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Moon SH, Park GN, Choe S, Song S, Le VP, Cho YS, An DJ. Molecular and phylogenetic analysis of transmissible gastroenteritis virus strain VET-16, isolated from piglets in Vietnam. Arch Virol 2024; 169:183. [PMID: 39164596 DOI: 10.1007/s00705-024-06101-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/17/2024] [Indexed: 08/22/2024]
Abstract
Porcine transmissible gastroenteritis virus (TGEV) is a major pathogen that causes viral enteritis and severe diarrhea in newborn piglets. TGEV strains have been isolated in the USA, Europe, and China, and their molecular characteristics are well known. However, there have been few reports of molecular analysis of TGEV strains isolated in Southeast Asia. In 2016, we isolated TGEV strain VET-16 from fecal samples collected from piglets in Vietnam and determined its complete genome sequence by Sanger sequencing. We found that, while the full genome of the VET-16 strain was 92.4-99.9% identical to those of other TGEV strains, the ORF3 gene showed very little sequence similarity. Phylogenetic analysis suggested that the VET-16 strain belongs to the Purdue subgroup. Comparison of the predicted amino acid (aa) sequence of the spike protein of strain VET-16 with those of other TGEV strains revealed three aa substitutions (V378L, S379T, and D380N) and a 3-aa insertion (F383_F387insWEK) in antigenic site D of the VET-16 strain. Also, a single aa deletion (∆F1413) was found in the transmembrane domain of the spike gene of VET-16. Like the ORF3 gene from the TGEV Miller M60 vaccine strain, the VET-16 strain has a large deletion (∆725 nt) in the ORF3 gene. Previous studies have suggested that these mutations in the spike and ORF3 genes might be associated with a reduction in pathogenicity. The data from this study will facilitate further genetic analysis and research into the evolution of TGEV in pigs in Vietnam.
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Affiliation(s)
- Soo Hyun Moon
- Viral Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 9660, Republic of Korea
| | - Gyu-Nam Park
- Viral Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 9660, Republic of Korea
| | - SeEun Choe
- Viral Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 9660, Republic of Korea
| | - Sok Song
- Viral Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 9660, Republic of Korea
| | - Van Phan Le
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, 100000, Vietnam
| | - Yun Sang Cho
- Viral Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 9660, Republic of Korea
| | - Dong-Jun An
- Viral Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 9660, Republic of Korea.
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Huerta L, Gamboa-Meraz A, Estrada-Ochoa PS. Relevance of the Entry by Fusion at the Cytoplasmic Membrane vs. Fusion After Endocytosis in the HIV and SARS-Cov-2 Infections. Results Probl Cell Differ 2024; 71:329-344. [PMID: 37996685 DOI: 10.1007/978-3-031-37936-9_16] [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: 11/25/2023]
Abstract
HIV-1 and SARS-Cov-2 fuse at the cell surface or at endosomal compartments for entry into target cells; entry at the cell surface associates to productive infection, whereas endocytosis of low pH-independent viruses may lead to virus inactivation, slow replication, or alternatively, to productive infection. Endocytosis and fusion at the cell surface are conditioned by cell type-specific restriction factors and the presence of enzymes required for activation of the viral fusogen. Whereas fusion with the plasma membrane is considered the main pathway to productive infection of low pH-independent entry viruses, endocytosis is also productive and may be the main route of the highly efficient cell-to-cell dissemination of viruses. Alternative receptors, membrane cofactors, and the presence of enzymes processing the fusion protein at the cell membrane, determine the balance between fusion and endocytosis in specific target cells. Characterization of the mode of entry in particular cell culture conditions is desirable to better assess the effect of neutralizing and blocking agents and their mechanism of action. Whatever the pathway of virus internalization, production of the viral proteins into the cells can lead to the expression of the viral fusion protein on the cell surface; if this protein is able to induce membrane fusion at physiological pH, it promotes the fusion of the infected cell with surrounding uninfected cells, leading to the formation of syncytia or heterokaryons. Importantly, particular membrane proteins and lipids act as cofactors to support fusion. Virus-induced cell-cell fusion leads to efficient virus replication into fused cells, cell death, inflammation, and severe disease.
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Affiliation(s)
- Leonor Huerta
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CDMX, Mexico.
| | - Alejandro Gamboa-Meraz
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CDMX, Mexico
- Posgrado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Pablo Samuel Estrada-Ochoa
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CDMX, Mexico
- Facultad de Ciencias, Universidad Autónoma del Estado de México, Ciudad de México, México
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3
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Aliper ET, Efremov RG. Inconspicuous Yet Indispensable: The Coronavirus Spike Transmembrane Domain. Int J Mol Sci 2023; 24:16421. [PMID: 38003610 PMCID: PMC10671605 DOI: 10.3390/ijms242216421] [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: 08/31/2023] [Revised: 11/07/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Membrane-spanning portions of proteins' polypeptide chains are commonly known as their transmembrane domains (TMDs). The structural organisation and dynamic behaviour of TMDs from proteins of various families, be that receptors, ion channels, enzymes etc., have been under scrutiny on the part of the scientific community for the last few decades. The reason for such attention is that, apart from their obvious role as an "anchor" in ensuring the correct orientation of the protein's extra-membrane domains (in most cases functionally important), TMDs often actively and directly contribute to the operation of "the protein machine". They are capable of transmitting signals across the membrane, interacting with adjacent TMDs and membrane-proximal domains, as well as with various ligands, etc. Structural data on TMD arrangement are still fragmentary at best due to their complex molecular organisation as, most commonly, dynamic oligomers, as well as due to the challenges related to experimental studies thereof. Inter alia, this is especially true for viral fusion proteins, which have been the focus of numerous studies for quite some time, but have provoked unprecedented interest in view of the SARS-CoV-2 pandemic. However, despite numerous structure-centred studies of the spike (S) protein effectuating target cell entry in coronaviruses, structural data on the TMD as part of the entire spike protein are still incomplete, whereas this segment is known to be crucial to the spike's fusogenic activity. Therefore, in attempting to bring together currently available data on the structure and dynamics of spike proteins' TMDs, the present review aims to tackle a highly pertinent task and contribute to a better understanding of the molecular mechanisms underlying virus-mediated fusion, also offering a rationale for the design of novel efficacious methods for the treatment of infectious diseases caused by SARS-CoV-2 and related viruses.
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Affiliation(s)
- Elena T. Aliper
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Roman G. Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
- Department of Applied Mathematics, National Research University Higher School of Economics, Moscow 101000, Russia
- L.D. Landau School of Physics, Moscow Institute of Physics and Technology (State University), Dolgoprudny 141701, Russia
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Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023; 52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Mateusz Sikora
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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Stincarelli MA, Quagliata M, Di Santo A, Pacini L, Fernandez FR, Arvia R, Rinaldi S, Papini AM, Rovero P, Giannecchini S. SARS-CoV-2 inhibitory activity of a short peptide derived from internal fusion peptide of S2 subunit of spike glycoprotein. Virus Res 2023; 334:199170. [PMID: 37422270 PMCID: PMC10384657 DOI: 10.1016/j.virusres.2023.199170] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/10/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has posed a great concern in human population. To fight coronavirus emergence, we have dissected the conserved amino acid region of the internal fusion peptide in the S2 subunit of Spike glycoprotein of SARS-CoV-2 to design new inhibitory peptides. Among the 11 overlapping peptides (9-23-mer), PN19, a 19-mer peptide, exhibited a powerful inhibitory activity against different SARS-CoV-2 clinical isolate variants in absence of cytotoxicity. The PN19 inhibitory activity was found to be dependent on conservation of the central Phe and C-terminal Tyr residues in the peptide sequence. Circular dichroism spectra of the active peptide exhibited an alpha-helix propensity, confirmed by secondary structure prediction analysis. The PN19 inhibitory activity, exerted in the first step of virus infection, was reduced after peptide adsorption treatment with virus-cell substrate during fusion interaction. Additionally, PN19 inhibitory activity was reduced by adding S2 membrane-proximal region derived peptides. PN19 showed binding ability to the S2 membrane proximal region derived peptides, confirmed by molecular modelling, playing a role in the mechanism of action. Collectively, these results confirm that the internal fusion peptide region is a good candidate on which develop peptidomimetic anti SARS-CoV-2 antivirals.
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Affiliation(s)
- Maria Alfreda Stincarelli
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, Florence 50134, Italy
| | - Michael Quagliata
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Andrea Di Santo
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Sesto Fiorentino 50019, Italy
| | - Lorenzo Pacini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Feliciana Real Fernandez
- CNR - Istituto di Chimica dei Composti Organometallici (CNR-ICCOM), Via Madonna del Piano 10, Sesto Fiorentino I-50019, Italy
| | - Rosaria Arvia
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, Florence 50134, Italy
| | - Silvia Rinaldi
- CNR - Istituto di Chimica dei Composti Organometallici (CNR-ICCOM), Via Madonna del Piano 10, Sesto Fiorentino I-50019, Italy
| | - Anna Maria Papini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Paolo Rovero
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Sesto Fiorentino 50019, Italy
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, Florence 50134, Italy.
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Ha YR, Kim HJ, Park JS, Chung YS. Genomic surveillance of genes encoding the SARS-CoV-2 spike protein to monitor for emerging variants on Jeju Island, Republic of Korea. Front Microbiol 2023; 14:1170766. [PMID: 37533831 PMCID: PMC10390832 DOI: 10.3389/fmicb.2023.1170766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/03/2023] [Indexed: 08/04/2023] Open
Abstract
Introduction The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been fueled by new variants emerging from circulating strains. Here, we report results from a genomic surveillance study of SARS-CoV-2 on Jeju Island, Republic of Korea, from February 2021 to September 2022. Methods A total of 3,585 SARS-CoV-2 positive samples were analyzed by Sanger sequencing of the gene encoding the spike protein before performing phylogenetic analyses. Results We found that the Alpha variant (B.1.1.7) was dominant in May 2021 before being replaced by the Delta variant (B.1.617.2) in July 2021, which was dominant until December 2021 before being replaced by the Omicron variant. Mutations in the spike protein, including N440K and G446S, have been proposed to contribute to immune evasion, accelerating the spread of Omicron variants. Discussion Our results from Juju Island, Republic of Korea, are consistent with and contribute to global surveillance efforts crucial for identifying new variants of concern of SARS-CoV-2 and for monitoring the transmission dynamics and characteristics of known strains.
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Affiliation(s)
- Young-Ran Ha
- Jeju Branch Office, Honam Regional Center for Disease Control and Prevention, Korea Disease Control and Prevention Agency, Jeju, Republic of Korea
| | - Hyun-Jeong Kim
- Jeju Branch Office, Honam Regional Center for Disease Control and Prevention, Korea Disease Control and Prevention Agency, Jeju, Republic of Korea
| | - Jae-Sung Park
- Jeju National Quarantine Station, Korea Disease Control and Prevention Agency, Jeju, Republic of Korea
| | - Yoon-Seok Chung
- Division of Infectious Disease Diagnosis Control, Honam Regional Center for Disease Control and Prevention, Korea Disease Control and Prevention Agency, Gwangju, Republic of Korea
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7
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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. Nature 2023; 619:403-409. [PMID: 37285872 DOI: 10.1038/s41586-023-06273-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
The entry of SARS-CoV-2 into host cells depends on the refolding of the virus-encoded spike protein from a prefusion conformation, which is metastable after cleavage, to a lower-energy stable postfusion conformation1,2. This transition overcomes kinetic barriers for fusion of viral and target cell membranes3,4. Here we report a cryogenic electron microscopy (cryo-EM) structure of the intact postfusion spike in a lipid bilayer that represents the single-membrane product of the fusion reaction. The structure provides structural definition of the functionally critical membrane-interacting 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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Affiliation(s)
- Wei Shi
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Yongfei Cai
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- CSL Seqirus, Waltham, MA, USA
| | - Haisun Zhu
- Institute for Protein Innovation, Harvard Institutes of Medicine, Boston, MA, USA
| | - Hanqin Peng
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Jewel Voyer
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | | | - Hong Cao
- Codex BioSolutions, Rockville, MD, USA
| | - Megan L Mayer
- The Harvard Cryo-EM Center for Structural Biology, Boston, MA, USA
| | - Kangkang Song
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Cryo-EM Core Facility, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Chen Xu
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Cryo-EM Core Facility, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jianming Lu
- Codex BioSolutions, Rockville, MD, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, USA
| | - Jun Zhang
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Bing Chen
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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Gopalan V, Chandran A, Arumugam K, Sundaram M, Velladurai S, Govindan K, Azhagesan N, Jeyavel P, Dhandapani P, Sivasubramanian S, Kitambi SS. Distribution and Functional Analyses of Mutations in Spike Protein and Phylogenic Diversity of SARS-CoV-2 Variants Emerged during the Year 2021 in India. J Glob Infect Dis 2023; 15:43-51. [PMID: 37469462 PMCID: PMC10353649 DOI: 10.4103/jgid.jgid_178_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/27/2022] [Accepted: 01/04/2023] [Indexed: 07/21/2023] Open
Abstract
Introduction Prolonged COVID-19 pandemic accelerates the emergence and transmissibility of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants through the accumulation of adaptive mutations. Particularly, adaptive mutations in spike (S) protein of SARS-CoV-2 leads to increased viral infectivity, severe morbidity and mortality, and immune evasion. This study focuses on the phylodynamic distribution of SARS-CoV-2 variants during the year 2021 in India besides analyzing the functional significance of mutations in S-protein of SARS-CoV-2 variants. Methods Whole genome of SARS-CoV-2 sequences (n = 87957) from the various parts of India over the period of January to December 2021 was retrieved from Global Initiative on Sharing All Influenza Data. All the S-protein sequences were subjected to clade analysis, variant calling, protein stability, immune escape potential, structural divergence, Furin cleavage efficiency, and phylogenetic analysis using various in silico tools. Results Delta variant belonging to 21A, 21I, and 21J clades was found to be predominant throughout the year 2021 though many variants were also present. A total of 4639 amino acid mutations were found in S-protein. D614G was the most predominant mutation in the S-protein followed by P681R, L452R, T19R, T478K, and D950N. The highest number of mutations was found in the N-terminal domain of S-protein. Mutations in the crucial sites of S-protein impacting pathogenicity, immunogenicity, and fusogenicity were identified. Intralineage diversity analysis showed that certain variants of SARS-CoV-2 possess high diversification. Conclusions The study has disclosed the distribution of various variants including the Delta, the predominant variant, in India throughout the year 2021. The study has identified mutations in S-protein of each SARS-CoV-2 variant that can significantly impact the virulence, immune evasion, increased transmissibility, high morbidity, and mortality. In addition, it is found that mutations acquired during each viral replication cycle introduce new sub-lineages as studied by intralineage diversity analysis.
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Affiliation(s)
- Vidya Gopalan
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Aswathi Chandran
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Kishore Arumugam
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Monisha Sundaram
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Selvakumar Velladurai
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Karthikeyan Govindan
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Nivetha Azhagesan
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Padmapriya Jeyavel
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Prabu Dhandapani
- Department of Microbiology, Dr. ALM Post Graduate, Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu, India
| | | | - Satish Srinivas Kitambi
- Department of Translational Sciences, Institute for Healthcare Education and Translational Sciences, Hyderabad, Telengana, India
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Cytoplasmic Tail Truncation Stabilizes S1-S2 Association and Enhances S Protein Incorporation into SARS-CoV-2 Pseudovirions. J Virol 2023; 97:e0165022. [PMID: 36790205 PMCID: PMC10062125 DOI: 10.1128/jvi.01650-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
Truncations of the cytoplasmic tail (CT) of entry proteins of enveloped viruses dramatically increase the infectivity of pseudoviruses (PVs) bearing these proteins. Several mechanisms have been proposed to explain this enhanced entry, including an increase in cell surface expression. However, alternative explanations have also been forwarded, and the underlying mechanisms for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) S protein remain undetermined. Here, we show that the partial or complete deletion of the CT (residues 19 to 35) does not modify SARS-CoV-2 S protein expression on the cell surface when the S2 subunit is measured, whereas it is significantly increased when the S1 subunit is measured. We also show that the higher level of S1 in these CT-truncated S proteins reflects the decreased dissociation of the S1 subunit from the S2 subunit. In addition, we demonstrate that CT truncation further promotes S protein incorporation into PV particles, as indicated by biochemical analyses and cryo-electron microscopy. Thus, our data show that two distinct mechanisms contribute to the markedly increased infectivity of PVs carrying CT-truncated SARS-CoV-2 S proteins and help clarify the interpretation of the results of studies employing such PVs. IMPORTANCE Various forms of PVs have been used as tools to evaluate vaccine efficacy and study virus entry steps. When PV infectivity is inherently low, such as that of SARS-CoV-2, a CT-truncated version of the viral entry glycoprotein is widely used to enhance PV infectivity, but the mechanism underlying this enhanced PV infectivity has been unclear. Here, our study identified two mechanisms by which the CT truncation of the SARS-CoV-2 S protein dramatically increases PV infectivity: a reduction of S1 shedding and an increase in S protein incorporation into PV particles. An understanding of these mechanisms can clarify the mechanistic bases for the differences observed among various assays employing such PVs.
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10
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Hu L, Tang Y, Mei L, Liang M, Huang J, Wang X, Wu L, Jiang J, Li L, Long F, Xiao J, Tan L, Lu S, Peng T. A new intracellular targeting motif in the cytoplasmic tail of the spike protein may act as a target to inhibit SARS-CoV-2 assembly. Antiviral Res 2023; 209:105509. [PMID: 36572190 PMCID: PMC9788845 DOI: 10.1016/j.antiviral.2022.105509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022]
Abstract
Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a threat to global public health, underscoring the urgent need for the development of preventive and therapeutic measures. The spike (S) protein of SARS-CoV-2, which mediates receptor binding and subsequent membrane fusion to promote viral entry, is a major target for current drug development and vaccine design. The S protein comprises a large N-terminal extracellular domain, a transmembrane domain, and a short cytoplasmic tail (CT) at the C-terminus. CT truncation of the S protein has been previously reported to promote the infectivity of SARS-CoV and SARS-CoV-2 pseudoviruses. However, the underlying molecular mechanism has not been precisely elucidated. In addition, the CT of various viral membrane glycoproteins play an essential role in the assembly of virions, yet the role of the S protein CT in SARS-CoV-2 infection remains unclear. In this study, through constructing a series of mutations of the CT of the S protein and analyzing their impact on the packaging of the SARS-CoV-2 pseudovirus and live SARS-CoV-2 virus, we identified V1264L1265 as a new intracellular targeting motif in the CT of the S protein, that regulates the transport and subcellular localization of the spike protein through the interactions with cytoskeleton and vesicular transport-related proteins, ARPC3, SCAMP3, and TUBB8, thereby modulating SARS-CoV-2 pseudovirus and live SARS-CoV-2 virion assembly. Either disrupting the V1264L1265 motif or reducing the expression of ARPC3, SCAMP3, and TUBB8 significantly repressed the assembly of the live SARS-CoV-2 virion, raising the possibility that the V1264L1265 motif and the host responsive pathways involved could be new drug targets for the treatment of SARS-CoV-2 infection. Our results extend the understanding of the role played by the S protein CT in the assembly of pseudoviruses and live SARS-CoV-2 virions, which will facilitate the application of pseudoviruses to the study of SARS-CoV-2 and provide potential strategies for the treatment of SARS-CoV-2 infection.
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Affiliation(s)
- Longbo Hu
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China,Corresponding author
| | - Yongjie Tang
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Lingling Mei
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Mengdi Liang
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Jinxian Huang
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Xufei Wang
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Liping Wu
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Jiajing Jiang
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Leyi Li
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Fei Long
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Jing Xiao
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Long Tan
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Shaohua Lu
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Tao Peng
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China,Guangdong South China Vaccine, Guangzhou, China,Greater Bay Area Innovative Vaccine Technology Development Center, Guangzhou International Bio-island Laboratory, China,Corresponding author. State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
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11
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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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12
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Aliper ET, Krylov NA, Nolde DE, Polyansky AA, Efremov RG. A Uniquely Stable Trimeric Model of SARS-CoV-2 Spike Transmembrane Domain. Int J Mol Sci 2022; 23:ijms23169221. [PMID: 36012488 PMCID: PMC9409440 DOI: 10.3390/ijms23169221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/13/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Understanding fusion mechanisms employed by SARS-CoV-2 spike protein entails realistic transmembrane domain (TMD) models, while no reliable approaches towards predicting the 3D structure of transmembrane (TM) trimers exist. Here, we propose a comprehensive computational framework to model the spike TMD only based on its primary structure. We performed amino acid sequence pattern matching and compared the molecular hydrophobicity potential (MHP) distribution on the helix surface against TM homotrimers with known 3D structures and selected an appropriate template for homology modeling. We then iteratively built a model of spike TMD, adjusting “dynamic MHP portraits” and residue variability motifs. The stability of this model, with and without palmitoyl modifications downstream of the TMD, and several alternative configurations (including a recent NMR structure), was tested in all-atom molecular dynamics simulations in a POPC bilayer mimicking the viral envelope. Our model demonstrated unique stability under the conditions applied and conforms to known basic principles of TM helix packing. The original computational framework looks promising and could potentially be employed in the construction of 3D models of TM trimers for a wide range of membrane proteins.
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Affiliation(s)
- Elena T. Aliper
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
| | - Nikolay A. Krylov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
- National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Dmitry E. Nolde
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
- National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Anton A. Polyansky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna BioCenter 5, A-1030 Vienna, Austria
| | - Roman G. Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
- National Research University Higher School of Economics, 101000 Moscow, Russia
- Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
- Correspondence:
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13
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Tioni MF, Jordan R, Pena AS, Garg A, Wu D, Phan SI, Weiss CM, Cheng X, Greenhouse J, Orekov T, Valentin D, Kar S, Pessaint L, Andersen H, Stobart CC, Bloodworth MH, Stokes Peebles R, Liu Y, Xie X, Shi PY, Moore ML, Tang RS. Mucosal administration of a live attenuated recombinant COVID-19 vaccine protects nonhuman primates from SARS-CoV-2. NPJ Vaccines 2022; 7:85. [PMID: 35906244 PMCID: PMC9334537 DOI: 10.1038/s41541-022-00509-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 07/01/2022] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 global pandemic. SARS-CoV-2 is an enveloped RNA virus that relies on its trimeric surface glycoprotein spike for entry into host cells. Here we describe the COVID-19 vaccine candidate MV-014-212, a live, attenuated, recombinant human respiratory syncytial virus expressing a chimeric SARS-CoV-2 spike as the only viral envelope protein. MV-014-212 was attenuated and immunogenic in African green monkeys (AGMs). One mucosal administration of MV-014-212 in AGMs protected against SARS-CoV-2 challenge, reducing by more than 200-fold the peak shedding of SARS-CoV-2 in the nose. MV-014-212 elicited mucosal immunoglobulin A in the nose and neutralizing antibodies in serum that exhibited cross-neutralization against virus variants of concern Alpha, Beta, and Delta. Intranasally delivered, live attenuated vaccines such as MV-014-212 entail low-cost manufacturing suitable for global deployment. MV-014-212 is currently in Phase 1 clinical trials as an intranasal COVID-19 vaccine.
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Affiliation(s)
| | - Robert Jordan
- Meissa Vaccines Inc, Redwood City, CA, USA.,Bill & Melinda Gates Foundation, Seattle, WA, USA
| | | | | | - Danlu Wu
- Meissa Vaccines Inc, Redwood City, CA, USA
| | | | | | - Xing Cheng
- Meissa Vaccines Inc, Redwood City, CA, USA
| | | | | | | | | | | | | | | | - Melissa H Bloodworth
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - R Stokes Peebles
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
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14
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Zainulabid UA, Mat Yassim AS, Hussain M, Aslam A, Soffian SN, Mohd Ibrahim MS, Kamarudin N, Kamarulzaman MN, Hin HS, Ahmad HF. Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. PLoS One 2022; 17:e0263678. [PMID: 35213571 PMCID: PMC8880882 DOI: 10.1371/journal.pone.0263678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/25/2022] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 has spread throughout the world since its discovery in China, and Malaysia is no exception. WGS has been a crucial approach in studying the evolution and genetic diversity of SARS-CoV-2 in the ongoing pandemic. Despite considerable number of SARS-CoV-2 genome sequences have been submitted to GISAID and NCBI databases, there is still scarcity of data from Malaysia. This study aims to report new Malaysian lineages of the virus, responsible for the sustained spikes in COVID-19 cases during the third wave of the pandemic. Patients with nasopharyngeal and/or oropharyngeal swabs confirmed COVID-19 positive by real-time RT-PCR with CT value < 25 were chosen for WGS. The selected SARS-CoV-2 isolates were then sequenced, characterized and analyzed along with 986 sequences of the dominant lineages of D614G variants currently circulating throughout Malaysia. The prevalence of clade GH and G formed strong ground for the presence of two Malaysian lineages of AU.2 and B.1.524 that has caused sustained spikes of cases in the country. Statistical analysis on the association of gender and age group with Malaysian lineages revealed a significant association (p <0.05). Phylogenetic analysis revealed dispersion of 41 lineages, of these, 22 lineages are still active. Mutational analysis showed presence of unique G1223C missense mutation in transmembrane domain of the spike protein. For better understanding of the SARS-CoV-2 evolution in Malaysia especially with reference to the reported lineages, large scale studies based on WGS are warranted.
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Affiliation(s)
- Ummu Afeera Zainulabid
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Gambang, Pahang, Malaysia
- Department of Internal Medicine, Kulliyyah of Medicine, International Islamic University of Malaysia, Kuantan, Pahang, Malaysia
| | | | - Mushtaq Hussain
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
| | - Ayesha Aslam
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
| | - Sharmeen Nellisa Soffian
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Gambang, Pahang, Malaysia
| | - Mohamad Shafiq Mohd Ibrahim
- Department of Paediatric and Dental Public Health, Kulliyyah of Dentistry, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Norhidayah Kamarudin
- Department of Pathology and Laboratory Medicine, Kulliyyah of Medicine, International Islamic University of Malaysia, Kuantan, Pahang, Malaysia
| | - Mohd Nazli Kamarulzaman
- Department of Surgery, Kulliyyah of Medicine, International Islamic University of Malaysia, Kuantan, Pahang, Malaysia
| | - How Soon Hin
- Department of Internal Medicine, Kulliyyah of Medicine, International Islamic University of Malaysia, Kuantan, Pahang, Malaysia
| | - Hajar Fauzan Ahmad
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Gambang, Pahang, Malaysia
- Centre for Research in Advanced Tropical Bioscience (Biotropic Centre), Universiti Malaysia Pahang, Gambang, Pahang, Malaysia
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15
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Analysis of Hendra Virus Fusion Protein N-Terminal Transmembrane Residues. Viruses 2021; 13:v13122353. [PMID: 34960622 PMCID: PMC8707071 DOI: 10.3390/v13122353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/17/2022] Open
Abstract
Hendra virus (HeV) is a zoonotic enveloped member of the family Paramyoxviridae. To successfully infect a host cell, HeV utilizes two surface glycoproteins: the attachment (G) protein to bind, and the trimeric fusion (F) protein to merge the viral envelope with the membrane of the host cell. The transmembrane (TM) region of HeV F has been shown to have roles in F protein stability and the overall trimeric association of F. Previously, alanine scanning mutagenesis has been performed on the C-terminal end of the protein, revealing the importance of β-branched residues in this region. Additionally, residues S490 and Y498 have been demonstrated to be important for F protein endocytosis, needed for the proteolytic processing of F required for fusion. To complete the analysis of the HeV F TM, we performed alanine scanning mutagenesis to explore the residues in the N-terminus of this region (residues 487-506). In addition to confirming the critical roles for S490 and Y498, we demonstrate that mutations at residues M491 and L492 alter F protein function, suggesting a role for these residues in the fusion process.
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16
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Tang Y, Hu L, Liu Y, Zhou B, Qin X, Ye J, Shen M, Wu Z, Zhang P. Possible mechanisms of cholesterol elevation aggravating COVID-19. Int J Med Sci 2021; 18:3533-3543. [PMID: 34522180 PMCID: PMC8436106 DOI: 10.7150/ijms.62021] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 08/04/2021] [Indexed: 12/23/2022] Open
Abstract
Importance: Despite the availability of a vaccine against the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), humans will have to live with this virus and the after-effects of the coronavirus disease 2019 (COVID-19) infection for a long time. Cholesterol plays an important role in the infection and prognosis of SARS-CoV-2, and the study of its mechanism is of great significance not only for the treatment of COVID-19 but also for research on generic antiviral drugs. Observations: Cholesterol promotes the development of atherosclerosis by activating NLR family pyrin domain containing 3 (NLRP3), and the resulting inflammatory environment indirectly contributes to COVID-19 infection and subsequent deterioration. In in vitro studies, membrane cholesterol increased the number of viral entry sites on the host cell membrane and the number of angiotensin-converting enzyme 2 (ACE2) receptors in the membrane fusion site. Previous studies have shown that the fusion protein of the virus interacts with cholesterol, and the spike protein of SARS-CoV-2 also requires cholesterol to enter the host cells. Cholesterol in blood interacts with the spike protein to promote the entry of spike cells, wherein the scavenger receptor class B type 1 (SR-B1) plays an important role. Because of the cardiovascular protective effects of lipid-lowering therapy and the additional anti-inflammatory effects of lipid-lowering drugs, it is currently recommended to continue lipid-lowering therapy for patients with COVID-19, but the safety of extremely low LDL-C is questionable. Conclusions and Relevance: Cholesterol can indirectly increase the susceptibility of patients to SARS-CoV-2 and increase the risk of death from COVID-19, which are mediated by NLRP3 and atherosclerotic plaques, respectively. Cholesterol present in the host cell membrane, virus, and blood may also directly participate in the virus cell entry process, but the specific mechanism still needs further study. Patients with COVID-19 are recommended to continue lipid-lowering therapy.
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Affiliation(s)
- Yan Tang
- Department of Cardiology, Heart Center, Zhujiang Hospital, Southern Medical University, 235 Industrial Avenue, Guangzhou, 510282, Guangdong, People's Republic of China
- Zhujiang Hospital, Southern Medical University/The Second School of Clinical Medicine, Southern Medical University, No. 6, Chenggui Road, East District, Zhongshan, 528403, Guangdong, People's Republic of China
| | - Longtai Hu
- Department of Cardiology, Heart Center, Zhujiang Hospital, Southern Medical University, 235 Industrial Avenue, Guangzhou, 510282, Guangdong, People's Republic of China
- School of Traditional Chinese Medicine, Southern Medical University, No. 6, Chenggui Road, East District, Zhongshan, 528403, Guangdong, People's Republic of China
| | - Yi Liu
- Department of Cardiology, Heart Center, Zhujiang Hospital, Southern Medical University, 235 Industrial Avenue, Guangzhou, 510282, Guangdong, People's Republic of China
- Zhujiang Hospital, Southern Medical University/The Second School of Clinical Medicine, Southern Medical University, No. 6, Chenggui Road, East District, Zhongshan, 528403, Guangdong, People's Republic of China
| | - Bangyi Zhou
- Department of Cardiology, Heart Center, Zhujiang Hospital, Southern Medical University, 235 Industrial Avenue, Guangzhou, 510282, Guangdong, People's Republic of China
- Zhujiang Hospital, Southern Medical University/The Second School of Clinical Medicine, Southern Medical University, No. 6, Chenggui Road, East District, Zhongshan, 528403, Guangdong, People's Republic of China
| | - Xiaohuan Qin
- Department of Cardiology, Heart Center, Zhujiang Hospital, Southern Medical University, 235 Industrial Avenue, Guangzhou, 510282, Guangdong, People's Republic of China
- Zhujiang Hospital, Southern Medical University/The Second School of Clinical Medicine, Southern Medical University, No. 6, Chenggui Road, East District, Zhongshan, 528403, Guangdong, People's Republic of China
| | - Jujian Ye
- Department of Cardiology, Heart Center, Zhujiang Hospital, Southern Medical University, 235 Industrial Avenue, Guangzhou, 510282, Guangdong, People's Republic of China
- Zhujiang Hospital, Southern Medical University/The Second School of Clinical Medicine, Southern Medical University, No. 6, Chenggui Road, East District, Zhongshan, 528403, Guangdong, People's Republic of China
| | - Maoze Shen
- Department of Cardiology, Raoping County People's Hospital, 161 Caichang Street, Huanggang Town, Chaozhou, 515700, Guangdong, People's Republic of China
| | - Zhijian Wu
- Department of Cardiology, Affiliated Boai Hospital of Zhongshan, Southern Medical University, No. 6, Chenggui Road, East District, Zhongshan, 528403, Guangdong, People's Republic of China
| | - Peidong Zhang
- Department of Cardiology, Heart Center, Zhujiang Hospital, Southern Medical University, 235 Industrial Avenue, Guangzhou, 510282, Guangdong, People's Republic of China
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17
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Fu Q, Chou JJ. A Trimeric Hydrophobic Zipper Mediates the Intramembrane Assembly of SARS-CoV-2 Spike. J Am Chem Soc 2021; 143:8543-8546. [PMID: 34086443 PMCID: PMC8204753 DOI: 10.1021/jacs.1c02394] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 01/09/2023]
Abstract
The S protein of SARS-CoV-2 is a type I membrane protein that mediates membrane fusion and viral entry. A vast amount of structural information is available for the ectodomain of S, a primary target by the host immune system, but much less is known regarding its transmembrane domain (TMD) and its membrane-proximal regions. Here, we determined the NMR structure of the S protein TMD in bicelles that closely mimic a lipid bilayer. The TMD structure is a transmembrane α-helix (TMH) trimer that assembles spontaneously in a membrane. The trimer structure shows an extensive hydrophobic core along the 3-fold axis that resembles that of a trimeric leucine/isoleucine zipper, but with tetrad, not heptad, repeats. The trimeric core is strong in bicelles, resisting hydrogen-deuterium exchange for weeks. Although highly stable, structural guided mutagenesis identified single mutations that can completely dissociate the TMD trimer. Multiple studies have shown that the membrane anchors of viral fusion proteins can form highly specific oligomers, but the exact function of these oligomers remains unclear. Our findings should guide future experiments to address the above question for SARS coronaviruses.
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Affiliation(s)
- Qingshan Fu
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard
Medical School, Boston, Massachusetts 02115, United States
| | - James J. Chou
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard
Medical School, Boston, Massachusetts 02115, United States
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18
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Nishima W, Kulik M. Full-Length Computational Model of the SARS-CoV-2 Spike Protein and Its Implications for a Viral Membrane Fusion Mechanism. Viruses 2021; 13:v13061126. [PMID: 34208191 PMCID: PMC8230804 DOI: 10.3390/v13061126] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/02/2021] [Accepted: 06/02/2021] [Indexed: 12/22/2022] Open
Abstract
The SARS-CoV-2 virus has now become one of the greatest causes of infectious death and morbidity since the 1918 flu pandemic. Substantial and unprecedented progress has been made in the elucidation of the viral infection process in a short time; however, our understanding of the structure–function dynamics of the spike protein during the membrane fusion process and viral uptake remains incomplete. Employing computational approaches, we use full-length structural models of the SARS-CoV-2 spike protein integrating Cryo-EM images and biophysical properties, which fill the gaps in our understanding. We propose a membrane fusion model incorporating structural transitions associated with the proteolytic processing of the spike protein, which initiates and regulates a series of events to facilitate membrane fusion and viral genome uptake. The membrane fusion mechanism highlights the notable role of the S1 subunit and eventual mature spike protein uptake through the host membrane. Our comprehensive view accounts for distinct neutralizing antibody binding effects targeting the spike protein and the enhanced infectivity of the SARS-CoV-2 variant.
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Affiliation(s)
- Wataru Nishima
- New Mexico Consortium, Los Alamos, NM 87545, USA
- University of New Mexico, Albuquerque, NM 87131, USA
- Correspondence:
| | - Marta Kulik
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-839 Warsaw, Poland;
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19
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A comparative analysis of SARS-CoV-2 antivirals characterizes 3CL pro inhibitor PF-00835231 as a potential new treatment for COVID-19. J Virol 2021; 95:JVI.01819-20. [PMID: 33622961 PMCID: PMC8139662 DOI: 10.1128/jvi.01819-20] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of Coronavirus Disease 2019 (COVID-19). There is a dire need for novel effective antivirals to treat COVID-19, as the only approved direct-acting antiviral to date is remdesivir, targeting the viral polymerase complex. A potential alternate target in the viral life cycle is the main SARS-CoV-2 protease 3CLpro (Mpro). The drug candidate PF-00835231 is the active compound of the first anti-3CLpro regimen in clinical trials. Here, we perform a comparative analysis of PF-00835231, the pre-clinical 3CLpro inhibitor GC-376, and the polymerase inhibitor remdesivir, in alveolar basal epithelial cells modified to express ACE2 (A549+ACE2 cells). We find PF-00835231 with at least similar or higher potency than remdesivir or GC-376. A time-of-drug-addition approach delineates the timing of early SARS-CoV-2 life cycle steps in A549+ACE2 cells and validates PF-00835231's early time of action. In a model of the human polarized airway epithelium, both PF-00835231 and remdesivir potently inhibit SARS-CoV-2 at low micromolar concentrations. Finally, we show that the efflux transporter P-glycoprotein, which was previously suggested to diminish PF-00835231's efficacy based on experiments in monkey kidney Vero E6 cells, does not negatively impact PF-00835231 efficacy in either A549+ACE2 cells or human polarized airway epithelial cultures. Thus, our study provides in vitro evidence for the potential of PF-00835231 as an effective SARS-CoV-2 antiviral and addresses concerns that emerged based on prior studies in non-human in vitro models.Importance:The arsenal of SARS-CoV-2 specific antiviral drugs is extremely limited. Only one direct-acting antiviral drug is currently approved, the viral polymerase inhibitor remdesivir, and it has limited efficacy. Thus, there is a substantial need to develop additional antiviral compounds with minimal side effects and alternate viral targets. One such alternate target is its main protease, 3CLpro (Mpro), an essential component of the SARS-CoV-2 life cycle processing the viral polyprotein into the components of the viral polymerase complex. In this study, we characterize a novel antiviral drug, PF-00835231, which is the active component of the first-in-class 3CLpro-targeting regimen in clinical trials. Using 3D in vitro models of the human airway epithelium, we demonstrate the antiviral potential of PF-00835231 for inhibition of SARS-CoV-2.
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20
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Sanders DW, Jumper CC, Ackerman PJ, Bracha D, Donlic A, Kim H, Kenney D, Castello-Serrano I, Suzuki S, Tamura T, Tavares AH, Saeed M, Holehouse AS, Ploss A, Levental I, Douam F, Padera RF, Levy BD, Brangwynne CP. SARS-CoV-2 requires cholesterol for viral entry and pathological syncytia formation. eLife 2021; 10:e65962. [PMID: 33890572 PMCID: PMC8104966 DOI: 10.7554/elife.65962] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/01/2021] [Indexed: 12/27/2022] Open
Abstract
Many enveloped viruses induce multinucleated cells (syncytia), reflective of membrane fusion events caused by the same machinery that underlies viral entry. These syncytia are thought to facilitate replication and evasion of the host immune response. Here, we report that co-culture of human cells expressing the receptor ACE2 with cells expressing SARS-CoV-2 spike, results in synapse-like intercellular contacts that initiate cell-cell fusion, producing syncytia resembling those we identify in lungs of COVID-19 patients. To assess the mechanism of spike/ACE2-driven membrane fusion, we developed a microscopy-based, cell-cell fusion assay to screen ~6000 drugs and >30 spike variants. Together with quantitative cell biology approaches, the screen reveals an essential role for biophysical aspects of the membrane, particularly cholesterol-rich regions, in spike-mediated fusion, which extends to replication-competent SARS-CoV-2 isolates. Our findings potentially provide a molecular basis for positive outcomes reported in COVID-19 patients taking statins and suggest new strategies for therapeutics targeting the membrane of SARS-CoV-2 and other fusogenic viruses.
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Affiliation(s)
- David W Sanders
- Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
| | - Chanelle C Jumper
- Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
| | - Paul J Ackerman
- Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
| | - Dan Bracha
- Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
| | - Anita Donlic
- Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
| | - Hahn Kim
- Princeton University Small Molecule Screening Center, Princeton UniversityPrincetonUnited States
- Department of Chemistry, Princeton UniversityPrincetonUnited States
| | - Devin Kenney
- Department of Microbiology, Boston University School of MedicineBostonUnited States
- National Emerging Infectious Diseases Laboratories, Boston UniversityBostonUnited States
| | - Ivan Castello-Serrano
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesvilleUnited States
| | - Saori Suzuki
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Tomokazu Tamura
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Alexander H Tavares
- National Emerging Infectious Diseases Laboratories, Boston UniversityBostonUnited States
- Department of Biochemistry, Boston University School of MedicineBostonUnited States
| | - Mohsan Saeed
- National Emerging Infectious Diseases Laboratories, Boston UniversityBostonUnited States
- Department of Biochemistry, Boston University School of MedicineBostonUnited States
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of MedicineSt. LouisUnited States
| | - Alexander Ploss
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Ilya Levental
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesvilleUnited States
| | - Florian Douam
- Department of Microbiology, Boston University School of MedicineBostonUnited States
- National Emerging Infectious Diseases Laboratories, Boston UniversityBostonUnited States
| | - Robert F Padera
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical SchoolBostonUnited States
| | - Bruce D Levy
- Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical SchoolBostonUnited States
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
- Howard Hughes Medical InstitutePrincetonUnited States
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21
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Fu Q, Chou JJ. A trimeric hydrophobic zipper mediates the intramembrane assembly of SARS-CoV-2 spike. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33851163 PMCID: PMC8043453 DOI: 10.1101/2021.04.09.439203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The S protein of the SARS-CoV-2 is a Type I membrane protein that mediates membrane fusion and viral entry. A vast amount of structural information is available for the ectodomain of S, a primary target by the host immune system, but much less is known regarding its transmembrane domain (TMD) and its membrane-proximal regions. Here, we determined the nuclear magnetic resonance (NMR) structure of the S protein TMD in bicelles that closely mimic a lipid bilayer. The TMD structure is a transmembrane α-helix (TMH) trimer that assembles spontaneously in membrane. The trimer structure shows an extensive hydrophobic core along the 3-fold axis that resembles that of a trimeric leucine/isoleucine zipper, but with tetrad, not heptad, repeat. The trimeric core is strong in bicelles, resisting hydrogen-deuterium exchange for weeks. Although highly stable, structural guided mutagenesis identified single mutations that can completely dissociate the TMD trimer. Multiple studies have shown that the membrane anchor of viral fusion protein can form highly specific oligomers, but the exact function of these oligomers remain unclear. Our findings should guide future experiments to address the above question for SARS coronaviruses.
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Affiliation(s)
- Qingshan Fu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - James J Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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22
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Garcia-Beltran WF, Lam EC, Astudillo MG, Yang D, Miller TE, Feldman J, Hauser BM, Caradonna TM, Clayton KL, Nitido AD, Murali MR, Alter G, Charles RC, Dighe A, Branda JA, Lennerz JK, Lingwood D, Schmidt AG, Iafrate AJ, Balazs AB. COVID-19-neutralizing antibodies predict disease severity and survival. Cell 2021; 184:476-488.e11. [PMID: 33412089 PMCID: PMC7837114 DOI: 10.1016/j.cell.2020.12.015] [Citation(s) in RCA: 492] [Impact Index Per Article: 164.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/17/2020] [Accepted: 12/09/2020] [Indexed: 12/26/2022]
Abstract
Coronavirus disease 2019 (COVID-19) exhibits variable symptom severity ranging from asymptomatic to life-threatening, yet the relationship between severity and the humoral immune response is poorly understood. We examined antibody responses in 113 COVID-19 patients and found that severe cases resulting in intubation or death exhibited increased inflammatory markers, lymphopenia, pro-inflammatory cytokines, and high anti-receptor binding domain (RBD) antibody levels. Although anti-RBD immunoglobulin G (IgG) levels generally correlated with neutralization titer, quantitation of neutralization potency revealed that high potency was a predictor of survival. In addition to neutralization of wild-type SARS-CoV-2, patient sera were also able to neutralize the recently emerged SARS-CoV-2 mutant D614G, suggesting cross-protection from reinfection by either strain. However, SARS-CoV-2 sera generally lacked cross-neutralization to a highly homologous pre-emergent bat coronavirus, WIV1-CoV, which has not yet crossed the species barrier. These results highlight the importance of neutralizing humoral immunity on disease progression and the need to develop broadly protective interventions to prevent future coronavirus pandemics.
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Affiliation(s)
| | - Evan C Lam
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Michael G Astudillo
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Diane Yang
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Tyler E Miller
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Blake M Hauser
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | | | - Kiera L Clayton
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Adam D Nitido
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Mandakolathur R Murali
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Richelle C Charles
- Infectious Disease Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Anand Dighe
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - John A Branda
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
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23
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Domains and Functions of Spike Protein in Sars-Cov-2 in the Context of Vaccine Design. Viruses 2021; 13:v13010109. [PMID: 33466921 PMCID: PMC7829931 DOI: 10.3390/v13010109] [Citation(s) in RCA: 174] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/10/2021] [Accepted: 01/12/2021] [Indexed: 12/11/2022] Open
Abstract
The spike protein in SARS-CoV-2 (SARS-2-S) interacts with the human ACE2 receptor to gain entry into a cell to initiate infection. Both Pfizer/BioNTech's BNT162b2 and Moderna's mRNA-1273 vaccine candidates are based on stabilized mRNA encoding prefusion SARS-2-S that can be produced after the mRNA is delivered into the human cell and translated. SARS-2-S is cleaved into S1 and S2 subunits, with S1 serving the function of receptor-binding and S2 serving the function of membrane fusion. Here, I dissect in detail the various domains of SARS-2-S and their functions discovered through a variety of different experimental and theoretical approaches to build a foundation for a comprehensive mechanistic understanding of how SARS-2-S works to achieve its function of mediating cell entry and subsequent cell-to-cell transmission. The integration of structure and function of SARS-2-S in this review should enhance our understanding of the dynamic processes involving receptor binding, multiple cleavage events, membrane fusion, viral entry, as well as the emergence of new viral variants. I highlighted the relevance of structural domains and dynamics to vaccine development, and discussed reasons for the spike protein to be frequently featured in the conspiracy theory claiming that SARS-CoV-2 is artificially created.
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24
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Rao PS, Bheemavarapu P, Kalyampudi PSL, Rao TVM. An Efficient Method for Coronavirus Detection Through X-rays using deep Neural Network. Curr Med Imaging 2021; 18:587-592. [PMID: 33438544 DOI: 10.2174/1573405617999210112193220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/23/2020] [Accepted: 10/15/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Coronavirus (COVID-19) is a group of infectious diseases caused by related viruses called coronaviruses. In humans, the seriousness of infection caused by a coronavirus in the respiratory tract can vary from mild to lethal. A serious illness can be developed in old people and those with underlying medical problems like diabetes, cardiovascular disease, cancer, and chronic respiratory disease. For the diagnosis of the coronavirus disease, due to the growing number of cases, a limited number of test kits for COVID-19 are available in the hospitals. Hence, it is important to implement an automated system as an immediate alternative diagnostic option to pause the spread of COVID-19 in the population. OBJECTIVE This paper proposes a deep learning model for classification of coronavirus infected patient detection using chest X-ray radiographs. METHODS A fully connected convolutional neural network model is developed to classify healthy and diseased X-ray radiographs. The proposed neural network model consists of seven convolutional layers with rectified linear unit, softmax (last layer) activation functions and max pooling layers which were trained using the publicly available COVID-19 dataset. RESULTS AND CONCLUSION For validation of the proposed model, the publicly available chest X-ray radiograph dataset consisting COVID-19 and normal patient's images were used. Considering the performance of the results that are evaluated based on various evaluation metrics such as precision, recall, MSE, RMSE & accuracy, it is seen that the accuracy of the proposed CNN model is 98.07%.
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Affiliation(s)
- P Srinivasa Rao
- Department of CSE MVGR College of Engineering(A). Vizianagaram,A.P.. India
| | | | | | - T V Madhusudhana Rao
- Department of CSE Vignan Institue of Information Technology Visakhapatnam, A.P.. India
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25
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Mariano G, Farthing RJ, Lale-Farjat SLM, Bergeron JRC. Structural Characterization of SARS-CoV-2: Where We Are, and Where We Need to Be. Front Mol Biosci 2020; 7:605236. [PMID: 33392262 PMCID: PMC7773825 DOI: 10.3389/fmolb.2020.605236] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/22/2020] [Indexed: 01/18/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread in humans in almost every country, causing the disease COVID-19. Since the start of the COVID-19 pandemic, research efforts have been strongly directed towards obtaining a full understanding of the biology of the viral infection, in order to develop a vaccine and therapeutic approaches. In particular, structural studies have allowed to comprehend the molecular basis underlying the role of many of the SARS-CoV-2 proteins, and to make rapid progress towards treatment and preventive therapeutics. Despite the great advances that have been provided by these studies, many knowledge gaps on the biology and molecular basis of SARS-CoV-2 infection still remain. Filling these gaps will be the key to tackle this pandemic, through development of effective treatments and specific vaccination strategies.
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Affiliation(s)
- Giuseppina Mariano
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Rebecca J. Farthing
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | | | - Julien R. C. Bergeron
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
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26
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Dunina-Barkovskaya AY, Vishnyakova KS. Modulation of the Cholesterol-Dependent Activity of Macrophages IC-21 by CRAC Peptides with Substituted Motif-Forming Amino Acids. BIOCHEMISTRY (MOSCOW) SUPPLEMENT. SERIES A, MEMBRANE AND CELL BIOLOGY 2020; 14:331-343. [PMID: 33288988 PMCID: PMC7709805 DOI: 10.1134/s1990747820040054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 12/16/2022]
Abstract
The activity of many membrane proteins, such as receptors, ionic channels, transporters, and enzymes, is cholesterol dependent; however, mechanisms of the cholesterol-dependent regulation of protein functions remain obscure. Recent studies suggest that membrane proteins can directly interact with cholesterol owing to the presence of the cholesterol-recognizing amino-acid consensus (CRAC) motifs. One of the ways to verify and further develop this notion is a design of CRAC-containing peptides and investigation of their effects on cholesterol-dependent cell functions. Previously we showed that a newly constructed peptide RTKLWEMLVELGNMDKAVKLWRKLKR (peptide P4) containing two CRAC motifs modulates cholesterol-dependent interactions of cultured macrophages IC-21 with 2-μm particles. In this work, in order to clarify the role of CRAC-forming amino acids, we employed the same experimental system to test the activity of peptides closely related to P4 but with modified CRAC motifs. We found that peptide STKLSEMLSELGNMDKASKLSRKLSR (Mut2) analogous to P4, except that all CRAC-forming amino acids (V, W, K/R) were substituted by serine, did not produce any effect in the concentration range 0.5-50 μM corresponding to the range of the P4 activity. Neither was effective peptide RTKLSEMLVELGNMDKAVKLSRKLKR (Mut3), in which only aromatic amino acids (W) of the CRAC motifs were substituted. Peptide STKLWEMLVELGNMDKAVKLWRKLSR (Mut4), in which only cationic amino acids (R/K) in the CRAC motifs were changed, produced almost the same effect as that of peptide P4 with a bell-shape dose-response curve. At low concentrations (1-4 μM) Mut4 notably increased the number of beads per cell, at higher concentrations this parameter diminished, and at 50 μM Mut4 produced a robust toxic effect. Finally, peptide EWGMAVLWERNRKLKKDLKVLKMLRT (Mut1) composed of the same amino acid residues as P4 but in a random order ("scramble") and possessing one CRAC motif, different from that in P4, produced a moderate stimulation at 4-10 μM but was not toxic at 50 μM. As in the case of peptide P4, the effects of Mut4 and Mut1 depended on the cholesterol content in the cell membrane: after the incubation of cells with cholesterol-extracting agent methyl-β-cyclodextrin stimulatory effects produced by Mut4 and Mut1 at low doses were suppressed. Our results indicate that CRAC motifs play an important role in the mechanisms of the peptide-induced modulations of cholesterol-dependent cell functions in the experimental system used and that of the three motif-forming amino acids, critical is the presence of the aromatic amino acid (W). Further research is required to comprehend the molecular mechanisms of interactions of CRAC-containing peptides with cell membrane components that lead to modulation of cell functions. We anticipate that CRAC-containing peptides may provide a basis for the development of new tools for directed regulation of the activity of target cholesterol-dependent membrane proteins and for the design of new antimicrobial and immunomodulating drugs in particular.
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Affiliation(s)
- A. Ya. Dunina-Barkovskaya
- Belozersky Institute of Physico-chemical Biology, Moscow Lomonosov State University, 119992 Moscow, Russia
| | - Kh. S. Vishnyakova
- Engelgardt Institute of Molecular Biology, Russian Academy of Sciences, 119191 Moscow, Russia
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27
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Garcia-Beltran WF, Lam EC, Astudillo MG, Yang D, Miller TE, Feldman J, Hauser BM, Caradonna TM, Clayton KL, Nitido AD, Murali MR, Alter G, Charles RC, Dighe A, Branda JA, Lennerz JK, Lingwood D, Schmidt AG, Iafrate AJ, Balazs AB. COVID-19 neutralizing antibodies predict disease severity and survival. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.10.15.20213512. [PMID: 33106822 PMCID: PMC7587842 DOI: 10.1101/2020.10.15.20213512] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
COVID-19 exhibits variable symptom severity ranging from asymptomatic to life-threatening, yet the relationship between severity and the humoral immune response is poorly understood. We examined antibody responses in 113 COVID-19 patients and found that severe cases resulting in intubation or death exhibited increased inflammatory markers, lymphopenia, and high anti-RBD antibody levels. While anti-RBD IgG levels generally correlated with neutralization titer, quantitation of neutralization potency revealed that high potency was a predictor of survival. In addition to neutralization of wild-type SARS-CoV-2, patient sera were also able to neutralize the recently emerged SARS-CoV-2 mutant D614G, suggesting protection from reinfection by this strain. However, SARS-CoV-2 sera was unable to cross-neutralize a highly-homologous pre-emergent bat coronavirus, WIV1-CoV, that has not yet crossed the species barrier. These results highlight the importance of neutralizing humoral immunity on disease progression and the need to develop broadly protective interventions to prevent future coronavirus pandemics.
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Affiliation(s)
| | - Evan C. Lam
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
| | | | - Diane Yang
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Tyler E. Miller
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
| | | | | | | | | | - Mandakolathur R. Murali
- Department of Pathology, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Massachusetts General, Hospital, Boston, MA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
| | | | - Anand Dighe
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - John A. Branda
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | | | | | | | - A. John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA
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28
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Azad T, Singaravelu R, Crupi MJ, Jamieson T, Dave J, Brown EE, Rezaei R, Taha Z, Boulton S, Martin NT, Surendran A, Poutou J, Ghahremani M, Nouri K, Whelan JT, Duong J, Tucker S, Diallo JS, Bell JC, Ilkow CS. Implications for SARS-CoV-2 Vaccine Design: Fusion of Spike Glycoprotein Transmembrane Domain to Receptor-Binding Domain Induces Trimerization. MEMBRANES 2020; 10:membranes10090215. [PMID: 32872641 PMCID: PMC7557813 DOI: 10.3390/membranes10090215] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 12/20/2022]
Abstract
The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic presents an urgent need for an effective vaccine. Molecular characterization of SARS-CoV-2 is critical to the development of effective vaccine and therapeutic strategies. In the present study, we show that the fusion of the SARS-CoV-2 spike protein receptor-binding domain to its transmembrane domain is sufficient to mediate trimerization. Our findings may have implications for vaccine development and therapeutic drug design strategies targeting spike trimerization. As global efforts for developing SARS-CoV-2 vaccines are rapidly underway, we believe this observation is an important consideration for identifying crucial epitopes of SARS-CoV-2.
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Affiliation(s)
- Taha Azad
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Ragunath Singaravelu
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Mathieu J.F. Crupi
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Taylor Jamieson
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Jaahnavi Dave
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Emily E.F. Brown
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Reza Rezaei
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Zaid Taha
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Stephen Boulton
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Nikolas T. Martin
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Abera Surendran
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Joanna Poutou
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Mina Ghahremani
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada;
| | - Kazem Nouri
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada;
| | - Jack T. Whelan
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Jessie Duong
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Sarah Tucker
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Jean-Simon Diallo
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - John C. Bell
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Carolina S. Ilkow
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Correspondence: ; Tel.: +1-613-737-8899 (ext. 75208)
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Barrett CT, Dutch RE. Viral Membrane Fusion and the Transmembrane Domain. Viruses 2020; 12:v12070693. [PMID: 32604992 PMCID: PMC7412173 DOI: 10.3390/v12070693] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 01/05/2023] Open
Abstract
Initiation of host cell infection by an enveloped virus requires a viral-to-host cell membrane fusion event. This event is mediated by at least one viral transmembrane glycoprotein, termed the fusion protein, which is a key therapeutic target. Viral fusion proteins have been studied for decades, and numerous critical insights into their function have been elucidated. However, the transmembrane region remains one of the most poorly understood facets of these proteins. In the past ten years, the field has made significant advances in understanding the role of the membrane-spanning region of viral fusion proteins. We summarize developments made in the past decade that have contributed to the understanding of the transmembrane region of viral fusion proteins, highlighting not only their critical role in the membrane fusion process, but further demonstrating their involvement in several aspects of the viral lifecycle.
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A Hydrophobic Target: Using the Paramyxovirus Fusion Protein Transmembrane Domain To Modulate Fusion Protein Stability. J Virol 2019; 93:JVI.00863-19. [PMID: 31217248 DOI: 10.1128/jvi.00863-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 06/12/2019] [Indexed: 12/15/2022] Open
Abstract
Enveloped viruses utilize surface glycoproteins to bind and fuse with a target cell membrane. The zoonotic Hendra virus (HeV), a member of the family Paramyxoviridae, utilizes the attachment protein (G) and the fusion protein (F) to perform these critical functions. Upon triggering, the trimeric F protein undergoes a large, irreversible conformation change to drive membrane fusion. Previously, we have shown that the transmembrane (TM) domain of the F protein, separate from the rest of the protein, is present in a monomer-trimer equilibrium. This TM-TM association contributes to the stability of the prefusion form of the protein, supporting a role for TM-TM interactions in the control of F protein conformational changes. To determine the impact of disrupting TM-TM interactions, constructs expressing the HeV F TM with limited flanking sequences were synthesized. Coexpression of these constructs with HeV F resulted in dramatic reductions in the stability of F protein expression and fusion activity. In contrast, no effects were observed when the HeV F TM constructs were coexpressed with the nonhomologous parainfluenza virus 5 (PIV5) fusion protein, indicating a requirement for specific interactions. To further examine this, a TM peptide homologous to the PIV5 F TM domain was synthesized. Addition of the peptide prior to infection inhibited infection with PIV5 but did not significantly affect infection with human metapneumovirus, a related virus. These results indicate that targeted disruption of TM-TM interactions significantly impact viral fusion protein stability and function, presenting these interactions as a novel target for antiviral development.IMPORTANCE Enveloped viruses require virus-cell membrane fusion to release the viral genome and replicate. The viral fusion protein triggers from the pre- to the postfusion conformation, an essentially irreversible change, to drive membrane fusion. We found that small proteins containing the TM and a limited flanking region homologous to the fusion protein of the zoonotic Hendra virus reduced protein expression and fusion activity. The introduction of exogenous TM peptides may displace a TM domain, disrupting native TM-TM interactions and globally destabilizing the fusion protein. Supporting this hypothesis, we showed that a sequence-specific transmembrane peptide dramatically reduced viral infection in another enveloped virus model, suggesting a broader inhibitory mechanism. Viral fusion protein TM-TM interactions are important for protein function, and disruption of these interactions dramatically reduces protein stability.
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Webb SR, Smith SE, Fried MG, Dutch RE. Transmembrane Domains of Highly Pathogenic Viral Fusion Proteins Exhibit Trimeric Association In Vitro. mSphere 2018; 3:e00047-18. [PMID: 29669880 PMCID: PMC5907656 DOI: 10.1128/msphere.00047-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 03/23/2018] [Indexed: 12/12/2022] Open
Abstract
Enveloped viruses require viral fusion proteins to promote fusion of the viral envelope with a target cell membrane. To drive fusion, these proteins undergo large conformational changes that must occur at the right place and at the right time. Understanding the elements which control the stability of the prefusion state and the initiation of conformational changes is key to understanding the function of these important proteins. The construction of mutations in the fusion protein transmembrane domains (TMDs) or the replacement of these domains with lipid anchors has implicated the TMD in the fusion process. However, the structural and molecular details of the role of the TMD in these fusion events remain unclear. Previously, we demonstrated that isolated paramyxovirus fusion protein TMDs associate in a monomer-trimer equilibrium, using sedimentation equilibrium analytical ultracentrifugation. Using a similar approach, the work presented here indicates that trimeric interactions also occur between the fusion protein TMDs of Ebola virus, influenza virus, severe acute respiratory syndrome coronavirus (SARS CoV), and rabies virus. Our results suggest that TM-TM interactions are important in the fusion protein function of diverse viral families.IMPORTANCE Many important human pathogens are enveloped viruses that utilize membrane-bound glycoproteins to mediate viral entry. Factors that contribute to the stability of these glycoproteins have been identified in the ectodomain of several viral fusion proteins, including residues within the soluble ectodomain. Although it is often thought to simply act as an anchor, the transmembrane domain of viral fusion proteins has been implicated in protein stability and function as well. Here, using a biophysical approach, we demonstrated that the fusion protein transmembrane domains of several deadly pathogens-Ebola virus, influenza virus, SARS CoV, and rabies virus-self-associate. This observation across various viral families suggests that transmembrane domain interactions may be broadly relevant and serve as a new target for therapeutic development.
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Affiliation(s)
- Stacy R Webb
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Stacy E Smith
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Michael G Fried
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Rebecca Ellis Dutch
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
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Liao Y, Zhang SM, Neo TL, Tam JP. Tryptophan-dependent membrane interaction and heteromerization with the internal fusion peptide by the membrane proximal external region of SARS-CoV spike protein. Biochemistry 2015; 54:1819-30. [PMID: 25668103 DOI: 10.1021/bi501352u] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The spike (S) protein of severe acute respiratory syndrome-associated CoV (SARS-CoV) mediates membrane fusion and viral entry. These events involve structural rearrangements, including heteromerization between two heptad repeats (HR1 and HR2) to form a trimer of dimers as a six-helix bundle (6-HB), a quaternary protein structure that brings two distant clusters of hydrophobic sequences into the proximity of each other, the internal fusion peptide (IFP) preceding HR1, and the highly conserved tryptophan (Trp)-rich membrane proximal external region (MPER) following HR2. Here, we show that MPER can undergo self-oligomerization and heteromerization with IFP, events that are Trp-dependent. To delineate the roles of Trp residues of MPER in forming these quaternary structures and interacting with membranes, we employed a panel of synthetic peptides: MPER peptide (M-wt) and its alanine (Ala) and phenylalanine (Phe) analogues. Ala substitutions of Trp inhibited its association with cellular membranes. Chemical cross-linking experiments showed that M-wt can self-interact to form oligomers and cross-interact with IFP23, a synthetic IFP peptide, to form a heterohexamer. In comparison, little high-order oligomer was formed between M-wt and fusion peptide. The specific interaction between M-wt and IFP23 was confirmed by immunofluorescence staining experiments. In aqueous solutions, both M-wt and IFP23 displayed random secondary structures that became helical in hydrophobic solvents. Triple-Ala substitutions of Trp in M-wt, but not the corresponding triple-Phe analogue, disrupted oligomerization of M-wt and hetero-oligomerization of M-wt with IFP23. Overall, our results show that Trp residues of MPER play a key role in maintaining the structure and functions of MPER, allowing it to interact with IFP to form a MPER-IFP heteromer, a putative quaternary structure extending from the 6-HB, and function in membrane fusion. Finally, we showed that a MPER peptide could serve as an inhibitor in the entry process.
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Affiliation(s)
- Ying Liao
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551
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