101
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He X, He C, Hong W, Yang J, Wei X. Research progress in spike mutations of SARS-CoV-2 variants and vaccine development. Med Res Rev 2023. [PMID: 36929527 DOI: 10.1002/med.21941] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 09/27/2022] [Accepted: 02/26/2023] [Indexed: 03/18/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic can hardly end with the emergence of different variants over time. In the past 2 years, several variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), such as the Delta and Omicron variants, have emerged with higher transmissibility, immune evasion and drug resistance, leading to higher morbidity and mortality in the population. The prevalent variants of concern (VOCs) share several mutations on the spike that can affect virus characteristics, including transmissibility, antigenicity, and immune evasion. Increasing evidence has demonstrated that the neutralization capacity of sera from COVID-19 convalescent or vaccinated individuals is decreased against SARS-CoV-2 variants. Moreover, the vaccine effectiveness of current COVID-19 vaccines against SARS-CoV-2 VOCs is not as high as that against wild-type SARS-CoV-2. Therefore, more attention might be paid to how the mutations impact vaccine effectiveness. In this review, we summarized the current studies on the mutations of the SARS-CoV-2 spike, particularly of the receptor binding domain, to elaborate on how the mutations impact the infectivity, transmissibility and immune evasion of the virus. The effects of mutations in the SARS-CoV-2 spike on the current therapeutics were highlighted, and potential strategies for future vaccine development were suggested.
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Affiliation(s)
- Xuemei He
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Cai He
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Weiqi Hong
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jingyun Yang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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102
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Kumar R. Cryo-EM technique and its application: Structure of steroid hormone receptors. VITAMINS AND HORMONES 2023; 123:385-397. [PMID: 37717991 DOI: 10.1016/bs.vh.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
In recent years, cryo-electron microscopy (cryo-EM) has become one of the most powerful tools to solve the 3-D structure of macromolecules. Unlike X-ray crystallography, the cryo-EM method has advantage of providing an in-depth insight into the dynamic behavior of macromolecules, which is particularly useful to determine 3-D structural analyses of large protein complexes. Due to recent technical advancements, cryo-EM has become the method of choice for the determination of protein structures. Among other proteins, solving 3-D structure of steroid hormone receptors (SHRs) complexed with DNA and coactivators has been a challenge for decades. The limitations with X-ray crystallography and NMR to solve SHR protein structures prompted investigators to move towards cryo-EM technique. The cryo-EM structural analyses have been successful in revealing structural dynamics of several SHRs in recent years. Though, limited by low-resolution, the structural analyses of these SHRs may be useful in understanding many receptor functions as well as provide a platform to refine high-resolution structural analyses in future. This review article discusses the cryo-EM technique in general as well as structural information gained for SHRs using cryo-EM.
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Affiliation(s)
- Raj Kumar
- Department of Pharmaceutical and Biomedical Sciences, Touro College of Pharmacy, New York, NY, United States.
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103
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Canton-Vitoria R, Sato K, Motooka Y, Toyokuni S, Liu Z, Kitaura R. Field-effect transistor antigen/antibody-TMDs sensors for the detection of COVID-19 samples. NANOSCALE 2023; 15:4570-4580. [PMID: 36762571 DOI: 10.1039/d2nr06630k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We fabricated sensors by modifying the surface of MoS2 and WS2 with COVID-19 antibodies and investigated their characteristics, including stability, reusability, sensitivity, and selectivity. Thiols and disulfanes in antibodies strongly interact with vacant Mo or W sites of MoS2 or WS2, yielding durable devices that are stable for several days in the air or water. More importantly, detachment of the antibodies is suppressed even during the aggressive cleaning process of the devices at pH 3, which allows reusing the same device in several experiments without appreciable loss of sensitivity. Therefore, the nanodevice may be employed in samples of different patients. Further, we found a limit of detection (LOD) of 1 fg ml-1 at room temperature, time responses of 1 second, and selectivity against interferences such as KLH protein or Albumin.
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Affiliation(s)
- Ruben Canton-Vitoria
- Department of Chemistry, Nagoya University, Nagoya, Aichi 464-8602, Japan.
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece.
| | - Kotaro Sato
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
- Department of Oral and Maxillofacial Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Yashiro Motooka
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Shinya Toyokuni
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Zheng Liu
- Innovative Functional Materials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Nagoya, Aichi 463-8560, Japan
| | - Ryo Kitaura
- Department of Chemistry, Nagoya University, Nagoya, Aichi 464-8602, Japan.
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Japan
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104
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Mizuta R, Inoue F, Sasaki Y, Sawada SI, Akiyoshi K. A Facile Method to Coat Nanoparticles with Lipid Bilayer Membrane: Hybrid Silica Nanoparticles Disguised as Biomembrane Vesicles by Particle Penetration of Concentrated Lipid Layers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206153. [PMID: 36634998 DOI: 10.1002/smll.202206153] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Natural membrane vesicles, including extracellular vesicles and enveloped viruses, participate in various events in vivo. To study and manipulate these events, biomembrane-coated nanoparticles inspired by natural membrane vesicles are developed. Herein, an efficient method is presented to prepare organic-inorganic hybrid materials in high yields that can accommodate various lipid compositions and particle sizes. To demonstrate this method, silica nanoparticles are passed through concentrated lipid layers prepared using density gradient centrifugation, followed by purification, to obtain lipid membrane-coated nanoparticles. Various lipids, including neutral, anionic, and cationic lipids, are used to prepare concentrated lipid layers. Single-particle analysis by imaging flow cytometry determines that silica nanoparticles are uniformly coated with a single lipid bilayer. Moreover, cellular uptake of silica nanoparticles is enhanced when covered with a lipid membrane containing cationic lipids. Finally, cell-free protein expression is applied to embed a membrane protein, namely the Spike protein of severe acute respiratory syndrome coronavirus 2, into the coating of the nanoparticles, with the correct orientation. Therefore, this method can be used to develop organic-inorganic hybrid nanomaterials with an inorganic core and a virus-like coating, serving as carriers for targeted delivery of cargos such as proteins, DNA, and drugs.
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Affiliation(s)
- Ryosuke Mizuta
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, A3-317, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Fumihito Inoue
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, A3-317, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Yoshihiro Sasaki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, A3-317, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Shin-Ichi Sawada
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, A3-317, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Kazunari Akiyoshi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, A3-317, Nishikyo-ku, Kyoto, 615-8510, Japan
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105
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Norris EG, Pan XS, Hocking DC. Receptor-binding domain of SARS-CoV-2 is a functional αv-integrin agonist. J Biol Chem 2023; 299:102922. [PMID: 36669646 PMCID: PMC9846890 DOI: 10.1016/j.jbc.2023.102922] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Among the novel mutations distinguishing SARS-CoV-2 from similar coronaviruses is a K403R substitution in the receptor-binding domain (RBD) of the viral spike (S) protein within its S1 region. This amino acid substitution occurs near the angiotensin-converting enzyme 2-binding interface and gives rise to a canonical RGD adhesion motif that is often found in native extracellular matrix proteins, including fibronectin. Here, the ability of recombinant S1-RBD to bind to cell surface integrins and trigger downstream signaling pathways was assessed and compared with RGD-containing, integrin-binding fragments of fibronectin. We determined that S1-RBD supported adhesion of fibronectin-null mouse embryonic fibroblasts as well as primary human small airway epithelial cells, while RBD-coated microparticles attached to epithelial monolayers in a cation-dependent manner. Cell adhesion to S1-RBD was RGD dependent and inhibited by blocking antibodies against αv and β3 but not α5 or β1 integrins. Similarly, we observed direct binding of S1-RBD to recombinant human αvβ3 and αvβ6 integrins, but not α5β1 integrins, using surface plasmon resonance. S1-RBD adhesion initiated cell spreading, focal adhesion formation, and actin stress fiber organization to a similar extent as fibronectin. Moreover, S1-RBD stimulated tyrosine phosphorylation of the adhesion mediators FAK, Src, and paxillin; triggered Akt activation; and supported cell proliferation. Thus, the RGD sequence of S1-RBD can function as an αv-selective integrin agonist. This study provides evidence that cell surface αv-containing integrins can respond functionally to spike protein and raises the possibility that S1-mediated dysregulation of extracellular matrix dynamics may contribute to the pathogenesis and/or post-acute sequelae of SARS-CoV-2 infection.
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Affiliation(s)
- Emma G Norris
- Department of Pharmacology and Physiology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Xuan Sabrina Pan
- Department of Biomedical Engineering, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Denise C Hocking
- Department of Pharmacology and Physiology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA; Department of Biomedical Engineering, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA.
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106
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Mironov AA, Savin MA, Beznoussenko GV. COVID-19 Biogenesis and Intracellular Transport. Int J Mol Sci 2023; 24:ijms24054523. [PMID: 36901955 PMCID: PMC10002980 DOI: 10.3390/ijms24054523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023] Open
Abstract
SARS-CoV-2 is responsible for the COVID-19 pandemic. The structure of SARS-CoV-2 and most of its proteins of have been deciphered. SARS-CoV-2 enters cells through the endocytic pathway and perforates the endosomes' membranes, and its (+) RNA appears in the cytosol. Then, SARS-CoV-2 starts to use the protein machines of host cells and their membranes for its biogenesis. SARS-CoV-2 generates a replication organelle in the reticulo-vesicular network of the zippered endoplasmic reticulum and double membrane vesicles. Then, viral proteins start to oligomerize and are subjected to budding within the ER exit sites, and its virions are passed through the Golgi complex, where the proteins are subjected to glycosylation and appear in post-Golgi carriers. After their fusion with the plasma membrane, glycosylated virions are secreted into the lumen of airways or (seemingly rarely) into the space between epithelial cells. This review focuses on the biology of SARS-CoV-2's interactions with cells and its transport within cells. Our analysis revealed a significant number of unclear points related to intracellular transport in SARS-CoV-2-infected cells.
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Affiliation(s)
- Alexander A. Mironov
- Department of Cell Biology, IFOM ETS—The AIRC Institute of Molecular Oncology, Via Adamello, 16, 20139 Milan, Italy
- Correspondence:
| | - Maksim A. Savin
- The Department for Welding Production and Technology of Constructional Materials, Perm National Research Polytechnic University, Komsomolsky Prospekt, 29, 614990 Perm, Russia
| | - Galina V. Beznoussenko
- Department of Cell Biology, IFOM ETS—The AIRC Institute of Molecular Oncology, Via Adamello, 16, 20139 Milan, Italy
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107
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Pedenko B, Sulbaran G, Guilligay D, Effantin G, Weissenhorn W. SARS-CoV-2 S Glycoprotein Stabilization Strategies. Viruses 2023; 15:v15020558. [PMID: 36851772 PMCID: PMC9960574 DOI: 10.3390/v15020558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The SARS-CoV-2 pandemic has again shown that structural biology plays an important role in understanding biological mechanisms and exploiting structural data for therapeutic interventions. Notably, previous work on SARS-related glycoproteins has paved the way for the rapid structural determination of the SARS-CoV-2 S glycoprotein, which is the main target for neutralizing antibodies. Therefore, all vaccine approaches aimed to employ S as an immunogen to induce neutralizing antibodies. Like all enveloped virus glycoproteins, SARS-CoV-2 S native prefusion trimers are in a metastable conformation, which primes the glycoprotein for the entry process via membrane fusion. S-mediated entry is associated with major conformational changes in S, which can expose many off-target epitopes that deviate vaccination approaches from the major aim of inducing neutralizing antibodies, which mainly target the native prefusion trimer conformation. Here, we review the viral glycoprotein stabilization methods developed prior to SARS-CoV-2, and applied to SARS-CoV-2 S, in order to stabilize S in the prefusion conformation. The importance of structure-based approaches is highlighted by the benefits of employing stabilized S trimers versus non-stabilized S in vaccines with respect to their protective efficacy.
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108
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Chmielewski D, Wilson EA, Pintilie G, Zhao P, Chen M, Schmid MF, Simmons G, Wells L, Jin J, Singharoy A, Chiu W. Integrated analyses reveal a hinge glycan regulates coronavirus spike tilting and virus infectivity. RESEARCH SQUARE 2023:rs.3.rs-2553619. [PMID: 36824920 PMCID: PMC9949256 DOI: 10.21203/rs.3.rs-2553619/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Coronavirus spike glycoproteins presented on the virion surface mediate receptor binding, and membrane fusion during virus entry and constitute the primary target for vaccine and drug development. How the structure dynamics of the full-length spikes incorporated in viral lipid envelope correlates with the virus infectivity remains poorly understood. Here we present structures and distributions of native spike conformations on vitrified human coronavirus NL63 (HCoV-NL63) virions without chemical fixation by cryogenic electron tomography (cryoET) and subtomogram averaging, along with site-specific glycan composition and occupancy determined by mass spectroscopy. The higher oligomannose glycan shield on HCoV-NL63 spikes than on SARS-CoV-2 spikes correlates with stronger immune evasion of HCoV-NL63. Incorporation of cryoET-derived native spike conformations into all-atom molecular dynamic simulations elucidate the conformational landscape of the glycosylated, full-length spike that reveals a novel role of stalk glycans in modulating spike bending. We show that glycosylation at N1242 at the upper portion of the stalk is responsible for the extensive orientational freedom of the spike crown. Subsequent infectivity assays support the hypothesis that this glycan-dependent motion impacts virus entry. Our results suggest a potential therapeutic target site for HCoV-NL63.
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Affiliation(s)
- David Chmielewski
- Biophysics Graduate Program, Stanford University, Stanford, CA 94305, USA
| | - Eric A. Wilson
- School of Molecular Sciences, Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Grigore Pintilie
- Department of Bioengineering, and of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Peng Zhao
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Muyuan Chen
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Michael F. Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Graham Simmons
- Vitalant Research Institute, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Lance Wells
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Jing Jin
- Department of Bioengineering, and of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
- Vitalant Research Institute, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Abhishek Singharoy
- School of Molecular Sciences, Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Wah Chiu
- Biophysics Graduate Program, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, and of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
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109
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Kohantorabi M, Wagstaffe M, Creutzburg M, Ugolotti A, Kulkarni S, Jeromin A, Krekeler T, Feuerherd M, Herrmann A, Ebert G, Protzer U, Guédez G, Löw C, Thuenauer R, Schlueter C, Gloskovskii A, Keller TF, Di Valentin C, Stierle A, Noei H. Adsorption and Inactivation of SARS-CoV-2 on the Surface of Anatase TiO 2(101). ACS APPLIED MATERIALS & INTERFACES 2023; 15:8770-8782. [PMID: 36723177 DOI: 10.1021/acsami.2c22078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We investigated the adsorption of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), the virus responsible for the current pandemic, on the surface of the model catalyst TiO2(101) using atomic force microscopy, transmission electron microscopy, fluorescence microscopy, and X-ray photoelectron spectroscopy, accompanied by density functional theory calculations. Three different methods were employed to inactivate the virus after it was loaded on the surface of TiO2(101): (i) ethanol, (ii) thermal, and (iii) UV treatments. Microscopic studies demonstrate that the denatured spike proteins and other proteins in the virus structure readsorb on the surface of TiO2 under thermal and UV treatments. The interaction of the virus with the surface of TiO2 was different for the thermally and UV treated samples compared to the sample inactivated via ethanol treatment. AFM and TEM results on the UV-treated sample suggested that the adsorbed viral particles undergo damage and photocatalytic oxidation at the surface of TiO2(101) which can affect the structural proteins of SARS-CoV-2 and denature the spike proteins in 30 min. The role of Pd nanoparticles (NPs) was investigated in the interaction between SARS-CoV-2 and TiO2(101). The presence of Pd NPs enhanced the adsorption of the virus due to the possible interaction of the spike protein with the NPs. This study is the first investigation of the interaction of SARS-CoV-2 with the surface of single crystalline TiO2(101) as a potential candidate for virus deactivation applications. Clarification of the interaction of the virus with the surface of semiconductor oxides will aid in obtaining a deeper understanding of the chemical processes involved in photoinactivation of microorganisms, which is important for the design of effective photocatalysts for air purification and self-cleaning materials.
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Affiliation(s)
- Mona Kohantorabi
- Center for X-ray and Nano Science (CXNS), Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, Hamburg 22607, Germany
| | - Michael Wagstaffe
- Center for X-ray and Nano Science (CXNS), Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, Hamburg 22607, Germany
| | - Marcus Creutzburg
- Center for X-ray and Nano Science (CXNS), Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, Hamburg 22607, Germany
| | - Aldo Ugolotti
- Dipartimento di Scienza dei Materiali, Università degli Studi di Milano-Bicocca, Via Cozzi 55, Milano 20125, Italy
| | - Satishkumar Kulkarni
- Center for X-ray and Nano Science (CXNS), Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, Hamburg 22607, Germany
| | - Arno Jeromin
- Center for X-ray and Nano Science (CXNS), Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, Hamburg 22607, Germany
| | - Tobias Krekeler
- Electron Microscopy Unit, Hamburg University of Technology, Eissendorfer Strasse 42, Hamburg 21073, Germany
| | - Martin Feuerherd
- Institute of Virology, Technical University of Munich/Helmholtz Munich, Munich 81675, Germany
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Alexander Herrmann
- Institute of Virology, Helmholtz Munich, Ingolstädter Landstraße 1, Neuherberg 85764, Germany
| | - Gregor Ebert
- Institute of Virology, Technical University of Munich/Helmholtz Munich, Munich 81675, Germany
| | - Ulrike Protzer
- Institute of Virology, Technical University of Munich/Helmholtz Munich, Munich 81675, Germany
| | - Gabriela Guédez
- Centre for Structural Systems Biology (CSSB), Deutsches Elektronen-Synchrotron (DESY), EMBL Hamburg, Notkestr. 85, Hamburg 22607, Germany
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), Deutsches Elektronen-Synchrotron (DESY), EMBL Hamburg, Notkestr. 85, Hamburg 22607, Germany
| | - Roland Thuenauer
- Technology Platform Light Microscopy and Image Analysis (TP MIA), Leibniz Institute for Experimental Virology (HPI), Hamburg 20251, Germany
- Centre for Structural Systems Biology (CSSB), Notkestr. 85, Hamburg 22607, Germany
| | - Christoph Schlueter
- Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, Hamburg 22607, Germany
| | - Andrei Gloskovskii
- Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, Hamburg 22607, Germany
| | - Thomas F Keller
- Center for X-ray and Nano Science (CXNS), Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, Hamburg 22607, Germany
- Department of Physics, University of Hamburg, Notkestraße 9-11, Hamburg 22607, Germany
| | - Cristiana Di Valentin
- Dipartimento di Scienza dei Materiali, Università degli Studi di Milano-Bicocca, Via Cozzi 55, Milano 20125, Italy
| | - Andreas Stierle
- Center for X-ray and Nano Science (CXNS), Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, Hamburg 22607, Germany
- Department of Physics, University of Hamburg, Notkestraße 9-11, Hamburg 22607, Germany
| | - Heshmat Noei
- Center for X-ray and Nano Science (CXNS), Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, Hamburg 22607, Germany
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110
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Marcink TC, Zipursky G, Cheng W, Stearns K, Stenglein S, Golub K, Cohen F, Bovier F, Pfalmer D, Greninger AL, Porotto M, des Georges A, Moscona A. Subnanometer structure of an enveloped virus fusion complex on viral surface reveals new entry mechanisms. SCIENCE ADVANCES 2023; 9:eade2727. [PMID: 36763666 PMCID: PMC9917000 DOI: 10.1126/sciadv.ade2727] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
Paramyxoviruses-including important pathogens like parainfluenza, measles, and Nipah viruses-use a receptor binding protein [hemagglutinin-neuraminidase (HN) for parainfluenza] and a fusion protein (F), acting in a complex, to enter cells. We use cryo-electron tomography to visualize the fusion complex of human parainfluenza virus 3 (HN/F) on the surface of authentic clinical viruses at a subnanometer resolution sufficient to answer mechanistic questions. An HN loop inserts in a pocket on F, showing how the fusion complex remains in a ready but quiescent state until activation. The globular HN heads are rotated with respect to each other: one downward to contact F, and the other upward to grapple cellular receptors, demonstrating how HN/F performs distinct steps before F activation. This depiction of viral fusion illuminates potentially druggable targets for paramyxoviruses and sheds light on fusion processes that underpin wide-ranging biological processes but have not been visualized in situ or at the present resolution.
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Affiliation(s)
- Tara C. Marcink
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Gillian Zipursky
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Wenjing Cheng
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Kyle Stearns
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Shari Stenglein
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Kate Golub
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Frances Cohen
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Francesca Bovier
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Daniel Pfalmer
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli,” 81100 Caserta, Italy
| | - Amedee des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, USA
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA
- PhD Programs in Chemistry and Biochemistry, The Graduate Center, City University of New York, New York, NY, USA
| | - Anne Moscona
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
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111
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Kordyukova LV, Moiseenko AV, Serebryakova MV, Shuklina MA, Sergeeva MV, Lioznov DA, Shanko AV. Structural and Immunoreactivity Properties of the SARS-CoV-2 Spike Protein upon the Development of an Inactivated Vaccine. Viruses 2023; 15:v15020480. [PMID: 36851694 PMCID: PMC9961907 DOI: 10.3390/v15020480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/21/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Inactivated vaccines are promising tools for tackling the COVID-19 pandemic. We applied several protocols for SARS-CoV-2 inactivation (by β-propiolactone, formaldehyde, and UV radiation) and examined the morphology of viral spikes, protein composition of the preparations, and their immunoreactivity in ELISA using two panels of sera collected from convalescents and people vaccinated by Sputnik V. Transmission electron microscopy (TEM) allowed us to distinguish wider flail-like spikes (supposedly the S-protein's pre-fusion conformation) from narrower needle-like ones (the post-fusion state). While the flails were present in all preparations studied, the needles were highly abundant in the β-propiolactone-inactivated samples only. Structural proteins S, N, and M of SARS-CoV-2 were detected via mass spectrometry. Formaldehyde and UV-inactivated samples demonstrated the highest affinity/immunoreactivity against the convalescent sera, while β-propiolactone (1:2000, 36 h) and UV-inactivated ones were more active against the sera of people vaccinated with Sputnik V. A higher concentration of β-propiolactone (1:1000, 2 h) led to a loss of antigenic affinity for both serum panels. Thus, although we did not analyze native SARS-CoV-2 for biosafety reasons, our comparative approach helped to exclude some destructive inactivation conditions and select suitable variants for future animal research. We believe that TEM is a valuable tool for inactivated COVID-19 vaccine quality control during the downstream manufacturing process.
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Affiliation(s)
- Larisa V. Kordyukova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (L.V.K.); (A.V.S.)
| | - Andrey V. Moiseenko
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Marina V. Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Marina A. Shuklina
- WHO National Influenza Center, Smorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, Russia
| | - Maria V. Sergeeva
- WHO National Influenza Center, Smorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, Russia
| | - Dmitry A. Lioznov
- WHO National Influenza Center, Smorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, Russia
| | - Andrei V. Shanko
- R&D Department, FORT LLC, 119435 Moscow, Russia
- Correspondence: (L.V.K.); (A.V.S.)
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112
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Kuhn CC, Basnet N, Bodakuntla S, Alvarez-Brecht P, Nichols S, Martinez-Sanchez A, Agostini L, Soh YM, Takagi J, Biertümpfel C, Mizuno N. Direct Cryo-ET observation of platelet deformation induced by SARS-CoV-2 spike protein. Nat Commun 2023; 14:620. [PMID: 36739444 PMCID: PMC9898865 DOI: 10.1038/s41467-023-36279-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
SARS-CoV-2 is a novel coronavirus responsible for the COVID-19 pandemic. Its high pathogenicity is due to SARS-CoV-2 spike protein (S protein) contacting host-cell receptors. A critical hallmark of COVID-19 is the occurrence of coagulopathies. Here, we report the direct observation of the interactions between S protein and platelets. Live imaging shows that the S protein triggers platelets to deform dynamically, in some cases, leading to their irreversible activation. Cellular cryo-electron tomography reveals dense decorations of S protein on the platelet surface, inducing filopodia formation. Hypothesizing that S protein binds to filopodia-inducing integrin receptors, we tested the binding to RGD motif-recognizing platelet integrins and find that S protein recognizes integrin αvβ3. Our results infer that the stochastic activation of platelets is due to weak interactions of S protein with integrin, which can attribute to the pathogenesis of COVID-19 and the occurrence of rare but severe coagulopathies.
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Affiliation(s)
- Christopher Cyrus Kuhn
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA
| | - Nirakar Basnet
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA
| | - Satish Bodakuntla
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA
| | - Pelayo Alvarez-Brecht
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA.,Department of Computer Sciences, Faculty of Sciences - Campus Llamaquique, University of Oviedo, Oviedo, 33007, Spain
| | - Scott Nichols
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA
| | - Antonio Martinez-Sanchez
- Department of Computer Sciences, Faculty of Sciences - Campus Llamaquique, University of Oviedo, Oviedo, 33007, Spain.,Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario s/n, 33011, Oviedo, Spain
| | - Lorenzo Agostini
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA
| | - Young-Min Soh
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA
| | - Junichi Takagi
- Osaka University Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Christian Biertümpfel
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA
| | - Naoko Mizuno
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA. .,National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA.
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113
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Structural ensembles of disordered proteins from hierarchical chain growth and simulation. Curr Opin Struct Biol 2023; 78:102501. [PMID: 36463772 DOI: 10.1016/j.sbi.2022.102501] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 12/03/2022]
Abstract
Disordered proteins and nucleic acids play key roles in cellular function and disease. Here, we review recent advances in the computational exploration of the conformational dynamics of flexible biomolecules. While atomistic molecular dynamics (MD) simulation has seen a lot of improvement in recent years, large-scale computing resources and careful validation are required to simulate full-length disordered biopolymers in solution. As a computationally efficient alternative, hierarchical chain growth (HCG) combines pre-sampled chain fragments in a statistically reproducible manner into ensembles of full-length atomically detailed biomolecular structures. Experimental data can be integrated during and after chain assembly. Applications to the neurodegeneration-linked proteins α-synuclein, tau, and TDP-43, including as condensate, illustrate the use of HCG. We conclude by highlighting the emerging connections to AI-based structural modeling including AlphaFold2.
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114
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Gomari MM, Tarighi P, Choupani E, Abkhiz S, Mohamadzadeh M, Rostami N, Sadroddiny E, Baammi S, Uversky VN, Dokholyan NV. Structural evolution of Delta lineage of SARS-CoV-2. Int J Biol Macromol 2023; 226:1116-1140. [PMID: 36435470 PMCID: PMC9683856 DOI: 10.1016/j.ijbiomac.2022.11.227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
One of the main obstacles in prevention and treatment of COVID-19 is the rapid evolution of the SARS-CoV-2 Spike protein. Given that Spike is the main target of common treatments of COVID-19, mutations occurring at this virulent factor can affect the effectiveness of treatments. The B.1.617.2 lineage of SARS-CoV-2, being characterized by many Spike mutations inside and outside of its receptor-binding domain (RBD), shows high infectivity and relative resistance to existing cures. Here, utilizing a wide range of computational biology approaches, such as immunoinformatics, molecular dynamics (MD), analysis of intrinsically disordered regions (IDRs), protein-protein interaction analyses, residue scanning, and free energy calculations, we examine the structural and biological attributes of the B.1.617.2 Spike protein. Furthermore, the antibody design protocol of Rosetta was implemented for evaluation the stability and affinity improvement of the Bamlanivimab (LY-CoV55) antibody, which is not capable of interactions with the B.1.617.2 Spike. We observed that the detected mutations in the Spike of the B1.617.2 variant of concern can cause extensive structural changes compatible with the described variation in immunogenicity, secondary and tertiary structure, oligomerization potency, Furin cleavability, and drug targetability. Compared to the Spike of Wuhan lineage, the B.1.617.2 Spike is more stable and binds to the Angiotensin-converting enzyme 2 (ACE2) with higher affinity.
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Affiliation(s)
- Mohammad Mahmoudi Gomari
- Student Research Committee, Iran University of Medical Sciences, Tehran 1449614535, Iran; Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Parastoo Tarighi
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Edris Choupani
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Shadi Abkhiz
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Masoud Mohamadzadeh
- Department of Chemistry, Faculty of Sciences, University of Hormozgan, Bandar Abbas 7916193145, Iran
| | - Neda Rostami
- Department of Chemical Engineering, Faculty of Engineering, Arak University, Arak 3848177584, Iran
| | - Esmaeil Sadroddiny
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran 1417613151, Iran
| | - Soukayna Baammi
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir 43150, Morocco
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia.
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 16802, USA.
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115
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Gupta S, Santangelo CD, Patteson AE, Schwarz JM. How cells wrap around virus-like particles using extracellular filamentous protein structures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526272. [PMID: 36778225 PMCID: PMC9915516 DOI: 10.1101/2023.01.30.526272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Nanoparticles, such as viruses, can enter cells via endocytosis. During endocytosis, the cell surface wraps around the nanoparticle to effectively eat it. Prior focus has been on how nanoparticle size and shape impacts endocytosis. However, inspired by the noted presence of extracellular vimentin affecting viral and bacteria uptake, as well as the structure of coronaviruses, we construct a computational model in which both the cell-like construct and the virus-like construct contain filamentous protein structures protruding from their surfaces. We then study the impact of these additional degrees of freedom on viral wrapping. We find that cells with an optimal density of filamentous extracellular components (ECCs) are more likely to be infected as they uptake the virus faster and use relatively less cell surface area per individual virus. At the optimal density, the cell surface folds around the virus, and folds are faster and more efficient at wrapping the virus than crumple-like wrapping. We also find that cell surface bending rigidity helps generate folds, as bending rigidity enhances force transmission across the surface. However, changing other mechanical parameters, such as the stretching stiffness of filamentous ECCs or virus spikes, can drive crumple-like formation of the cell surface. We conclude with the implications of our study on the evolutionary pressures of virus-like particles, with a particular focus on the cellular microenvironment that may include filamentous ECCs.
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Affiliation(s)
- Sarthak Gupta
- Physics Department and BioInspired Institute, Syracuse University Syracuse, NY USA
| | | | - Alison E Patteson
- Physics Department and BioInspired Institute, Syracuse University Syracuse, NY USA
| | - J M Schwarz
- Physics Department and BioInspired Institute, Syracuse University Syracuse, NY USA
- Indian Creek Farm, Ithaca, NY USA
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116
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Lim K, Nishide G, Sajidah ES, Yamano T, Qiu Y, Yoshida T, Kobayashi A, Hazawa M, Ando T, Hanayama R, Wong RW. Nanoscopic Assessment of Anti-SARS-CoV-2 Spike Neutralizing Antibody Using High-Speed AFM. NANO LETTERS 2023; 23:619-628. [PMID: 36641798 PMCID: PMC9881159 DOI: 10.1021/acs.nanolett.2c04270] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Anti-spike neutralizing antibodies (S NAbs) have been developed for prevention and treatment against COVID-19. The nanoscopic characterization of the dynamic interaction between spike proteins and S NAbs remains difficult. By using high-speed atomic force microscopy (HS-AFM), we elucidate the molecular property of an S NAb and its interaction with spike proteins. The S NAb appeared as monomers with a Y conformation at low density and formed hexameric oligomers at high density. The dynamic S NAb-spike protein interaction at RBD induces neither RBD opening nor S1 subunit shedding. Furthermore, the interaction was stable at endosomal pH. These findings indicated that the S NAb could have a negligible risk of antibody-dependent enhancement. Dynamic movement of spike proteins on small extracellular vesicles (S sEV) resembled that on SARS-CoV-2. The sensitivity of variant S sEVs to S NAb could be evaluated using HS-AFM. Altogether, we demonstrate a nanoscopic assessment platform for evaluating the binding property of S NAbs.
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Affiliation(s)
- Keesiang Lim
- WPI-Nano
Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Goro Nishide
- Division
of Nano Life Science in the Graduate School of Frontier Science Initiative,
WISE Program for Nano-Precision Medicine, Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Elma Sakinatus Sajidah
- Division
of Nano Life Science in the Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa Ishikawa 920-1192, Japan
| | - Tomoyoshi Yamano
- WPI-Nano
Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Department
of Immunology, Kanazawa University Graduate
School of Medical Sciences, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Yujia Qiu
- Division
of Nano Life Science in the Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa Ishikawa 920-1192, Japan
| | - Takeshi Yoshida
- Department
of Immunology, Kanazawa University Graduate
School of Medical Sciences, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Akiko Kobayashi
- Cell-Bionomics
Research Unit, Institute for Frontier Science Initiative (INFINITI), Kanazawa University,
Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Masaharu Hazawa
- WPI-Nano
Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Cell-Bionomics
Research Unit, Institute for Frontier Science Initiative (INFINITI), Kanazawa University,
Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Toshio Ando
- WPI-Nano
Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Rikinari Hanayama
- WPI-Nano
Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Department
of Immunology, Kanazawa University Graduate
School of Medical Sciences, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Richard W. Wong
- WPI-Nano
Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Cell-Bionomics
Research Unit, Institute for Frontier Science Initiative (INFINITI), Kanazawa University,
Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
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117
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Gupta S, Santangelo CD, Patteson AE, Schwarz JM. How cells wrap around virus-like particles using extracellular filamentous protein structures. ARXIV 2023:arXiv:2301.08776v2. [PMID: 36747999 PMCID: PMC9900966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Nanoparticles, such as viruses, can enter cells via endocytosis. During endocytosis, the cell surface wraps around the nanoparticle to effectively eat it. Prior focus has been on how nanoparticle size and shape impacts endocytosis. However, inspired by the noted presence of extracellular vimentin affecting viral and bacteria uptake, as well as the structure of coronaviruses, we construct a computational model in which both the cell-like construct and the virus-like construct contain filamentous protein structures protruding from their surfaces. We then study the impact of these additional degrees of freedom on viral wrapping. We find that cells with an optimal density of filamentous extracellular components (ECCs) are more likely to be infected as they uptake the virus faster and use relatively less cell surface area per individual virus. At the optimal density, the cell surface folds around the virus, and folds are faster and more efficient at wrapping the virus than crumple-like wrapping. We also find that cell surface bending rigidity helps generate folds, as bending rigidity enhances force transmission across the surface. However, changing other mechanical parameters, such as the stretching stiffness of filamentous ECCs or virus spikes, can drive crumple-like formation of the cell surface. We conclude with the implications of our study on the evolutionary pressures of virus-like particles, with a particular focus on the cellular microenvironment that may include filamentous ECCs.
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Affiliation(s)
- Sarthak Gupta
- Physics Department and BioInspired Institute, Syracuse University Syracuse, NY USA
| | | | - Alison E Patteson
- Physics Department and BioInspired Institute, Syracuse University Syracuse, NY USA
| | - J M Schwarz
- Physics Department and BioInspired Institute, Syracuse University Syracuse, NY USA
- Indian Creek Farm, Ithaca, NY USA
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118
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Erickson HP, Corbin Goodman L. Recently Designed Multivalent Spike Binders Cannot Bind Multivalently─How Do They Achieve Enhanced Avidity to SARS-CoV-2? Biochemistry 2023; 62:163-168. [PMID: 35943748 DOI: 10.1021/acs.biochem.2c00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The trimeric spike protein of SARS-CoV-2 has been targeted by antibody mimics that bind near or at the receptor-binding domain to neutralize the virus. Several independent studies have reported enhanced binding avidity for dimers and trimers, where binding domains are connected by short peptides. The enhanced avidity of the multivalent constructs was attributed to their simultaneously binding two or three sites within a single spike trimer. We argue here that the 15-20 amino acid peptide linkers, when considered as worm-like-chains, are too short to span the binding sites within a single spike. The enhanced avidity of the multivalent constructs may be explained by a rebinding mechanism, which does not involve multivalent binding.
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119
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K U S, Hunakunti BB, Le Gratiet A, Gogoi A, Mazumder N. Stokes-Mueller polarization-based analysis of model SARS-CoV-2 virions. Lasers Med Sci 2023; 38:35. [PMID: 36622455 PMCID: PMC9827445 DOI: 10.1007/s10103-022-03680-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/12/2022] [Indexed: 01/10/2023]
Abstract
Understanding the virology of the coronavirus at the structural level has gained utmost importance to overcome the constant and long-term health complications induced by them. In this work, the light scattering properties of SARS-CoV-2 of size 140 nm were simulated by using discrete dipole approximation (DDA) for two incident wavelengths 200 nm and 350 nm, respectively. Three different 3-dimensional (3D) models of SARS-CoV-2 corresponding to 15, 20, and 40 numbers of spike proteins on the viral capsid surface were constructed as target geometries for the DDA calculations. These models were assessed by employing Stokes-Mueller polarimetry to obtain individual polarization properties such as degree of polarization (DOP), degree of linear polarization (DOLP), and degree of circular polarization (DOCP). Irrespective of its spike numbers, all the coronavirus models were found to display higher DOP and DOCP values and negligibly small DOLP values for circularly polarized incident light, indicating the presence of chiral structures. On the other hand, the lack of understanding about the dependence of the Mueller matrix on its microstructural properties was overcome by transforming 16 Mueller elements into sub-matrices with specific structural and physical properties using Lu-Chipman-based Mueller matrix polar decomposition method. The obtained properties such as retardance, diattenuation, and depolarization were used for investigating the composition and microstructural information. The approach presented in this work has the potential to understand the virology of the coronavirus at the structural level and, therefore, will be beneficial in developing effective detection strategies by exploiting their characteristic electromagnetic scattering signatures.
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Affiliation(s)
- Spandana K U
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India, 576104
| | - Bhagesh Basavraj Hunakunti
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India, 576104
| | - Aymeric Le Gratiet
- Université de Rennes, CNRS, Institut FOTON - UMR 6082, F-22305, Lannion, France.
| | - Ankur Gogoi
- Department of Physics, Jagannath Barooah College, Jorhat, 785001, Assam, India.
| | - Nirmal Mazumder
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India, 576104.
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120
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Maryam S, Ul Haq I, Yahya G, Ul Haq M, Algammal AM, Saber S, Cavalu S. COVID-19 surveillance in wastewater: An epidemiological tool for the monitoring of SARS-CoV-2. Front Cell Infect Microbiol 2023; 12:978643. [PMID: 36683701 PMCID: PMC9854263 DOI: 10.3389/fcimb.2022.978643] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/03/2022] [Indexed: 01/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has prompted a lot of questions globally regarding the range of information about the virus's possible routes of transmission, diagnostics, and therapeutic tools. Worldwide studies have pointed out the importance of monitoring and early surveillance techniques based on the identification of viral RNA in wastewater. These studies indicated the presence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in human feces, which is shed via excreta including mucus, feces, saliva, and sputum. Subsequently, they get dumped into wastewater, and their presence in wastewater provides a possibility of using it as a tool to help prevent and eradicate the virus. Its monitoring is still done in many regions worldwide and serves as an early "warning signal"; however, a lot of limitations of wastewater surveillance have also been identified.
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Affiliation(s)
- Sajida Maryam
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
| | - Ihtisham Ul Haq
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
- Department of Physical Chemistry and Polymers Technology, Silesian University of Technology, Gliwice, Poland
- Joint Doctoral School, Silesian University of Technology, Gliwice, Poland
| | - Galal Yahya
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Mehboob Ul Haq
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
| | - Abdelazeem M. Algammal
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Sameh Saber
- Department of Pharmacology, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa, Egypt
| | - Simona Cavalu
- Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
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121
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Anwar F, Altayeb H, Alhayyani S, Kumar V, Al-Abbasi FA, Ashraf GM. Analysis of Interaction Between Odorant Receptors and Flexible Spike of SARS CoV-2- Key to Loss of Smell. Curr Neuropharmacol 2023; 21:151-159. [PMID: 35761501 PMCID: PMC10193757 DOI: 10.2174/1570159x20666220627165846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/06/2022] [Accepted: 06/13/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The development of a vaccine for SARS-CoV-2 is primarily focused on the structure of the spike (S) protein. The heavy glycosylation of S with flexible hinges at the stalk shields from antibody attachment. OBJECTIVE This study deciphers the flexible nature of hinges responsible for binding the odorant receptor on neurons responsible for the loss of smell in COVID-19 patients. METHODS The 3D structure via EPIK in Maestro, protein docking with ligands via Maestro protein analysis tool, and molecular dynamic simulation at 30 ns run using DESMOND was prepared. RESULTS The data of the study strongly suggest that strong and stable bond formation results from the reaction between R:14: Trp and Phe at the residue, targeting the flexible hinges of SARS-CoV-2. The difference in the conformational structure of the S protein and its binding with the odorant receptor in COVID-19 is the prime factor for the loss of smell and taste in patients, as supported by the concept of Antigen (epitope) Antibody interaction by the stable formation of a hydrogen bond among odorant receptor and the S protein. The flexibility of structural proteins determines the binding potential of antibodies or other defense proteins produced to participate in the antigen-antibody reaction. CONCLUSION Molecular and atomic details potentiate the design and screening of small molecules that can inhibit the fusion at entry level or odorant receptors and potentially be used in the prevention and treatment of infection, particularly when formulated as nasal drops, paving a new approach for pharmacologists in the treatment of COVID-19 infection.
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Affiliation(s)
- Firoz Anwar
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Hisham Altayeb
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Sultan Alhayyani
- Department of Chemistry, College of Sciences & Arts, King Abdulaziz University, Rabigh King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Vikas Kumar
- Department of Pharmaceutical Sciences, Natural Product Discovery Laboratory, Shalom Institute of Health and Allied Sciences. SHUATS, Naini, Prayagraj, India
| | - Fahad A Al-Abbasi
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Ghulam Md Ashraf
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
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122
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Vijayakrishnan S. In Situ Imaging of Virus-Infected Cells by Cryo-Electron Tomography: An Overview. Subcell Biochem 2023; 106:3-36. [PMID: 38159222 DOI: 10.1007/978-3-031-40086-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Cryo-electron tomography (cryo-ET) has emerged as a powerful tool in structural biology to study viruses and is undergoing a resolution revolution. Enveloped viruses comprise several RNA and DNA pleomorphic viruses that are pathogens of clinical importance to humans and animals. Considerable efforts in cryogenic correlative light and electron microscopy (cryo-CLEM), cryogenic focused ion beam milling (cryo-FIB), and integrative structural techniques are helping to identify virus structures within cells leading to a rise of in situ discoveries shedding light on how viruses interact with their hosts during different stages of infection. This chapter reviews recent advances in the application of cryo-ET in imaging enveloped viruses and the structural and mechanistic insights revealed studying the viral infection cycle within their eukaryotic cellular hosts, with particular attention to viral entry, replication, assembly, and egress during infection.
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Affiliation(s)
- Swetha Vijayakrishnan
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, Glasgow, Scotland, UK.
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123
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von Bülow S, Sikora M, Blanc FEC, Covino R, Hummer G. Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants. PLoS Comput Biol 2023; 19:e1010822. [PMID: 36693110 PMCID: PMC9897577 DOI: 10.1371/journal.pcbi.1010822] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 02/03/2023] [Accepted: 12/17/2022] [Indexed: 01/25/2023] Open
Abstract
The steady emergence of SARS-CoV-2 variants gives us a real-time view of the interplay between viral evolution and the host immune defense. The spike protein of SARS-CoV-2 is the primary target of antibodies. Here, we show that steric accessibility to antibodies provides a strong predictor of mutation activity in the spike protein of SARS-CoV-2 variants, including Omicron. We introduce an antibody accessibility score (AAS) that accounts for the steric shielding effect of glycans at the surface of spike. We find that high values of the AAS correlate strongly with the sites of mutations in the spike proteins of newly emerging SARS-CoV-2 variants. We use the AAS to assess the escapability of variant spike proteins, i.e., their ability to escape antibody-based immune responses. The high calculated escapability of the Omicron variant BA.5 with respect to both wild-type (WT) vaccination and BA.1 infection is consistent with its rapid spread despite high rates of vaccination and prior infection with earlier variants. We calculated the AAS from structural and molecular dynamics simulation data that were available early in the pandemic, in the spring of 2020. The AAS thus allows us to prospectively assess the ability of variant spike proteins to escape antibody-based immune responses and to pinpoint regions of expected mutation activity in future variants.
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Affiliation(s)
- Sören von Bülow
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mateusz Sikora
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Florian E. C. Blanc
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Roberto Covino
- Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany
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124
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Dommer A, Casalino L, Kearns F, Rosenfeld M, Wauer N, Ahn SH, Russo J, Oliveira S, Morris C, Bogetti A, Trifan A, Brace A, Sztain T, Clyde A, Ma H, Chennubhotla C, Lee H, Turilli M, Khalid S, Tamayo-Mendoza T, Welborn M, Christensen A, Smith DG, Qiao Z, Sirumalla SK, O'Connor M, Manby F, Anandkumar A, Hardy D, Phillips J, Stern A, Romero J, Clark D, Dorrell M, Maiden T, Huang L, McCalpin J, Woods C, Gray A, Williams M, Barker B, Rajapaksha H, Pitts R, Gibbs T, Stone J, Zuckerman DM, Mulholland AJ, Miller T, Jha S, Ramanathan A, Chong L, Amaro RE. #COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. THE INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS 2023; 37:28-44. [PMID: 36647365 PMCID: PMC9527558 DOI: 10.1177/10943420221128233] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus obscure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized.
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Affiliation(s)
| | | | | | | | | | | | - John Russo
- Oregon Health & Science University, Portland, OR, USA
| | | | | | | | - Anda Trifan
- Argonne National Laboratory, Lemont, IL, USA
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alexander Brace
- Argonne National Laboratory, Lemont, IL, USA
- University of Chicago, Chicago, IL, USA
| | - Terra Sztain
- UC San Diego, La Jolla, CA, USA
- Freie Universitat Berlin
| | - Austin Clyde
- Argonne National Laboratory, Lemont, IL, USA
- University of Chicago, Chicago, IL, USA
| | - Heng Ma
- Argonne National Laboratory, Lemont, IL, USA
| | | | - Hyungro Lee
- Brookhaven National Lab and Rutgers University
| | | | | | | | | | | | | | - Zhuoran Qiao
- California Institute of Technology, Pasadena, CA, USA
| | | | | | | | - Anima Anandkumar
- California Institute of Technology, Pasadena, CA, USA
- NVIDIA Corp, Santa Clara, CA, USA
| | - David Hardy
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - James Phillips
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | | | | | | | - Tom Maiden
- Pittsburgh Supercomputing Center, Pittsburgh, PA, USA
| | - Lei Huang
- Texas Advanced Computing Center, Austin, TX, USA
| | | | | | | | | | | | | | | | | | - John Stone
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
- NVIDIA Corp, Santa Clara, CA, USA
| | | | | | - Thomas Miller
- Entos, Inc., San Diego, CA, USA
- California Institute of Technology, Pasadena, CA, USA
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125
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Casalino L, Seitz C, Lederhofer J, Tsybovsky Y, Wilson IA, Kanekiyo M, Amaro RE. Breathing and Tilting: Mesoscale Simulations Illuminate Influenza Glycoprotein Vulnerabilities. ACS CENTRAL SCIENCE 2022; 8:1646-1663. [PMID: 36589893 PMCID: PMC9801513 DOI: 10.1021/acscentsci.2c00981] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Indexed: 05/28/2023]
Abstract
Influenza virus has resurfaced recently from inactivity during the early stages of the COVID-19 pandemic, raising serious concerns about the nature and magnitude of future epidemics. The main antigenic targets of influenza virus are two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA). Whereas the structural and dynamical properties of both glycoproteins have been studied previously, the understanding of their plasticity in the whole-virion context is fragmented. Here, we investigate the dynamics of influenza glycoproteins in a crowded protein environment through mesoscale all-atom molecular dynamics simulations of two evolutionary-linked glycosylated influenza A whole-virion models. Our simulations reveal and kinetically characterize three main molecular motions of influenza glycoproteins: NA head tilting, HA ectodomain tilting, and HA head breathing. The flexibility of HA and NA highlights antigenically relevant conformational states, as well as facilitates the characterization of a novel monoclonal antibody, derived from convalescent human donor, that binds to the underside of the NA head. Our work provides previously unappreciated views on the dynamics of HA and NA, advancing the understanding of their interplay and suggesting possible strategies for the design of future vaccines and antivirals against influenza.
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Affiliation(s)
- Lorenzo Casalino
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California92093, United States
| | - Christian Seitz
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California92093, United States
| | - Julia Lederhofer
- Vaccine
Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland20892, United States
| | - Yaroslav Tsybovsky
- Electron
Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research
Sponsored by the National Cancer Institute, Frederick, Maryland21702, United States
| | - Ian A. Wilson
- Department
of Integrative Structural and Computational Biology and the Skaggs
Institute for Chemical Biology, The Scripps
Research Institute, La Jolla, California92037, United States
| | - Masaru Kanekiyo
- Vaccine
Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland20892, United States
| | - Rommie E. Amaro
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California92093, United States
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126
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Zhu R, Canena D, Sikora M, Klausberger M, Seferovic H, Mehdipour AR, Hain L, Laurent E, Monteil V, Wirnsberger G, Wieneke R, Tampé R, Kienzl NF, Mach L, Mirazimi A, Oh YJ, Penninger JM, Hummer G, Hinterdorfer P. Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level. Nat Commun 2022; 13:7926. [PMID: 36566234 PMCID: PMC9789309 DOI: 10.1038/s41467-022-35641-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/14/2022] [Indexed: 12/25/2022] Open
Abstract
Recent waves of COVID-19 correlate with the emergence of the Delta and the Omicron variant. We report that the Spike trimer acts as a highly dynamic molecular caliper, thereby forming up to three tight bonds through its RBDs with ACE2 expressed on the cell surface. The Spike of both Delta and Omicron (B.1.1.529) Variant enhance and markedly prolong viral attachment to the host cell receptor ACE2, as opposed to the early Wuhan-1 isolate. Delta Spike shows rapid binding of all three Spike RBDs to three different ACE2 molecules with considerably increased bond lifetime when compared to the reference strain, thereby significantly amplifying avidity. Intriguingly, Omicron (B.1.1.529) Spike displays less multivalent bindings to ACE2 molecules, yet with a ten time longer bond lifetime than Delta. Delta and Omicron (B.1.1.529) Spike variants enhance and prolong viral attachment to the host, which likely not only increases the rate of viral uptake, but also enhances the resistance of the variants against host-cell detachment by shear forces such as airflow, mucus or blood flow. We uncover distinct binding mechanisms and strategies at single-molecule resolution, employed by circulating SARS-CoV-2 variants to enhance infectivity and viral transmission.
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Affiliation(s)
- Rong Zhu
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Daniel Canena
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Mateusz Sikora
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Faculty of Physics, University of Vienna, Vienna, Austria
- Malopolska Centre of Biotechnology, Gronostajowa 7A, 30-387, Kraków, Poland
| | - Miriam Klausberger
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Hannah Seferovic
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Ahmad Reza Mehdipour
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Center for Molecular Modeling, University of Ghent, Ghent, Belgium
| | - Lisa Hain
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Elisabeth Laurent
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
- Core Facility Biomolecular & Cellular Analysis, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Vanessa Monteil
- Department of Laboratory Medicine, Unit of Clinical Microbiology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | | | - Ralph Wieneke
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Nikolaus F Kienzl
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Lukas Mach
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Ali Mirazimi
- Department of Laboratory Medicine, Unit of Clinical Microbiology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
- National Veterinary Institute, Uppsala, Sweden
| | - Yoo Jin Oh
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria.
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany.
| | - Peter Hinterdorfer
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria.
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127
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Bowen JE, Park YJ, Stewart C, Brown JT, Sharkey WK, Walls AC, Joshi A, Sprouse KR, McCallum M, Tortorici MA, Franko NM, Logue JK, Mazzitelli IG, Nguyen AW, Silva RP, Huang Y, Low JS, Jerak J, Tiles SW, Ahmed K, Shariq A, Dan JM, Zhang Z, Weiskopf D, Sette A, Snell G, Posavad CM, Iqbal NT, Geffner J, Bandera A, Gori A, Sallusto F, Maynard JA, Crotty S, Van Voorhis WC, Simmerling C, Grifantini R, Chu HY, Corti D, Veesler D. SARS-CoV-2 spike conformation determines plasma neutralizing activity elicited by a wide panel of human vaccines. Sci Immunol 2022; 7:eadf1421. [PMID: 36356052 PMCID: PMC9765460 DOI: 10.1126/sciimmunol.adf1421] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022]
Abstract
Numerous safe and effective coronavirus disease 2019 vaccines have been developed worldwide that use various delivery technologies and engineering strategies. We show here that vaccines containing prefusion-stabilizing S mutations elicit antibody responses in humans with enhanced recognition of S and the S1 subunit relative to postfusion S as compared with vaccines lacking these mutations or natural infection. Prefusion S and S1 antibody binding titers positively and equivalently correlated with neutralizing activity, and depletion of S1-directed antibodies completely abrogated plasma neutralizing activity. We show that neutralizing activity is almost entirely directed to the S1 subunit and that variant cross-neutralization is mediated solely by receptor binding domain-specific antibodies. Our data provide a quantitative framework for guiding future S engineering efforts to develop vaccines with higher resilience to the emergence of variants than current technologies.
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Affiliation(s)
- John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jack T. Brown
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - William K. Sharkey
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Anshu Joshi
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Kaitlin R. Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Nicholas M. Franko
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Jennifer K. Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Ignacio G. Mazzitelli
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Facultad de Medicina, Buenos Aires C1121ABG, Argentina
| | - Annalee W. Nguyen
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX
| | - Rui P. Silva
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX
| | - Yimin Huang
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX
| | - Jun Siong Low
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Josipa Jerak
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Sasha W Tiles
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Kumail Ahmed
- Department of Paediatrics and Child Health, and Biological & Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
| | - Asefa Shariq
- Department of Paediatrics and Child Health, and Biological & Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
| | - Jennifer M. Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA
| | - Zeli Zhang
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA
| | | | - Christine M. Posavad
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Najeeha Talat Iqbal
- Department of Paediatrics and Child Health, and Biological & Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
| | - Jorge Geffner
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Facultad de Medicina, Buenos Aires C1121ABG, Argentina
| | - Alessandra Bandera
- Infectious Diseases Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Andrea Gori
- Infectious Diseases Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Jennifer A. Maynard
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA
| | - Wesley C. Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - Renata Grifantini
- INGM, Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, 20122 Milan, Italy
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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128
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Funari R, Bhalla N, Gentile L. Measuring the Radius of Gyration and Intrinsic Flexibility of Viral Proteins in Buffer Solution Using Small-Angle X-ray Scattering. ACS MEASUREMENT SCIENCE AU 2022; 2:547-552. [PMID: 36573077 PMCID: PMC9783065 DOI: 10.1021/acsmeasuresciau.2c00048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 06/17/2023]
Abstract
Measuring structural features of proteins dispersed in buffer solution, in contrast to crystal form, is indispensable in understanding morphological characteristics of the biomolecule in a native environment. We report on the structure and apparent viscosity of unfolded α and β variants of SARS-CoV-2 spike proteins dispersed in buffer solutions. The radius of gyration of the β variant is found to be larger than that of the α variant, while the ab initio computation of one of the possible particle-like bodies is consistent with the small-angle X-ray scattering (SAXS) profiles resembling a conformation similar to the three-dimensional structure of the folded state of the corresponding α and β spike variant. However, a smaller radius of gyration with respect to the predicted folded state of 2.4 and 2.7 is observed for both α and β variants, respectively. Our work complements the structural characterization of spike proteins using cryo-electron microscopy techniques. The measurement/analysis discussed here might be useful for quick and cost-effective evaluation of several protein structures, let alone mutated viral proteins, which is useful for drug discovery/development applications.
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Affiliation(s)
- Riccardo Funari
- Department
of Physics “M. Merlin”, University
of Bari Aldo Moro, Via Amendola, 173, Bari 70125, Italy
- Institute
for Photonics and Nanotechnologies, CNR, Via Amendola, 173, Bari, 70125, Italy
| | - Nikhil Bhalla
- Nanotechnology
and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, Jordanstown, Shore Road, Northern Ireland BT37 0QB, United Kingdom
- Healthcare
Technology Hub, Ulster University, Jordanstown Shore Road, Northern Ireland BT37 0QB, United Kingdom
| | - Luigi Gentile
- Department
of Chemistry, University of Bari Aldo Moro, Edoardo Orabona 4, Bari 70125, Italy
- Bari
unit,
Center for Colloid and Surface Science (CSGI), via della Lastruccia 3, Sesto Fiorentino 50019, Italy
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129
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Abstract
The global spread of the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the continuously emerging new variants underscore an urgent need for effective therapeutics for the treatment of coronavirus disease 2019 (COVID-19). Here, we screened several FDA-approved amphiphilic drugs and determined that sertraline (SRT) exhibits potent antiviral activity against infection of SARS-CoV-2 pseudovirus (PsV) and authentic virus in vitro. It effectively inhibits SARS-CoV-2 spike (S)-mediated cell-cell fusion. SRT targets the early stage of viral entry. It can bind to the S1 subunit of the S protein, especially the receptor binding domain (RBD), thus blocking S-hACE2 interaction and interfering with the proteolysis process of S protein. SRT is also effective against infection with SARS-CoV-2 PsV variants, including the newly emerging Omicron. The combination of SRT and other antivirals exhibits a strong synergistic effect against infection of SARS-CoV-2 PsV. The antiviral activity of SRT is independent of serotonin transporter expression. Moreover, SRT effectively inhibits infection of SARS-CoV-2 PsV and alleviates the inflammation process and lung pathological alterations in transduced mice in vivo. Therefore, SRT shows promise as a treatment option for COVID-19. IMPORTANCE The study shows SRT is an effective entry inhibitor against infection of SARS-CoV-2, which is currently prevalent globally. SRT targets the S protein of SARS-CoV-2 and is effective against a panel of SARS-CoV-2 variants. It also could be used in combination to prevent SARS-CoV-2 infection. More importantly, with long history of clinical use and proven safety, SRT might be particularly suitable to treat infection of SARS-CoV-2 in the central nervous system and optimized for treatment in older people, pregnant women, and COVID-19 patients with heart complications, which are associated with severity and mortality of COVID-19.
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130
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Zhao F, Zai X, Zhang Z, Xu J, Chen W. Challenges and developments in universal vaccine design against SARS-CoV-2 variants. NPJ Vaccines 2022; 7:167. [PMID: 36535982 PMCID: PMC9761649 DOI: 10.1038/s41541-022-00597-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had become a global concern because of its unexpectedly high pathogenicity and transmissibility. SARS-CoV-2 variants that reduce the immune protection elicited from previous vaccination or natural infection raise challenges in controlling the spread of the pandemic. The development of universal vaccines against these variants seems to be a practical solution to alleviate the physical and economic effects caused by this disease, but it is hard to achieve. In this review, we describe the high mutation rate of RNA viruses and dynamic molecular structures of SARS-CoV-2 variants in several major neutralizing epitopes, trying to answer the question of why universal vaccines are difficult to design. Understanding the biological basis of immune evasion is crucial for combating these obstacles. We then summarize several advancements worthy of further study, including heterologous prime-boost regimens, construction of chimeric immunogens, design of protein nanoparticle antigens, and utilization of conserved neutralizing epitopes. The fact that some immunogens can induce cross-reactive immune responses against heterologous coronaviruses provides hints for universal vaccine development. We hope this review can provide inspiration to current universal vaccine studies.
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Affiliation(s)
- Fangxin Zhao
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, 10071, China
- School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Xiaodong Zai
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, 10071, China
| | - Zhiling Zhang
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, 10071, China
- College of pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Junjie Xu
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, 10071, China.
| | - Wei Chen
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, 10071, China.
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131
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Verkhivker GM, Agajanian S, Oztas D, Gupta G. Computational analysis of protein stability and allosteric interaction networks in distinct conformational forms of the SARS-CoV-2 spike D614G mutant: reconciling functional mechanisms through allosteric model of spike regulation. J Biomol Struct Dyn 2022; 40:9724-9741. [PMID: 34060425 DOI: 10.1080/07391102.2021.1933594] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this study, we used an integrative computational approach to examine molecular mechanisms underlying functional effects of the D614G mutation by exploring atomistic modeling of the SARS-CoV-2 spike proteins as allosteric regulatory machines. We combined coarse-grained simulations, protein stability and dynamic fluctuation communication analysis with network-based community analysis to examine structures of the native and mutant SARS-CoV-2 spike proteins in different functional states. Through distance fluctuations communication analysis, we probed stability and allosteric communication propensities of protein residues in the native and mutant SARS-CoV-2 spike proteins, providing evidence that the D614G mutation can enhance long-range signaling of the allosteric spike engine. By combining functional dynamics analysis and ensemble-based alanine scanning of the SARS-CoV-2 spike proteins we found that the D614G mutation can improve stability of the spike protein in both closed and open forms, but shifting thermodynamic preferences towards the open mutant form. Our results revealed that the D614G mutation can promote the increased number of stable communities and allosteric hub centers in the open form by reorganizing and enhancing the stability of the S1-S2 inter-domain interactions and restricting mobility of the S1 regions. This study provides atomistic-based view of allosteric communications in the SARS-CoV-2 spike proteins, suggesting that the D614G mutation can exert its primary effect through allosterically induced changes on stability and communications in the residue interaction networks.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gennady M Verkhivker
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA, USA.,Depatment of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, USA
| | - Steve Agajanian
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA, USA
| | - Deniz Oztas
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA, USA
| | - Grace Gupta
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA, USA
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132
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Pipitò L, Reynolds CA, Deganutti G. Is the Stalk of the SARS-CoV-2 Spike Protein Druggable? Viruses 2022; 14:2789. [PMID: 36560795 PMCID: PMC9786045 DOI: 10.3390/v14122789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/28/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
The spike protein is key to SARS-CoV-2 high infectivity because it facilitates the receptor binding domain (RBD) encounter with ACE2. As targeting subunit S1 has not yet delivered an ACE2-binding inhibitor, we have assessed the druggability of the conserved segment of the spike protein stalk within subunit S2 by means of an integrated computational approach that combines the molecular docking of an optimized library of fragments with high-throughput molecular dynamics simulations. The high propensity of the spike protein to mutate in key regions that are responsible for the recognition of the human angiotensin-converting enzyme 2 (hACE2) or for the recognition of antibodies, has made subunit S1 of the spike protein difficult to target. Despite the inherent flexibility of the stalk region, our results suggest two hidden interhelical binding sites, whose accessibility is only partially hampered by glycan residues.
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Affiliation(s)
| | | | - Giuseppe Deganutti
- Centre for Sport, Exercise and Life Sciences, Faculty of Health and Life Sciences, Coventry University, Coventry CV1 5FB, UK
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133
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Shi W, Cai Y, Zhu H, Peng H, Voyer J, Rits-Volloch S, Cao H, Mayer ML, Song K, Xu C, Lu J, Zhang J, Chen B. Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.05.519151. [PMID: 36523411 PMCID: PMC9753783 DOI: 10.1101/2022.12.05.519151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into host cells depends on refolding of the virus-encoded spike protein from a prefusion conformation, metastable after cleavage, to a lower energy, stable postfusion conformation. This transition overcomes kinetic barriers for fusion of viral and target cell membranes. We report here a cryo-EM structure of the intact postfusion spike in a lipid bilayer that represents single-membrane product of the fusion reaction. The structure provides structural definition of the functionally critical membraneinteracting segments, including the fusion peptide and transmembrane anchor. The internal fusion peptide forms a hairpin-like wedge that spans almost the entire lipid bilayer and the transmembrane segment wraps around the fusion peptide at the last stage of membrane fusion. These results advance our understanding of the spike protein in a membrane environment and may guide development of intervention strategies.
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134
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Harastani M, Vuillemot R, Hamitouche I, Moghadam NB, Jonic S. ContinuousFlex: Software package for analyzing continuous conformational variability of macromolecules in cryo electron microscopy and tomography data. J Struct Biol 2022; 214:107906. [PMID: 36244611 DOI: 10.1016/j.jsb.2022.107906] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 09/02/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
ContinuousFlex is a user-friendly open-source software package for analyzing continuous conformational variability of macromolecules in cryo electron microscopy (cryo-EM) and cryo electron tomography (cryo-ET) data. In 2019, ContinuousFlex became available as a plugin for Scipion, an image processing software package extensively used in the cryo-EM field. Currently, ContinuousFlex contains software for running (1) recently published methods HEMNMA-3D, TomoFlow, and NMMD; (2) earlier published methods HEMNMA and StructMap; and (3) methods for simulating cryo-EM and cryo-ET data with conformational variability and methods for data preprocessing. It also includes external software for molecular dynamics simulation (GENESIS) and normal mode analysis (ElNemo), used in some of the mentioned methods. The HEMNMA software has been presented in the past, but not the software of other methods. Besides, ContinuousFlex currently also offers a deep learning extension of HEMNMA, named DeepHEMNMA. In this article, we review these methods in the context of the ContinuousFlex package, developed to facilitate their use by the community.
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Affiliation(s)
- Mohamad Harastani
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Rémi Vuillemot
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Ilyes Hamitouche
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Nima Barati Moghadam
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Slavica Jonic
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France.
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135
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Cryo-electron tomography: The power of seeing the whole picture. Biochem Biophys Res Commun 2022; 633:26-28. [DOI: 10.1016/j.bbrc.2022.08.078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 08/25/2022] [Indexed: 11/06/2022]
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136
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Rodríguez de Francisco B, Bezault A, Xu XP, Hanein D, Volkmann N. MEPSi: A tool for simulating tomograms of membrane-embedded proteins. J Struct Biol 2022; 214:107921. [PMID: 36372192 DOI: 10.1016/j.jsb.2022.107921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 10/27/2022] [Accepted: 11/05/2022] [Indexed: 11/11/2022]
Abstract
The throughput and fidelity of cryogenic cellular electron tomography (cryo-ET) is constantly increasing through advances in cryogenic electron microscope hardware, direct electron detection devices, and powerful image processing algorithms. However, the need for careful optimization of sample preparations and for access to expensive, high-end equipment, make cryo-ET a costly and time-consuming technique. Generally, only after the last step of the cryo-ET workflow, when reconstructed tomograms are available, it becomes clear whether the chosen imaging parameters were suitable for a specific type of sample in order to answer a specific biological question. Tools for a-priory assessment of the feasibility of samples to answer biological questions and how to optimize imaging parameters to do so would be a major advantage. Here we describe MEPSi (Membrane Embedded Protein Simulator), a simulation tool aimed at rapid and convenient evaluation and optimization of cryo-ET data acquisition parameters for studies of transmembrane proteins in their native environment. We demonstrate the utility of MEPSi by showing how to detangle the influence of different data collection parameters and different orientations in respect to tilt axis and electron beam for two examples: (1) simulated plasma membranes with embedded single-pass transmembrane αIIbβ3 integrin receptors and (2) simulated virus membranes with embedded SARS-CoV-2 spike proteins.
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Affiliation(s)
- Borja Rodríguez de Francisco
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Studies of Macromolecular Machines in Cellulo Unit, Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Image Analysis Unit, Paris, France
| | - Armel Bezault
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Studies of Macromolecular Machines in Cellulo Unit, Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Image Analysis Unit, Paris, France
| | | | - Dorit Hanein
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Studies of Macromolecular Machines in Cellulo Unit, Paris, France; Scintillon Institute, San Diego, CA 92121, USA
| | - Niels Volkmann
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Image Analysis Unit, Paris, France.
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137
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Novel chimeric proteins mimicking SARS-CoV-2 spike epitopes with broad inhibitory activity. Int J Biol Macromol 2022; 222:2467-2478. [PMID: 36220405 PMCID: PMC9546781 DOI: 10.1016/j.ijbiomac.2022.10.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/29/2022] [Accepted: 10/05/2022] [Indexed: 11/05/2022]
Abstract
SARS-CoV-2 spike (S) protein mediates virus attachment to the cells and fusion between viral and cell membranes. Membrane fusion is driven by mutual interaction between the highly conserved heptad-repeat regions 1 and 2 (HR1 and HR2) of the S2 subunit of the spike. For this reason, these S2 regions are interesting therapeutic targets for COVID-19. Although HR1 and HR2 have been described as transiently exposed during the fusion process, no significant antibody responses against these S2 regions have been reported. Here we designed chimeric proteins that imitate highly stable HR1 helical trimers and strongly bind to HR2. The proteins have broad inhibitory activity against WT B.1 and BA.1 viruses. Sera from COVID-19 convalescent donors showed significant levels of reactive antibodies (IgG and IgA) against the HR1 mimetic proteins, whereas these antibody responses were absent in sera from uninfected donors. Moreover, both inhibitory activity and antigenicity of the proteins correlate positively with their structural stability but not with the number of amino acid changes in their HR1 sequences, indicating a conformational and conserved nature of the involved epitopes. Our results reveal previously undetected spike epitopes that may guide the design of new robust COVID-19 vaccines and therapies.
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138
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Ling Z, Yi C, Sun X, Yang Z, Sun B. Broad strategies for neutralizing SARS-CoV-2 and other human coronaviruses with monoclonal antibodies. SCIENCE CHINA. LIFE SCIENCES 2022; 66:658-678. [PMID: 36443513 PMCID: PMC9707277 DOI: 10.1007/s11427-022-2215-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/04/2022] [Indexed: 11/30/2022]
Abstract
Antibody therapeutics and vaccines for coronavirus disease 2019 (COVID-19) have been approved in many countries, with most being developed based on the original strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 has an exceptional ability to mutate under the pressure of host immunity, especially the immune-dominant spike protein of the virus, which is the target of both antibody drugs and vaccines. Given the continuous evolution of the virus and the identification of critical mutation sites, the World Health Organization (WHO) has named 5 variants of concern (VOCs): 4 are previously circulating VOCs, and 1 is currently circulating (Omicron). Due to multiple mutations in the spike protein, the recently emerged Omicron and descendent lineages have been shown to have the strongest ability to evade the neutralizing antibody (NAb) effects of current antibody drugs and vaccines. The development and characterization of broadly neutralizing antibodies (bNAbs) will provide broad strategies for the control of the sophisticated virus SARS-CoV-2. In this review, we describe how the virus evolves to escape NAbs and the potential neutralization mechanisms that associated with bNAbs. We also summarize progress in the development of bNAbs against SARS-CoV-2, human coronaviruses (CoVs) and other emerging pathogens and highlight their scientific and clinical significance.
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Affiliation(s)
- Zhiyang Ling
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunyan Yi
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyu Sun
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhuo Yang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing Sun
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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139
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Acosta‐Gutiérrez S, Buckley J, Battaglia G. The Role of Host Cell Glycans on Virus Infectivity: The SARS-CoV-2 Case. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 10:e2201853. [PMID: 36417571 PMCID: PMC9811451 DOI: 10.1002/advs.202201853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Glycans are ubiquitously expressed sugars, coating the cell and protein surfaces. They are found on many proteins as either short and branched chains or long chains sticking out from special membrane proteins, known as proteoglycans. This sugar cushion, the glycocalyx, modulates specific interactions and protects the cell. Here it is shown that both the expression of proteoglycans and the glycans expressed on the surface of both the host and virus proteins have a critical role in modulating viral attachment to the cell. A mathematical model using SARS-Cov-2 as an archetypical virus to study the glycan role during infection is proposed. It is shown that this occurs via a tug-of-war of forces. On one side, the multivalent molecular recognition that viral proteins have toward specific host glycans and receptors. On the other side, the glycan steric repulsion that a virus must overcome to approach such specific receptors. By balancing both interactions, viral tropism can be predicted. In other words, the authors can map out the cells susceptible to virus infection in terms of receptors and proteoglycans compositions.
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Affiliation(s)
- Silvia Acosta‐Gutiérrez
- Institute for the Physics of Living SystemsUniversity College LondonLondonCentral LondonUK
- Institute of Structural and Molecular BiologyUniversity College LondonLondonCentral LondonUK
- Department of ChemistryUniversity College London20 Gordon StLondonCentral LondonWC1H 0AJUK
| | - Joseph Buckley
- Institute for the Physics of Living SystemsUniversity College LondonLondonCentral LondonUK
- Institute of Structural and Molecular BiologyUniversity College LondonLondonCentral LondonUK
- Department of ChemistryUniversity College London20 Gordon StLondonCentral LondonWC1H 0AJUK
| | - Giuseppe Battaglia
- Institute for the Physics of Living SystemsUniversity College LondonLondonCentral LondonUK
- Institute of Structural and Molecular BiologyUniversity College LondonLondonCentral LondonUK
- Department of ChemistryUniversity College London20 Gordon StLondonCentral LondonWC1H 0AJUK
- Institute for Bioengineering of Catalunya (IBEC)The Barcelona Institute of Science and TechnologyBarcelonaBarcelona08028Spain
- Catalan Institution for Research and Advances Studies (ICREA)BarcelonaSpain
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140
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Kuhn CC, Basnet N, Bodakuntla S, Alvarez-Brecht P, Nichols S, Martinez-Sanchez A, Agostini L, Soh YM, Takagi J, Biertümpfel C, Mizuno N. Direct Cryo-ET observation of platelet deformation induced by SARS-CoV-2 Spike protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.11.22.517574. [PMID: 36451880 PMCID: PMC9709796 DOI: 10.1101/2022.11.22.517574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
SARS-CoV-2 is a novel coronavirus responsible for the COVID-19 pandemic. Its high pathogenicity is due to SARS-CoV-2 spike protein (S protein) contacting host-cell receptors. A critical hallmark of COVID-19 is the occurrence of coagulopathies. Here, we report the direct observation of the interactions between S protein and platelets. Live imaging showed that the S protein triggers platelets to deform dynamically, in some cases, leading to their irreversible activation. Strikingly, cellular cryo-electron tomography revealed dense decorations of S protein on the platelet surface, inducing filopodia formation. Hypothesizing that S protein binds to filopodia-inducing integrin receptors, we tested the binding to RGD motif-recognizing platelet integrins and found that S protein recognizes integrin α v β 3 . Our results infer that the stochastic activation of platelets is due to weak interactions of S protein with integrin, which can attribute to the pathogenesis of COVID-19 and the occurrence of rare but severe coagulopathies.
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Affiliation(s)
- Christopher Cyrus Kuhn
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA
| | - Nirakar Basnet
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA
| | - Satish Bodakuntla
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA
| | - Pelayo Alvarez-Brecht
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA.,Department of Computer Sciences, Faculty of Sciences - Campus Llamaquique, University of Oviedo, Oviedo 33007, Spain
| | - Scott Nichols
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA
| | - Antonio Martinez-Sanchez
- Department of Computer Sciences, Faculty of Sciences - Campus Llamaquique, University of Oviedo, Oviedo 33007, Spain.,Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario s/n, 33011, Oviedo, Spain
| | - Lorenzo Agostini
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA
| | - Young-Min Soh
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA
| | - Junichi Takagi
- Osaka University Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Christian Biertümpfel
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA
| | - Naoko Mizuno
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA.,National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA
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141
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Calder LJ, Calcraft T, Hussain S, Harvey R, Rosenthal PB. Electron cryotomography of SARS-CoV-2 virions reveals cylinder-shaped particles with a double layer RNP assembly. Commun Biol 2022; 5:1210. [PMID: 36357779 PMCID: PMC9648435 DOI: 10.1038/s42003-022-04183-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022] Open
Abstract
SARS-CoV-2 is a lipid-enveloped Betacoronavirus and cause of the Covid-19 pandemic. To study the three-dimensional architecture of the virus, we perform electron cryotomography (cryo-ET) on SARS-Cov-2 virions and three variants revealing particles of regular cylindrical morphology. The ribonucleoprotein particles packaging the genome in the virion interior form a dense, double layer assembly with a cylindrical shape related to the overall particle morphology. This organisation suggests structural interactions important to virus assembly.
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Affiliation(s)
- Lesley J. Calder
- grid.451388.30000 0004 1795 1830Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Thomas Calcraft
- grid.451388.30000 0004 1795 1830Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Saira Hussain
- grid.451388.30000 0004 1795 1830Worldwide Influenza Centre, The Francis Crick Institute, NW1 1AT London, UK ,grid.451388.30000 0004 1795 1830RNA Virus Replication Laboratory, The Francis Crick Institute, NW1 1AT London, UK
| | - Ruth Harvey
- grid.451388.30000 0004 1795 1830Worldwide Influenza Centre, The Francis Crick Institute, NW1 1AT London, UK
| | - Peter B. Rosenthal
- grid.451388.30000 0004 1795 1830Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
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142
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Garza-Domínguez R, Torres-Quiroz F. Evolutionary Signals in Coronaviral Structural Proteins Suggest Possible Complex Mechanisms of Post-Translational Regulation in SARS-CoV-2 Virus. Viruses 2022; 14:v14112469. [PMID: 36366566 PMCID: PMC9696223 DOI: 10.3390/v14112469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/18/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022] Open
Abstract
Post-translational regulation of proteins has emerged as a central topic of research in the field of functional proteomics. Post-translational modifications (PTMs) dynamically control the activities of proteins and are involved in a wide range of biological processes. Crosstalk between different types of PTMs represents a key mechanism of regulation and signaling. Due to the current pandemic of the novel and dangerous SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) virus, here we present an in silico analysis of different types of PTMs in structural proteins of coronaviruses. A dataset of PTM sites was studied at three levels: conservation analysis, mutational analysis and crosstalk analysis. We identified two sets of PTMs which could have important functional roles in the regulation of the structural proteins of coronaviruses. Additionally, we found seven interesting signals of potential crosstalk events. These results reveal a higher level of complexity in the mechanisms of post-translational regulation of coronaviral proteins and provide new insights into the adaptation process of the SARS-CoV-2 virus.
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143
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Nattich-Rak M, Sadowska M, Motyczyńska M, Adamczyk Z. Mimicking Pseudo-Virion Interactions with Abiotic Surfaces: Deposition of Polymer Nanoparticles with Albumin Corona. Biomolecules 2022; 12:1658. [PMID: 36359008 PMCID: PMC9687657 DOI: 10.3390/biom12111658] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/02/2022] [Accepted: 11/02/2022] [Indexed: 10/14/2023] Open
Abstract
Adsorption of human serum albumin (HSA) molecules on negatively charged polystyrene microparticles was studied using the dynamic light scattering, the electrophoretic and the solution depletion methods involving atomic force microscopy. Initially, the physicochemical characteristics of the albumin comprising the hydrodynamic diameter, the zeta potential and the isoelectric point were determined as a function of pH. Analogous characteristics of the polymer particles were acquired, including their size and zeta potential. The formation of albumin corona on the particles was investigated in situ by electrophoretic mobility measurements. The size, stability and electrokinetic properties of the particles with the corona were also determined. The particle diameter was equal to 125 nm, which coincides with the size of the SARS-CoV-2 virion. The isoelectric point of the particles appeared at a pH of 5. The deposition kinetics of the particles was determined by atomic force microscopy (AFM) under diffusion and by quartz microbalance (QCM) under flow conditions. It was shown that the deposition rate at a gold sensor abruptly vanished with pH following the decrease in the zeta potential of the particles. It is postulated that the acquired results can be used as useful reference systems mimicking virus adsorption on abiotic surfaces.
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Affiliation(s)
- Małgorzata Nattich-Rak
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Cracow, Poland
| | - Marta Sadowska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Cracow, Poland
| | - Maja Motyczyńska
- The Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Cracow, Poland
| | - Zbigniew Adamczyk
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Cracow, Poland
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144
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Siavash Moakhar R, del Real Mata C, Jalali M, Shafique H, Sanati A, de Vries J, Strauss J, AbdElFatah T, Ghasemi F, McLean M, I. Hosseini I, Lu Y, Yedire SG, Mahshid SS, Tabatabaiefar MA, Liang C, Mahshid S. A Versatile Biomimic Nanotemplating Fluidic Assay for Multiplex Quantitative Monitoring of Viral Respiratory Infections and Immune Responses in Saliva and Blood. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2204246. [PMID: 36253095 PMCID: PMC9685479 DOI: 10.1002/advs.202204246] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Indexed: 05/17/2023]
Abstract
The last pandemic exposed critical gaps in monitoring and mitigating the spread of viral respiratory infections at the point-of-need. A cost-effective multiplexed fluidic device (NFluidEX), as a home-test kit analogous to a glucometer, that uses saliva and blood for parallel quantitative detection of viral infection and body's immune response in an automated manner within 11 min is proposed. The technology integrates a versatile biomimetic receptor based on molecularly imprinted polymers in a core-shell structure with nano gold electrodes, a multiplexed fluidic-impedimetric readout, built-in saliva collection/preparation, and smartphone-enabled data acquisition and interpretation. NFluidEX is validated with Influenza A H1N1 and SARS-CoV-2 (original strain and variants of concern), and achieves low detection limit in saliva and blood for the viral proteins and the anti-receptor binding domain (RBD) Immunoglobulin G (IgG) and Immunoglobulin M (IgM), respectively. It is demonstrated that nanoprotrusions of gold electrodes are essential for the fine templating of antibodies and spike proteins during molecular imprinting, and differentiation of IgG and IgM in whole blood. In the clinical setting, NFluidEX achieves 100% sensitivity and 100% specificity by testing 44 COVID-positive and 25 COVID-negative saliva and blood samples on par with the real-time quantitative polymerase chain reaction (p < 0.001, 95% confidence) and the enzyme-linked immunosorbent assay.
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Affiliation(s)
| | | | - Mahsa Jalali
- Department of BioengineeringMcGill UniversityMontrealQuebecH3A 0E9Canada
| | - Houda Shafique
- Department of BioengineeringMcGill UniversityMontrealQuebecH3A 0E9Canada
| | - Alireza Sanati
- Biosensor Research CenterIsfahan University of Medical SciencesIsfahan81746‐73461Iran
| | - Justin de Vries
- Department of BioengineeringMcGill UniversityMontrealQuebecH3A 0E9Canada
| | - Julia Strauss
- Department of BioengineeringMcGill UniversityMontrealQuebecH3A 0E9Canada
| | - Tamer AbdElFatah
- Department of BioengineeringMcGill UniversityMontrealQuebecH3A 0E9Canada
| | - Fahimeh Ghasemi
- Biosensor Research CenterIsfahan University of Medical SciencesIsfahan81746‐73461Iran
| | - Myles McLean
- Department of MedicineMcGill UniversityMontrealQuebecH4A 3J1Canada
- Lady Davis Institute for Medical Research and McGill AIDS CentreJewish General HospitalMontrealQCH3T 1E2Canada
| | - Imman I. Hosseini
- Department of BioengineeringMcGill UniversityMontrealQuebecH3A 0E9Canada
| | - Yao Lu
- Department of BioengineeringMcGill UniversityMontrealQuebecH3A 0E9Canada
| | | | - Sahar Sadat Mahshid
- Biological SciencesSunnybrook Research InstituteSunnybrook Health Sciences CentreTorontoONM4N 3M5Canada
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular BiologySchool of MedicineIsfahan University of Medical SciencesIsfahan81746‐73461Iran
| | - Chen Liang
- Department of MedicineMcGill UniversityMontrealQuebecH4A 3J1Canada
- Lady Davis Institute for Medical Research and McGill AIDS CentreJewish General HospitalMontrealQCH3T 1E2Canada
| | - Sara Mahshid
- Department of BioengineeringMcGill UniversityMontrealQuebecH3A 0E9Canada
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145
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Isotropic reconstruction for electron tomography with deep learning. Nat Commun 2022; 13:6482. [PMID: 36309499 PMCID: PMC9617606 DOI: 10.1038/s41467-022-33957-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/05/2022] [Indexed: 12/25/2022] Open
Abstract
Cryogenic electron tomography (cryoET) allows visualization of cellular structures in situ. However, anisotropic resolution arising from the intrinsic "missing-wedge" problem has presented major challenges in visualization and interpretation of tomograms. Here, we have developed IsoNet, a deep learning-based software package that iteratively reconstructs the missing-wedge information and increases signal-to-noise ratio, using the knowledge learned from raw tomograms. Without the need for sub-tomogram averaging, IsoNet generates tomograms with significantly reduced resolution anisotropy. Applications of IsoNet to three representative types of cryoET data demonstrate greatly improved structural interpretability: resolving lattice defects in immature HIV particles, establishing architecture of the paraflagellar rod in Eukaryotic flagella, and identifying heptagon-containing clathrin cages inside a neuronal synapse of cultured cells. Therefore, by overcoming two fundamental limitations of cryoET, IsoNet enables functional interpretation of cellular tomograms without sub-tomogram averaging. Its application to high-resolution cellular tomograms should also help identify differently oriented complexes of the same kind for sub-tomogram averaging.
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146
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Xu Z, Zou Y, Gao X, Niu MM, Li J, Xue L, Jiang S. Dual-targeting cyclic peptides of receptor-binding domain (RBD) and main protease (Mpro) as potential drug leads for the treatment of SARS-CoV-2 infection. Front Pharmacol 2022; 13:1041331. [PMID: 36339564 PMCID: PMC9627161 DOI: 10.3389/fphar.2022.1041331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/10/2022] [Indexed: 12/01/2023] Open
Abstract
The receptor-binding domain (RBD) and the main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) play a crucial role in the entry and replication of viral particles, and co-targeting both of them could be an attractive approach for the treatment of SARS-CoV-2 infection by setting up a "double lock" in the viral lifecycle. However, few dual RBD/Mpro-targeting agents have been reported. Here, four novel RBD/Mpro dual-targeting peptides, termed as MRs 1-4, were discovered by an integrated virtual screening scheme combining molecular docking-based screening and molecular dynamics simulation. All of them possessed nanomolar binding affinities to both RBD and Mpro ranging from 14.4 to 39.2 nM and 22.5-40.4 nM, respectively. Further pseudovirus infection assay revealed that the four selected peptides showed >50% inhibition against SARS-CoV-2 pseudovirus at a concentration of 5 µM without significant cytotoxicity to host cells. This study leads to the identification of a class of dual RBD/Mpro-targeting agents, which may be developed as potential and effective SARS-CoV-2 therapeutics.
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Affiliation(s)
- Zhen Xu
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Yunting Zou
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Xi Gao
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Jindong Li
- Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Lu Xue
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Su Jiang
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
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147
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Żeliszewska P, Wasilewska M, Batys P, Pogoda K, Deptuła P, Bucki R, Adamczyk Z. SARS-CoV-2 Spike Protein (RBD) Subunit Adsorption at Abiotic Surfaces and Corona Formation at Polymer Particles. Int J Mol Sci 2022; 23:ijms232012374. [PMID: 36293231 PMCID: PMC9604293 DOI: 10.3390/ijms232012374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 12/29/2022] Open
Abstract
The adsorption kinetics of the SARS-CoV-2 spike protein subunit with the receptor binding domain at abiotic surfaces was investigated. A combination of sensitive methods was used such as atomic force microscopy yielding a molecular resolution, a quartz microbalance, and optical waveguide lightmode spectroscopy. The two latter methods yielded in situ information about the protein adsorption kinetics under flow conditions. It was established that at pH 3.5-4 the protein adsorbed on mica and silica surfaces in the form of compact quasi-spherical aggregates with an average size of 14 nm. The maximum coverage of the layers was equal to 3 and 1 mg m-2 at pH 4 and 7.4, respectively. The experimental data were successfully interpreted in terms of theoretical results derived from modeling. The experiments performed for flat substrates were complemented by investigations of the protein corona formation at polymer particles carried out using in situ laser Doppler velocimetry technique. In this way, the zeta potential of the protein layers was acquired as a function of the coverage. Applying the electrokinetic model, these primary data were converted to the dependence of the subunit zeta potential on pH. It was shown that a complete acid-base characteristic of the layer can be acquired only using nanomolar quantities of the protein.
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Affiliation(s)
- Paulina Żeliszewska
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, 30-239 Cracow, Poland
- Correspondence: (P.Ż.); (Z.A.)
| | - Monika Wasilewska
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, 30-239 Cracow, Poland
| | - Piotr Batys
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, 30-239 Cracow, Poland
| | - Katarzyna Pogoda
- Institute of Nuclear Physics, Polish Academy of Sciences, 31-342 Kraków, Poland
| | - Piotr Deptuła
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, 15-222 Białystok, Poland
| | - Robert Bucki
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, 15-222 Białystok, Poland
| | - Zbigniew Adamczyk
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, 30-239 Cracow, Poland
- Correspondence: (P.Ż.); (Z.A.)
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148
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Valério M, Borges-Araújo L, Melo MN, Lousa D, Soares CM. SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility. FRONTIERS IN MEDICAL TECHNOLOGY 2022; 4:1009451. [PMID: 36277437 PMCID: PMC9581196 DOI: 10.3389/fmedt.2022.1009451] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/20/2022] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 6 million people and is having a devastating social and economic impact around the world. The rise of new variants of concern (VOCs) represents a difficult challenge due to the loss of vaccine and natural immunity, as well as increased transmissibility. All VOCs contain mutations in the spike glycoprotein, which mediates fusion between the viral and host cell membranes. The spike glycoprotein binds to angiotensin-converting enzyme 2 (ACE2) via its receptor binding domain (RBD) initiating the infection process. Attempting to understand the effect of RBD mutations in VOCs, a lot of attention has been given to the RBD-ACE2 interaction. However, this type of analysis ignores more indirect effects, such as the conformational dynamics of the RBD itself. Observing that some mutations occur in residues that are not in direct contact with ACE2, we hypothesized that they could affect the RBD conformational dynamics. To test this, we performed long atomistic (AA) molecular dynamics (MD) simulations to investigate the structural dynamics of wt RBD, and that of four VOCs (Alpha, Beta, Delta, and Omicron). Our results show that the wt RBD presents two distinct conformations: an "open" conformation where it is free to bind ACE2; and a "closed" conformation, where the RBM ridge blocks the binding surface. The Alpha and Beta variants shift the open/closed equilibrium towards the open conformation by roughly 20%, likely increasing ACE2 binding affinity. Simulations of the Delta and Omicron variants showed extreme results, with the closed conformation being rarely observed. The Delta variant also differed substantially from the other variants, alternating between the open conformation and an alternative "reversed" one, with a significantly changed orientation of the RBM ridge. This alternate conformation could provide a fitness advantage due to increased availability for ACE2 binding, and by aiding antibody escape through epitope occlusion. These results support the hypothesis that VOCs, and particularly the Omicron and Delta variants, impact RBD conformational dynamics in a direction that promotes efficient binding to ACE2 and, in the case of Delta, may assist antibody escape.
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Affiliation(s)
- Mariana Valério
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Luís Borges-Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Diana Lousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cláudio M. Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
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149
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Verma S, Patil VM, Gupta MK. Mutation informatics: SARS-CoV-2 receptor-binding domain of the spike protein. Drug Discov Today 2022; 27:103312. [PMID: 35787481 PMCID: PMC9250815 DOI: 10.1016/j.drudis.2022.06.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/06/2022] [Accepted: 06/29/2022] [Indexed: 01/31/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) undergoes mutations at a high rate and with frequent genetic reassortment (antigenic drift/shift), leading to variability in targets. The receptor-binding domain (RBD) of the spike (S) protein has a major role in the binding of SARS-CoV-2 with human angiotensin-converting enzyme 2 (ACE2). Mutations at the RBD influence the binding interaction at the SARS-CoV-2 S-ACE2 interface and impact viral pathogenicity. Here, we discuss different reported mutations of concern in RBD, physicochemical characteristic changes resulting from mutated amino acids and their effect on binding between the RBD and ACE2. Along with mutation informatics, we highlight recently developed small-molecule inhibitors of RBD and the ACE2 interface. This information provides a rational basis for the design of inhibitors against the multivariant strains of SARS-CoV-2.
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Affiliation(s)
- Saroj Verma
- Department of Pharmaceutical Chemistry, SGT College of Pharmacy, SGT University, Gurugram, Haryana 122505, India,Corresponding author
| | - Vaishali M. Patil
- Department of Pharmaceutical Chemistry, KIET School of Pharmacy, KIET Group of Institutions, Delhi-NCR, Ghaziabad, Uttar Pradesh 201206, India
| | - Manish K. Gupta
- Department of Pharmaceutical Chemistry, SGT College of Pharmacy, SGT University, Gurugram, Haryana 122505, India
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150
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Xu X, Li G, Sun B, Zuo YY. S2 Subunit of SARS-CoV-2 Spike Protein Induces Domain Fusion in Natural Pulmonary Surfactant Monolayers. J Phys Chem Lett 2022; 13:8359-8364. [PMID: 36043851 PMCID: PMC9454269 DOI: 10.1021/acs.jpclett.2c01998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Pulmonary surfactant has been attempted as a supportive therapy to treat COVID-19. Although it is mechanistically accepted that the fusion peptide in the S2 subunit of the S protein plays a predominant role in mediating viral fusion with the host cell membrane, it is still unknown how the S2 subunit interacts with the natural surfactant film. Using combined bio-physicochemical assays and atomic force microscopy imaging, it was found that the S2 subunit inhibited the biophysical properties of the surfactant and induced microdomain fusion in the surfactant monolayer. The surfactant inhibition has been attributed to membrane fluidization caused by insertion of the S2 subunit mediated by its fusion peptide. These findings may provide novel insight into the understanding of bio-physicochemical mechanisms responsible for surfactant interactions with SARS-CoV-2 and may have translational implications in the further development of surfactant replacement therapy for COVID-19 patients.
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Affiliation(s)
- Xiaojie Xu
- Department
of Mechanical Engineering, University of
Hawaii at Manoa, Honolulu 96822, Hawaii, United States
| | - Guangle Li
- Department
of Mechanical Engineering, University of
Hawaii at Manoa, Honolulu 96822, Hawaii, United States
| | - Bingbing Sun
- State
Key Laboratory of Fine Chemicals and School of Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Yi Y. Zuo
- Department
of Mechanical Engineering, University of
Hawaii at Manoa, Honolulu 96822, Hawaii, United States
- Department
of Pediatrics, John A. Burns School of Medicine, University of Hawaii, Honolulu 96826, Hawaii, United States
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