney
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Hannah Rickman
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | | | - Catherine F Houlihan
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK
| | - Kirsty Thomson
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Emilie Sanchez
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Gee Yen Shin
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Moira J Spyer
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
- Department of Population, Policy and Practice, Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Dhira Joshi
- Peptide Chemistry, The Francis Crick Institute, London NW1 1AT, UK
| | - Nicola O'Reilly
- Peptide Chemistry, The Francis Crick Institute, London NW1 1AT, UK
| | - Philip A Walker
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Svend Kjaer
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Andrew Riddell
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Catherine Moore
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Bethany R Jebson
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Meredyth Wilkinson
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Lucy R Marshall
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Elizabeth C Rosser
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Anna Radziszewska
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Hannah Peckham
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Coziana Ciurtin
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Lucy R Wedderburn
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Sonia Gandhi
- Neurodegeneration Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | | | - John McCauley
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Steve J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Laura E McCoy
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK.
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
| | - Eleni Nastouli
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK.
- Department of Population, Policy and Practice, Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK.
- Department of Medicine, Faculty of Medicine, Imperial College London, London W2 1PG, UK
| |
Collapse
|
430
|
Zhou T, Tsybovsky Y, Gorman J, Rapp M, Cerutti G, Chuang GY, Katsamba PS, Sampson JM, Schön A, Bimela J, Boyington JC, Nazzari A, Olia AS, Shi W, Sastry M, Stephens T, Stuckey J, Teng IT, Wang P, Wang S, Zhang B, Friesner RA, Ho DD, Mascola JR, Shapiro L, Kwong PD. Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains. Cell Host Microbe 2020; 28:867-879.e5. [PMID: 33271067 PMCID: PMC7670890 DOI: 10.1016/j.chom.2020.11.004] [Citation(s) in RCA: 250] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/20/2020] [Accepted: 11/09/2020] [Indexed: 01/21/2023]
Abstract
The SARS-CoV-2 spike employs mobile receptor-binding domains (RBDs) to engage the human ACE2 receptor and to facilitate virus entry, which can occur through low-pH-endosomal pathways. To understand how ACE2 binding and low pH affect spike conformation, we determined cryo-electron microscopy structures-at serological and endosomal pH-delineating spike recognition of up to three ACE2 molecules. RBDs freely adopted "up" conformations required for ACE2 interaction, primarily through RBD movement combined with smaller alterations in neighboring domains. In the absence of ACE2, single-RBD-up conformations dominated at pH 5.5, resolving into a solitary all-down conformation at lower pH. Notably, a pH-dependent refolding region (residues 824-858) at the spike-interdomain interface displayed dramatic structural rearrangements and mediated RBD positioning through coordinated movements of the entire trimer apex. These structures provide a foundation for understanding prefusion-spike mechanics governing endosomal entry; we suggest that the low pH all-down conformation potentially facilitates immune evasion from RBD-up binding antibody.
Collapse
Affiliation(s)
- Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Micah Rapp
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Gabriele Cerutti
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Phinikoula S Katsamba
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Jared M Sampson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Arne Schön
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jude Bimela
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Jeffrey C Boyington
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra Nazzari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mallika Sastry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jonathan Stuckey
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
431
|
Celik U, Celik K, Celik S, Abayli H, Sahna KC, Tonbak Ş, Toraman ZA, Oral A. Interpretation of SARS-CoV-2 behaviour on different substrates and denaturation of virions using ethanol: an atomic force microscopy study. RSC Adv 2020; 10:44079-44086. [PMID: 35517177 PMCID: PMC9058402 DOI: 10.1039/d0ra09083b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 12/01/2020] [Indexed: 01/18/2023] Open
Abstract
Coronavirus (SARS-CoV-2) is a respiratory infection virus that was first detected in Wuhan, China. The virus causes COVID-19 disease and the outbreak was recognised as a pandemic by the World Health Organization (WHO) in March 2020. SARS-CoV-2 virion was first imaged using cryo-electron microscopy by the Chinese Center for Disease Control and Prevention (CDC). Atomic Force Microscopy is a unique technique that can allow imaging of biomolecules under different conditions. In this work, we used Atomic Force Microscopy to characterize SARS-CoV-2 on tissue culture polystyrene (TCPS) and glass coverslip surfaces. We isolated SARS-CoV-2 and drop casted it on coverslip glass and tissue culture polystyrene surfaces. We analyzed height profiles, density, and aggregation behavior of the virion on glass and polystyrene surfaces. We observed the coffee ring effect on the drop casted samples and close packing of virions near the coffee rings on both surfaces with relatively higher virion distribution on the tissue culture polystyrene (TCPS) substrates. We compare virion agglomeration on the two types of surfaces. Finally, we applied ethanol disinfectant to virions on the surface to visualize the effect of ethanol and image the ultrastructure of SARS-CoV-2.
Collapse
Affiliation(s)
- Umit Celik
- School of Civil Aviation, Firat University Elazig 23119 Turkey
| | - Kubra Celik
- School of Civil Aviation, Firat University Elazig 23119 Turkey
| | - Suleyman Celik
- Sabanci University Nanotechnology and Applications Center (SUNUM), Sabanci University Tuzla Istanbul 34956 Turkey
| | - Hasan Abayli
- Department of Virology, Faculty of Veterinary Medicine, Firat University Elazig 23119 Turkey
| | - Kezban Can Sahna
- Department of Virology, Faculty of Veterinary Medicine, Firat University Elazig 23119 Turkey
| | - Şükrü Tonbak
- Department of Virology, Faculty of Veterinary Medicine, Firat University Elazig 23119 Turkey
| | - Zulal Asci Toraman
- Department of Microbiology, Faculty of Medicine, Firat University Elazig 23119 Turkey
| | - Ahmet Oral
- Department of Physics, Middle East Technical University Çankaya Ankara 06800 Turkey
- NanoMagnetics Instruments Ltd Ankara Turkey
| |
Collapse
|
432
|
Mugnai ML, Templeton C, Elber R, Thirumalai D. Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.11.30.405340. [PMID: 33299995 PMCID: PMC7724663 DOI: 10.1101/2020.11.30.405340] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Severe acute respiratory syndrome (SARS) and novel coronavirus disease (COVID-19) are caused by two closely related beta-coronaviruses, SARS-CoV and SARS-CoV-2, respectively. The envelopes surrounding these viruses are decorated with spike proteins, whose receptor binding domains (RBDs) initiate invasion by binding to the human angiotensin-converting enzyme 2 (ACE2). Subtle changes at the interface with ACE2 seem to be responsible for the enhanced affinity for the receptor of the SARS-CoV-2 RBD compared to SARS-CoV RBD. Here, we use Elastic Network Models (ENMs) to study the response of the viral RBDs and ACE2 upon dissassembly of the complexes. We identify a dominant detachment mode, in which the RBD rotates away from the surface of ACE2, while the receptor undergoes a conformational transition which stretches the active-site cleft. Using the Structural Perturbation Method, we determine the network of residues, referred to as the Allostery Wiring Diagram (AWD), which drives the large-scale motion activated by the detachment of the complex. The AWD for SARS-CoV and SARS-CoV-2 are remarkably similar, showing a network that spans the interface of the complex and reaches the active site of ACE2, thus establishing an allosteric connection between RBD binding and receptor catalytic function. Informed in part by the AWD, we used Molecular Dynamics simulations to probe the effect of interfacial mutations in which SARS-CoV-2 residues are replaced by their SARS-CoV counterparts. We focused on a conserved glycine (G502 in SARS-CoV-2, G488 in SARS-CoV) because it belongs to a region that initiates the dissociation of the complex along the dominant detachment mode, and is prominent in the AWD. Molecular Dynamics simulations of SARS-CoV-2 wild-type and G502P mutant show that the affinity for the human receptor of the mutant is drastically diminished. Our results suggest that in addition to residues that are in direct contact with the interface those involved in long range allosteric communication are also a determinant of the stability of the RBD-ACE2 complex.
Collapse
Affiliation(s)
- Mauro L Mugnai
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
| | - Clark Templeton
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ron Elber
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
- Institute for Computational Engineering and Science, The University of Texas at Austin, Austin, TX 78712
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
| |
Collapse
|
433
|
Moreira RA, Guzman HV, Boopathi S, Baker JL, Poma AB. Characterization of Structural and Energetic Differences between Conformations of the SARS-CoV-2 Spike Protein. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E5362. [PMID: 33255977 PMCID: PMC7730245 DOI: 10.3390/ma13235362] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 01/27/2023]
Abstract
The novel coronavirus disease 2019 (COVID-19) pandemic has disrupted modern societies and their economies. The resurgence in COVID-19 cases as part of the second wave is observed across Europe and the Americas. The scientific response has enabled a complete structural characterization of the Severe Acute Respiratory Syndrome-novel Coronavirus 2 (SARS-CoV-2). Among the most relevant proteins required by the novel coronavirus to facilitate the cell entry mechanism is the spike protein. This protein possesses a receptor-binding domain (RBD) that binds the cellular angiotensin-converting enzyme 2 (ACE2) and then triggers the fusion of viral and host cell membranes. In this regard, a comprehensive characterization of the structural stability of the spike protein is a crucial step to find new therapeutics to interrupt the process of recognition. On the other hand, it has been suggested that the participation of more than one RBD is a possible mechanism to enhance cell entry. Here, we discuss the protein structural stability based on the computational determination of the dynamic contact map and the energetic difference of the spike protein conformations via the mapping of the hydration free energy by the Poisson-Boltzmann method. We expect our result to foster the discussion of the number of RBD involved during recognition and the repurposing of new drugs to disable the recognition by discovering new hotspots for drug targets apart from the flexible loop in the RBD that binds the ACE2.
Collapse
Affiliation(s)
- Rodrigo A. Moreira
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland;
| | - Horacio V. Guzman
- Department of Theoretical Physics, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia;
| | - Subramanian Boopathi
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico;
| | - Joseph L. Baker
- Department of Chemistry, The College of New Jersey, 2000 Pennington Road, Ewing, NJ 08628, USA;
| | - Adolfo B. Poma
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland;
| |
Collapse
|
434
|
Casalino L, Dommer A, Gaieb Z, Barros EP, Sztain T, Ahn SH, Trifan A, Brace A, Bogetti A, Ma H, Lee H, Turilli M, Khalid S, Chong L, Simmerling C, Hardy DJ, Maia JDC, Phillips JC, Kurth T, Stern A, Huang L, McCalpin J, Tatineni M, Gibbs T, Stone JE, Jha S, Ramanathan A, Amaro RE. AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.11.19.390187. [PMID: 33236007 PMCID: PMC7685317 DOI: 10.1101/2020.11.19.390187] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spike's full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Anda Trifan
- Argonne National Lab
- University of Illinois at Urbana-Champaign
| | | | | | | | - Hyungro Lee
- Rutgers University & Brookhaven National Lab
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
435
|
Klein S, Cortese M, Winter SL, Wachsmuth-Melm M, Neufeldt CJ, Cerikan B, Stanifer ML, Boulant S, Bartenschlager R, Chlanda P. SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography. Nat Commun 2020; 11:5885. [PMID: 33208793 PMCID: PMC7676268 DOI: 10.1038/s41467-020-19619-7] [Citation(s) in RCA: 454] [Impact Index Per Article: 113.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/23/2020] [Indexed: 01/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID19 pandemic, is a highly pathogenic β-coronavirus. As other coronaviruses, SARS-CoV-2 is enveloped, replicates in the cytoplasm and assembles at intracellular membranes. Here, we structurally characterize the viral replication compartment and report critical insights into the budding mechanism of the virus, and the structure of extracellular virions close to their native state by in situ cryo-electron tomography and subtomogram averaging. We directly visualize RNA filaments inside the double membrane vesicles, compartments associated with viral replication. The RNA filaments show a diameter consistent with double-stranded RNA and frequent branching likely representing RNA secondary structures. We report that assembled S trimers in lumenal cisternae do not alone induce membrane bending but laterally reorganize on the envelope during virion assembly. The viral ribonucleoprotein complexes (vRNPs) are accumulated at the curved membrane characteristic for budding sites suggesting that vRNP recruitment is enhanced by membrane curvature. Subtomogram averaging shows that vRNPs are distinct cylindrical assemblies. We propose that the genome is packaged around multiple separate vRNP complexes, thereby allowing incorporation of the unusually large coronavirus genome into the virion while maintaining high steric flexibility between the vRNPs.
Collapse
Affiliation(s)
- Steffen Klein
- Schaller Research Groups, Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany.,Research Group "Membrane Biology of Viral Infection," Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany
| | - Mirko Cortese
- Department of Infectious Diseases-Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Sophie L Winter
- Schaller Research Groups, Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany.,Research Group "Membrane Biology of Viral Infection," Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany
| | - Moritz Wachsmuth-Melm
- Schaller Research Groups, Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany.,Research Group "Membrane Biology of Viral Infection," Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany
| | - Christopher J Neufeldt
- Department of Infectious Diseases-Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Berati Cerikan
- Department of Infectious Diseases-Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Megan L Stanifer
- Department of Infectious Diseases-Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Steeve Boulant
- Research Group "Host/Pathogen Interactions at Intestinal Epithelial Surfaces," Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases-Molecular Virology, Heidelberg University, Heidelberg, Germany. .,Division Virus-Associated Carcinogenesis, German Cancer Research Center, Heidelberg, Germany. .,German Center for Infection Research (DZIF), (Heidelberg Partner Site), Heidelberg, Germany.
| | - Petr Chlanda
- Schaller Research Groups, Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany. .,Research Group "Membrane Biology of Viral Infection," Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany.
| |
Collapse
|
436
|
Barros EP, Casalino L, Gaieb Z, Dommer AC, Wang Y, Fallon L, Raguette L, Belfon K, Simmerling C, Amaro RE. The flexibility of ACE2 in the context of SARS-CoV-2 infection. Biophys J 2020; 120:1072-1084. [PMID: 33189680 PMCID: PMC7661960 DOI: 10.1016/j.bpj.2020.10.036] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/22/2020] [Accepted: 10/27/2020] [Indexed: 12/13/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has swept over the world in the past months, causing significant loss of life and consequences to human health. Although numerous drug and vaccine development efforts are underway, there are many outstanding questions on the mechanism of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral association to angiotensin-converting enzyme 2 (ACE2), its main host receptor, and host cell entry. Structural and biophysical studies indicate some degree of flexibility in the viral extracellular spike glycoprotein and at the receptor-binding domain (RBD)-receptor interface, suggesting a role in infection. Here, we perform explicitly solvated, all-atom, molecular dynamics simulations of the glycosylated, full-length, membrane-bound ACE2 receptor in both an apo and spike RBD-bound state to probe the intrinsic dynamics of the ACE2 receptor in the context of the cell surface. A large degree of fluctuation in the full-length structure is observed, indicating hinge bending motions at the linker region connecting the head to the transmembrane helix while still not disrupting the ACE2 homodimer or ACE2-RBD interfaces. This flexibility translates into an ensemble of ACE2 homodimer conformations that could sterically accommodate binding of the spike trimer to more than one ACE2 homodimer and suggests a mechanical contribution of the host receptor toward the large spike conformational changes required for cell fusion. This work presents further structural and functional insights into the role of ACE2 in viral infection that can potentially be exploited for the rational design of effective SARS-CoV-2 therapeutics.
Collapse
Affiliation(s)
- Emilia P Barros
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Zied Gaieb
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Abigail C Dommer
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Yuzhang Wang
- Department of Chemistry, Stony Brook University, Stony Brook, New York
| | - Lucy Fallon
- Department of Chemistry, Stony Brook University, Stony Brook, New York
| | - Lauren Raguette
- Department of Chemistry, Stony Brook University, Stony Brook, New York
| | - Kellon Belfon
- Department of Chemistry, Stony Brook University, Stony Brook, New York
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, New York; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California.
| |
Collapse
|
437
|
Piccoli L, Park YJ, Tortorici MA, Czudnochowski N, Walls AC, Beltramello M, Silacci-Fregni C, Pinto D, Rosen LE, Bowen JE, Acton OJ, Jaconi S, Guarino B, Minola A, Zatta F, Sprugasci N, Bassi J, Peter A, De Marco A, Nix JC, Mele F, Jovic S, Rodriguez BF, Gupta SV, Jin F, Piumatti G, Lo Presti G, Pellanda AF, Biggiogero M, Tarkowski M, Pizzuto MS, Cameroni E, Havenar-Daughton C, Smithey M, Hong D, Lepori V, Albanese E, Ceschi A, Bernasconi E, Elzi L, Ferrari P, Garzoni C, Riva A, Snell G, Sallusto F, Fink K, Virgin HW, Lanzavecchia A, Corti D, Veesler D. Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology. Cell 2020; 183:1024-1042.e21. [PMID: 32991844 PMCID: PMC7494283 DOI: 10.1016/j.cell.2020.09.037] [Citation(s) in RCA: 998] [Impact Index Per Article: 249.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/28/2020] [Accepted: 09/11/2020] [Indexed: 12/28/2022]
Abstract
Analysis of the specificity and kinetics of neutralizing antibodies (nAbs) elicited by SARS-CoV-2 infection is crucial for understanding immune protection and identifying targets for vaccine design. In a cohort of 647 SARS-CoV-2-infected subjects, we found that both the magnitude of Ab responses to SARS-CoV-2 spike (S) and nucleoprotein and nAb titers correlate with clinical scores. The receptor-binding domain (RBD) is immunodominant and the target of 90% of the neutralizing activity present in SARS-CoV-2 immune sera. Whereas overall RBD-specific serum IgG titers waned with a half-life of 49 days, nAb titers and avidity increased over time for some individuals, consistent with affinity maturation. We structurally defined an RBD antigenic map and serologically quantified serum Abs specific for distinct RBD epitopes leading to the identification of two major receptor-binding motif antigenic sites. Our results explain the immunodominance of the receptor-binding motif and will guide the design of COVID-19 vaccines and therapeutics.
Collapse
MESH Headings
- Angiotensin-Converting Enzyme 2
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antigen-Antibody Reactions
- Betacoronavirus/immunology
- Betacoronavirus/isolation & purification
- Betacoronavirus/metabolism
- Binding Sites
- COVID-19
- Coronavirus Infections/pathology
- Coronavirus Infections/virology
- Epitope Mapping/methods
- Epitopes/chemistry
- Epitopes/immunology
- Humans
- Immunoglobulin A/blood
- Immunoglobulin A/immunology
- Immunoglobulin G/blood
- Immunoglobulin G/immunology
- Immunoglobulin M/blood
- Immunoglobulin M/immunology
- Kinetics
- Molecular Dynamics Simulation
- Pandemics
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/metabolism
- Pneumonia, Viral/pathology
- Pneumonia, Viral/virology
- Protein Binding
- Protein Domains/immunology
- Protein Structure, Quaternary
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
Collapse
Affiliation(s)
- Luca Piccoli
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - M Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, 75015 Paris, France
| | | | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | | | - Dora Pinto
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Oliver J Acton
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Stefano Jaconi
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Barbara Guarino
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Andrea Minola
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Fabrizia Zatta
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Jessica Bassi
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alessia Peter
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Anna De Marco
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Jay C Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Federico Mele
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Sandra Jovic
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | | | | | - Feng Jin
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Giovanni Piumatti
- Division of Primary Care, Geneva University Hospitals, 1205 Geneva, Switzerland; Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
| | - Giorgia Lo Presti
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | | | - Maira Biggiogero
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Maciej Tarkowski
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy
| | - Matteo S Pizzuto
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | | | - David Hong
- Vir Biotechnology, San Francisco, CA 94158, USA
| | | | - Emiliano Albanese
- Institute of Public Health, Università della Svizzera italiana, 6900 Lugano, Switzerland
| | - Alessandro Ceschi
- Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland; Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland; Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Ente Ospedaliero Cantonale, Ospedale Civico and Ospedale Italiano, 6900 Lugano, Switzerland
| | - Luigia Elzi
- Division of Infectious Diseases, Ente Ospedaliero Cantonale, Ospedale Regionale Bellinzona e Valli and Ospedale Regionale, 6600 Locarno, Switzerland
| | - Paolo Ferrari
- Department of Nephrology, Ospedale Civico Lugano, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland; Prince of Wales Hospital Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Agostino Riva
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy
| | | | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Katja Fink
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | - Davide Corti
- Humabs BioMed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland.
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
438
|
Abstract
COVID19 has changed life for people worldwide. Despite lockdowns globally, computational research has pressed on, working remotely and collaborating virtually on research questions in COVID19 and the virus it is caused by, SARS-CoV-2. Molecular simulations can help to characterize the function of viral and host proteins and have the potential to contribute to the search for vaccines and treatments. Changes in the modus operandi of research groups include broader adoption of the use of preprint servers, earlier and more open sharing of methods, models, and data, the use of social media to rapidly disseminate information, online seminars, and cloud-based virtual collaboration. Research funders and computing providers worldwide recognized the need to provide rapid and significant access to computational architectures. In this review, we discuss how the interplay of all of these factors is influencing the impact - both potential and realized - of biomolecular simulations in the fight against SARS-CoV-2.
Collapse
|
439
|
Berkenbrock JA, Grecco-Machado R, Achenbach S. Microfluidic devices for the detection of viruses: aspects of emergency fabrication during the COVID-19 pandemic and other outbreaks. Proc Math Phys Eng Sci 2020; 476:20200398. [PMID: 33363440 PMCID: PMC7735301 DOI: 10.1098/rspa.2020.0398] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/05/2020] [Indexed: 12/17/2022] Open
Abstract
Extensive testing of populations against COVID-19 has been suggested as a game-changer quest to control the spread of this contagious disease and to avoid further disruption in our social, healthcare and economical systems. Nonetheless, testing millions of people for a new virus brings about quite a few challenges. The development of effective tests for the new coronavirus has become a worldwide task that relies on recent discoveries and lessons learned from past outbreaks. In this work, we review the most recent publications on microfluidics devices for the detection of viruses. The topics of discussion include different detection approaches, methods of signalling and fabrication techniques. Besides the miniaturization of traditional benchtop detection assays, approaches such as electrochemical analyses, field-effect transistors and resistive pulse sensors are considered. For emergency fabrication of quick test kits, the local capabilities must be evaluated, and the joint work of universities, industries, and governments seems to be an unequivocal necessity.
Collapse
Affiliation(s)
- José Alvim Berkenbrock
- Department of Electrical and Computer Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Rafaela Grecco-Machado
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sven Achenbach
- Department of Electrical and Computer Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| |
Collapse
|
440
|
Guruprasad L. Human coronavirus spike protein-host receptor recognition. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 161:39-53. [PMID: 33137344 PMCID: PMC7604128 DOI: 10.1016/j.pbiomolbio.2020.10.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/12/2020] [Accepted: 10/23/2020] [Indexed: 01/06/2023]
Abstract
A variety of coronaviruses (CoVs) have infected humans and caused mild to severe respiratory diseases that could result in mortality. The human CoVs (HCoVs) belong to the genera of α- and β-CoVs that originate in rodents and bats and are transmitted to humans via zoonotic contacts. The binding of viral spike proteins to the host cell receptors is essential for mediating fusion of viral and host cell membranes to cause infection. The SARS-CoV-2 originated in bats (RaTG13 SARS-CoV) and is transmitted to humans via pangolins. The presence of 'PRRA' sequence motif in SARS-CoV-2 spike proteins from human, dog, cat, mink, tiger and lion suggests a common viral entry mechanism into host cells. In this review, we discuss structural features of HCoV spike proteins and recognition of host protein and carbohydrate receptors.
Collapse
|
441
|
SARS-CoV-2 spike protein: flexibility as a new target for fighting infection. Signal Transduct Target Ther 2020; 5:254. [PMID: 33127889 PMCID: PMC7597425 DOI: 10.1038/s41392-020-00369-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 11/09/2022] Open
|
442
|
Yao H, Song Y, Chen Y, Wu N, Xu J, Sun C, Zhang J, Weng T, Zhang Z, Wu Z, Cheng L, Shi D, Lu X, Lei J, Crispin M, Shi Y, Li L, Li S. Molecular Architecture of the SARS-CoV-2 Virus. Cell 2020; 183:730-738.e13. [PMID: 32979942 PMCID: PMC7474903 DOI: 10.1016/j.cell.2020.09.018] [Citation(s) in RCA: 677] [Impact Index Per Article: 169.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/10/2020] [Accepted: 09/03/2020] [Indexed: 01/16/2023]
Abstract
SARS-CoV-2 is an enveloped virus responsible for the COVID-19 pandemic. Despite recent advances in the structural elucidation of SARS-CoV-2 proteins, the detailed architecture of the intact virus remains to be unveiled. Here we report the molecular assembly of the authentic SARS-CoV-2 virus using cryoelectron tomography (cryo-ET) and subtomogram averaging (STA). Native structures of the S proteins in pre- and postfusion conformations were determined to average resolutions of 8.7-11 Å. Compositions of the N-linked glycans from the native spikes were analyzed by mass spectrometry, which revealed overall processing states of the native glycans highly similar to that of the recombinant glycoprotein glycans. The native conformation of the ribonucleoproteins (RNPs) and their higher-order assemblies were revealed. Overall, these characterizations revealed the architecture of the SARS-CoV-2 virus in exceptional detail and shed light on how the virus packs its ∼30-kb-long single-segmented RNA in the ∼80-nm-diameter lumen.
Collapse
Affiliation(s)
- Hangping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China; National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Yutong Song
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China
| | - Yong Chen
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China
| | - Nanping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China; National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Jialu Xu
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Chujie Sun
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Jiaxing Zhang
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China
| | - Tianhao Weng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China; National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Zheyuan Zhang
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China
| | - Zhigang Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China; National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Linfang Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China; National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Danrong Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China; National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Xiangyun Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China; National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Jianlin Lei
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Yigong Shi
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China; National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China.
| | - Sai Li
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
| |
Collapse
|
443
|
Arantes P, Saha A, Palermo G. Fighting COVID-19 Using Molecular Dynamics Simulations. ACS CENTRAL SCIENCE 2020; 6:1654-1656. [PMID: 33140032 PMCID: PMC7571292 DOI: 10.1021/acscentsci.0c01236] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- Pablo
R. Arantes
- Department
of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, California 92512, United States
| | - Aakash Saha
- Department
of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, California 92512, United States
| | - Giulia Palermo
- Department
of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, California 92512, United States
| |
Collapse
|
444
|
Gecht M, Siggel M, Linke M, Hummer G, Köfinger J. MDBenchmark: A toolkit to optimize the performance of molecular dynamics simulations. J Chem Phys 2020; 153:144105. [PMID: 33086826 DOI: 10.1063/5.0019045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Despite the impending flattening of Moore's law, the system size, complexity, and length of molecular dynamics (MD) simulations keep on increasing, thanks to effective code parallelization and optimization combined with algorithmic developments. Going forward, exascale computing poses new challenges to the efficient execution and management of MD simulations. The diversity and rapid developments of hardware architectures, software environments, and MD engines make it necessary that users can easily run benchmarks to optimally set up simulations, both with respect to time-to-solution and overall efficiency. To this end, we have developed the software MDBenchmark to streamline the setup, submission, and analysis of simulation benchmarks and scaling studies. The software design is open and as such not restricted to any specific MD engine or job queuing system. To illustrate the necessity and benefits of running benchmarks and the capabilities of MDBenchmark, we measure the performance of a diverse set of 23 MD simulation systems using GROMACS 2018. We compare the scaling of simulations with the number of nodes for central processing unit (CPU)-only and mixed CPU-graphics processing unit (GPU) nodes and study the performance that can be achieved when running multiple simulations on a single node. In all these cases, we optimize the numbers of message passing interface (MPI) ranks and open multi-processing (OpenMP) threads, which is crucial to maximizing performance. Our results demonstrate the importance of benchmarking for finding the optimal system and hardware specific simulation parameters. Running MD simulations with optimized settings leads to a significant performance increase that reduces the monetary, energetic, and environmental costs of MD simulations.
Collapse
Affiliation(s)
- Michael Gecht
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Marc Siggel
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Max Linke
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Jürgen Köfinger
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| |
Collapse
|
445
|
Turk M, Baumeister W. The promise and the challenges of cryo-electron tomography. FEBS Lett 2020; 594:3243-3261. [PMID: 33020915 DOI: 10.1002/1873-3468.13948] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 01/11/2023]
Abstract
Structural biologists have traditionally approached cellular complexity in a reductionist manner in which the cellular molecular components are fractionated and purified before being studied individually. This 'divide and conquer' approach has been highly successful. However, awareness has grown in recent years that biological functions can rarely be attributed to individual macromolecules. Most cellular functions arise from their concerted action, and there is thus a need for methods enabling structural studies performed in situ, ideally in unperturbed cellular environments. Cryo-electron tomography (Cryo-ET) combines the power of 3D molecular-level imaging with the best structural preservation that is physically possible to achieve. Thus, it has a unique potential to reveal the supramolecular architecture or 'molecular sociology' of cells and to discover the unexpected. Here, we review state-of-the-art Cryo-ET workflows, provide examples of biological applications, and discuss what is needed to realize the full potential of Cryo-ET.
Collapse
Affiliation(s)
- Martin Turk
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| |
Collapse
|
446
|
Zimmerman MI, Porter JR, Ward MD, Singh S, Vithani N, Meller A, Mallimadugula UL, Kuhn CE, Borowsky JH, Wiewiora RP, Hurley MFD, Harbison AM, Fogarty CA, Coffland JE, Fadda E, Voelz VA, Chodera JD, Bowman GR. SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.27.175430. [PMID: 32637963 PMCID: PMC7337393 DOI: 10.1101/2020.06.27.175430] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
SARS-CoV-2 has intricate mechanisms for initiating infection, immune evasion/suppression, and replication, which depend on the structure and dynamics of its constituent proteins. Many protein structures have been solved, but far less is known about their relevant conformational changes. To address this challenge, over a million citizen scientists banded together through the Folding@home distributed computing project to create the first exascale computer and simulate an unprecedented 0.1 seconds of the viral proteome. Our simulations capture dramatic opening of the apo Spike complex, far beyond that seen experimentally, which explains and successfully predicts the existence of 'cryptic' epitopes. Different Spike homologues modulate the probabilities of open versus closed structures, balancing receptor binding and immune evasion. We also observe dramatic conformational changes across the proteome, which reveal over 50 'cryptic' pockets that expand targeting options for the design of antivirals. All data and models are freely available online, providing a quantitative structural atlas.
Collapse
Affiliation(s)
- Maxwell I. Zimmerman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Justin R. Porter
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Michael D. Ward
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Sukrit Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Neha Vithani
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Artur Meller
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Upasana L. Mallimadugula
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Catherine E. Kuhn
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jonathan H. Borowsky
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Rafal P. Wiewiora
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Computational and Systems Biology Program, Sloan Kettering Institute, New York, New York 10065, United States
| | - Matthew F. D. Hurley
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Aoife M Harbison
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland
| | - Carl A Fogarty
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland
| | | | - Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland
| | - Vincent A. Voelz
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - John D. Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, New York, New York 10065, United States
| | - Gregory R. Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| |
Collapse
|
447
|
Duan L, Zheng Q, Zhang H, Niu Y, Lou Y, Wang H. The SARS-CoV-2 Spike Glycoprotein Biosynthesis, Structure, Function, and Antigenicity: Implications for the Design of Spike-Based Vaccine Immunogens. Front Immunol 2020; 11:576622. [PMID: 33117378 PMCID: PMC7575906 DOI: 10.3389/fimmu.2020.576622] [Citation(s) in RCA: 241] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/16/2020] [Indexed: 12/20/2022] Open
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses a grave threat to global public health and imposes a severe burden on the entire human society. Like other coronaviruses, the SARS-CoV-2 genome encodes spike (S) glycoproteins, which protrude from the surface of mature virions. The S glycoprotein plays essential roles in virus attachment, fusion and entry into the host cell. Surface location of the S glycoprotein renders it a direct target for host immune responses, making it the main target of neutralizing antibodies. In the light of its crucial roles in viral infection and adaptive immunity, the S protein is the focus of most vaccine strategies as well as therapeutic interventions. In this review, we highlight and describe the recent progress that has been made in the biosynthesis, structure, function, and antigenicity of the SARS-CoV-2 S glycoprotein, aiming to provide valuable insights into the design and development of the S protein-based vaccines as well as therapeutics.
Collapse
Affiliation(s)
- Liangwei Duan
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Qianqian Zheng
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Hongxia Zhang
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Yuna Niu
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Yunwei Lou
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Hui Wang
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| |
Collapse
|
448
|
McCallum M, Walls AC, Bowen JE, Corti D, Veesler D. Structure-guided covalent stabilization of coronavirus spike glycoprotein trimers in the closed conformation. Nat Struct Mol Biol 2020. [PMID: 32753755 DOI: 10.1038/s41594-41020-40483-41598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
SARS-CoV-2 is the causative agent of the COVID-19 pandemic, with 10 million infections and more than 500,000 fatalities by June 2020. To initiate infection, the SARS-CoV-2 spike (S) glycoprotein promotes attachment to the host cell surface and fusion of the viral and host membranes. Prefusion SARS-CoV-2 S is the main target of neutralizing antibodies and the focus of vaccine design. However, its limited stability and conformational dynamics are limiting factors for developing countermeasures against this virus. We report here the design of a construct corresponding to the prefusion SARS-CoV-2 S ectodomain trimer, covalently stabilized by a disulfide bond in the closed conformation. Structural and antigenicity analyses show we successfully shut S in the closed state without otherwise altering its architecture. We demonstrate that this strategy is applicable to other β-coronaviruses, such as SARS-CoV and MERS-CoV, and might become an important tool for structural biology, serology, vaccine design and immunology studies.
Collapse
Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Davide Corti
- Humabs Biomed SA, a Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| |
Collapse
|
449
|
Barros EP, Casalino L, Gaieb Z, Dommer AC, Wang Y, Fallon L, Raguette L, Belfon K, Simmerling C, Amaro RE. The flexibility of ACE2 in the context of SARS-CoV-2 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.09.16.300459. [PMID: 32995769 PMCID: PMC7523095 DOI: 10.1101/2020.09.16.300459] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The COVID-19 pandemic has swept over the world in the past months, causing significant loss of life and consequences to human health. Although numerous drug and vaccine developments efforts are underway, many questions remain outstanding on the mechanism of SARS-CoV-2 viral association to angiotensin-converting enzyme 2 (ACE2), its main host receptor, and entry in the cell. Structural and biophysical studies indicate some degree of flexibility in the viral extracellular Spike glycoprotein and at the receptor binding domain-receptor interface, suggesting a role in infection. Here, we perform all-atom molecular dynamics simulations of the glycosylated, full-length membrane-bound ACE2 receptor, in both an apo and spike receptor binding domain (RBD) bound state, in order to probe the intrinsic dynamics of the ACE2 receptor in the context of the cell surface. A large degree of fluctuation in the full length structure is observed, indicating hinge bending motions at the linker region connecting the head to the transmembrane helix, while still not disrupting the ACE2 homodimer or ACE2-RBD interfaces. This flexibility translates into an ensemble of ACE2 homodimer conformations that could sterically accommodate binding of the spike trimer to more than one ACE2 homodimer, and suggests a mechanical contribution of the host receptor towards the large spike conformational changes required for cell fusion. This work presents further structural and functional insights into the role of ACE2 in viral infection that can be exploited for the rational design of effective SARS-CoV-2 therapeutics. STATEMENT OF SIGNIFICANCE As the host receptor of SARS-CoV-2, ACE2 has been the subject of extensive structural and antibody design efforts in aims to curtail COVID-19 spread. Here, we perform molecular dynamics simulations of the homodimer ACE2 full-length structure to study the dynamics of this protein in the context of the cellular membrane. The simulations evidence exceptional plasticity in the protein structure due to flexible hinge motions in the head-transmembrane domain linker region and helix mobility in the membrane, resulting in a varied ensemble of conformations distinct from the experimental structures. Our findings suggest a dynamical contribution of ACE2 to the spike glycoprotein shedding required for infection, and contribute to the question of stoichiometry of the Spike-ACE2 complex.
Collapse
|
450
|
Powell AE, Zhang K, Sanyal M, Tang S, Weidenbacher PA, Li S, Pham TD, Pak JE, Chiu W, Kim PS. A single immunization with spike-functionalized ferritin vaccines elicits neutralizing antibody responses against SARS-CoV-2 in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.08.28.272518. [PMID: 32869030 PMCID: PMC7457616 DOI: 10.1101/2020.08.28.272518] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Development of a safe and effective SARS-CoV-2 vaccine is a public health priority. We designed subunit vaccine candidates using self-assembling ferritin nanoparticles displaying one of two multimerized SARS-CoV-2 spikes: full-length ectodomain (S-Fer) or a C-terminal 70 amino-acid deletion (SΔC-Fer). Ferritin is an attractive nanoparticle platform for production of vaccines and ferritin-based vaccines have been investigated in humans in two separate clinical trials. We confirmed proper folding and antigenicity of spike on the surface of ferritin by cryo-EM and binding to conformation-specific monoclonal antibodies. After a single immunization of mice with either of the two spike ferritin particles, a lentiviral SARS-CoV-2 pseudovirus assay revealed mean neutralizing antibody titers at least 2-fold greater than those in convalescent plasma from COVID-19 patients. Additionally, a single dose of SΔC-Fer elicited significantly higher neutralizing responses as compared to immunization with the spike receptor binding domain (RBD) monomer or spike ectodomain trimer alone. After a second dose, mice immunized with SΔC-Fer exhibited higher neutralizing titers than all other groups. Taken together, these results demonstrate that multivalent presentation of SARS-CoV-2 spike on ferritin can notably enhance elicitation of neutralizing antibodies, thus constituting a viable strategy for single-dose vaccination against COVID-19.
Collapse
Affiliation(s)
- Abigail E. Powell
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Kaiming Zhang
- Department of Bioengineering & James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Mrinmoy Sanyal
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Shaogeng Tang
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Payton A. Weidenbacher
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Shanshan Li
- Department of Bioengineering & James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Tho D. Pham
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Stanford Blood Center, Palo Alto, CA 94304, USA
| | - John E. Pak
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Wah Chiu
- Department of Bioengineering & James H. Clark Center, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Peter S. Kim
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| |
Collapse
|