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Journal articles on the topic 'Spike protein'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Bosch, Berend Jan, Willem Bartelink, and Peter J. M. Rottier. "Cathepsin L Functionally Cleaves the Severe Acute Respiratory Syndrome Coronavirus Class I Fusion Protein Upstream of Rather than Adjacent to the Fusion Peptide." Journal of Virology 82, no. 17 (2008): 8887–90. http://dx.doi.org/10.1128/jvi.00415-08.

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ABSTRACT Unlike other class I viral fusion proteins, spike proteins on severe acute respiratory sydrome coronavirus virions are uncleaved. As we and others have demonstrated, infection by this virus depends on cathepsin proteases present in endosomal compartments of the target cell, suggesting that the spike protein acquires its fusion competence by cleavage during cell entry rather than during virion biogenesis. Here we demonstrate that cathepsin L indeed activates the membrane fusion function of the spike protein. Moreover, cleavage was mapped to the same region where, in coronaviruses carry

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Pino, Paco, Joeri Kint, Divor Kiseljak, et al. "Trimeric SARS-CoV-2 Spike Proteins Produced from CHO Cells in Bioreactors Are High-Quality Antigens." Processes 8, no. 12 (2020): 1539. http://dx.doi.org/10.3390/pr8121539.

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The spike protein of the pandemic human corona virus is essential for its entry into human cells. In fact, most neutralizing antibodies against Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) are directed against the Virus-surface exposed spike protein, making it the antigen of choice for use in vaccines and diagnostic tests. In the current pandemic context, global demand for spike proteins has rapidly increased and could exceed hundreds of grams to kilograms annually. Coronavirus spikes are large heavily glycosylated homo-trimeric complexes, with inherent instability. The poor m

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Liu, Rong, Janhavi P. Natekar, Ki-Hye Kim, et al. "Multivalent and Sequential Heterologous Spike Protein Vaccinations Effectively Induce Protective Humoral Immunity against SARS-CoV-2 Variants." Vaccines 12, no. 4 (2024): 362. http://dx.doi.org/10.3390/vaccines12040362.

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The emergence of new SARS-CoV-2 variants continues to cause challenging problems for the effective control of COVID-19. In this study, we tested the hypothesis of whether a strategy of multivalent and sequential heterologous spike protein vaccinations would induce a broader range and higher levels of neutralizing antibodies against SARS-CoV-2 variants and more effective protection than homologous spike protein vaccination in a mouse model. We determined spike-specific IgG, receptor-binding inhibition titers, and protective efficacy in the groups of mice that were vaccinated with multivalent re

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Bejoy, Jennyfer, Tinatin I. Brelidze, and Yuichiro J. Suzuki. "Roles of glycosylation and redox states on SARS-CoV-2 spike protein actions." Journal of Immunology 210, no. 1_Supplement (2023): 235.17. http://dx.doi.org/10.4049/jimmunol.210.supp.235.17.

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Abstract The pandemic of Coronavirus Disease 2019 (COVID-19) is caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The viral fusion protein, spike protein, binds to its receptor Angiotensin-Converting Enzyme 2 (ACE2) to enter host cells. Further, the S1 subunit of the spike protein may be cleaved off the virus and affect various organs. In addition to tightly binding to ACE2, S1 spike protein also enhances the peptidase activity of ACE2 and activate cell signaling. The present study compared effects of recombinant S1 spike proteins expressed in HEK cells and in E. coli. Th

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Lee, Myeongsang, Marian Major, and Huixiao Hong. "Distinct Conformations of SARS-CoV-2 Omicron Spike Protein and Its Interaction with ACE2 and Antibody." International Journal of Molecular Sciences 24, no. 4 (2023): 3774. http://dx.doi.org/10.3390/ijms24043774.

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Since November 2021, Omicron has been the dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant that causes the coronavirus disease 2019 (COVID-19) and has continuously impacted human health. Omicron sublineages are still increasing and cause increased transmission and infection rates. The additional 15 mutations on the receptor binding domain (RBD) of Omicron spike proteins change the protein conformation, enabling the Omicron variant to evade neutralizing antibodies. For this reason, many efforts have been made to design new antigenic variants to induce effective anti

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Walter, Monika, Christian Fiedler, Renate Grassl, et al. "Structure of the Receptor-Binding Protein of Bacteriophage Det7: a Podoviral Tail Spike in a Myovirus." Journal of Virology 82, no. 5 (2007): 2265–73. http://dx.doi.org/10.1128/jvi.01641-07.

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ABSTRACT A new Salmonella enterica phage, Det7, was isolated from sewage and shown by electron microscopy to belong to the Myoviridae morphogroup of bacteriophages. Det7 contains a 75-kDa protein with 50% overall sequence identity to the tail spike endorhamnosidase of podovirus P22. Adsorption of myoviruses to their bacterial hosts is normally mediated by long and short tail fibers attached to a contractile tail, whereas podoviruses do not contain fibers but attach to host cells through stubby tail spikes attached to a very short, noncontractile tail. The amino-terminal 150 residues of the Det

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Simsar, Merve, Erkan Rayaman, Elif Çağlayan, and Kadir Turan. "Production and intracellular trafficking of SARS CoV-2 spike protein in insect cells infected with recombinant baculovirus." Journal of Research in Pharmacy 29, no. 1 (2025): 65–74. https://doi.org/10.12991/jrespharm.1626413.

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SARS CoV-2 belongs to the Coronaviridae family and is an enveloped virus with a positive polarity single stranded RNA genome. The virus's spike protein, embedded in the viral membrane, is the most important antigenic protein involved in binding the virus to the host cell receptor. This protein is the basic component of vaccines developed against the virus due to its antigenic character. Therefore, it is crucial to produce this protein heterologously. This study evaluated the potential of ExpiSf9 and Hi5 insect cells infected with recombinant baculoviruses carrying the spike gene to synthesize

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Shneider, Mikhail, Sergey Buth, Brian Ho, Marek Basler, John Mekalanos, and Petr Leiman. "Central spike proteins of contractile ejection systems." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C579. http://dx.doi.org/10.1107/s2053273314094200.

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Contractile tails of bacteriophages and related systems - R-type pyocins, the Serratia entomophila antifeeding prophage, the Photorhabdus Virulence Cassette, and the Type VI Secretion System (T6SS) - contain a special spike-shaped protein complex, which is involved in breaching the target cell envelope during infection. We have identified the genes and determined crystal structures for several spike proteins from phages, pyocins, and T6SS, and established a paradigm for their organization and function. The architecture of spike proteins is remarkably well conserved at the level of tertiary str

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Yamamoto, Yuichiro, Tetsuya Inoue, Miyu Inoue, et al. "SARS-CoV-2 Spike Protein Mutation at Cysteine-488 Impairs Its Golgi Localization and Intracellular S1/S2 Processing." International Journal of Molecular Sciences 23, no. 24 (2022): 15834. http://dx.doi.org/10.3390/ijms232415834.

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein binds to the cellular receptor—angiotensin-converting enzyme-2 (ACE2) as the first step in viral cell entry. SARS-CoV-2 spike protein expression in the ACE2-expressing cell surface induces cell–cell membrane fusion, thus forming syncytia. To exert its fusogenic activity, the spike protein is typically processed at a specific site (the S1/S2 site) by cellular proteases such as furin. The C488 residue, located at the spike–ACE2 interacting surface, is critical for the fusogenic and infectious roles of the SARS-CoV-2 s

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Azmi, Syifa Zahara Kultsum, Sunarno Sunarno, Sinta Aulia Rahmah, Melisa Andriani, Azlya Reza Lailul Farobi, and Luke Nur Ahlina. "Utilization of Quercetin Flavonoid Compounds in Red Onion (Allium cepa L.) as Inhibitor of Spike Sars-CoV-2 Protein against ACE2 Receptors." Biosaintifika: Journal of Biology & Biology Education 13, no. 3 (2021): 356–62. http://dx.doi.org/10.15294/biosaintifika.v13i3.32027.

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The world is facing the challenge of the COVID-19 disease, which is now stated as a pandemic. Inside the host cell, spike envelope protein (spike) of SARS-CoV-2 interact with the Angiotensin-converting Enzyme 2 (ACE2) receptor. It can be inhibited by bioactive compounds such as flavonoids which have anti-viral and broad pharmacological effect. This study aimed to determine the spike protein inhibitory activity by quercetin against the ACE2 receptor using the molecular docking method. This study focused on the inhibitory of the penetration activity of s proteins in ACE2 by utilizing natural mat

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Katzmann, Jerry A., Melissa R. Snyder, S. Vincent Rajkumar, et al. "Long-Term Biological Variation of Serum Protein Electrophoresis M-Spike, Urine M-Spike, and Monoclonal Serum Free Light Chain Quantification: Implications for Monitoring Monoclonal Gammopathies." Clinical Chemistry 57, no. 12 (2011): 1687–92. http://dx.doi.org/10.1373/clinchem.2011.171314.

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BACKGROUND We analyzed serial data in patients with clinically stable monoclonal gammopathy to determine the total variation of serum M-spikes [measured with serum protein electrophoresis (SPEP)], urine M-spikes [measured with urine protein electrophoresis (UPEP)], and monoclonal serum free light chain (FLC) concentrations measured with immunoassay. METHODS Patients to be studied were identified by (a) no treatment during the study interval, (b) no change in diagnosis and &lt;5 g/L change in serum M-spike over the course of observation; (c) performance of all 3 tests (SPEP, UPEP, FLC immun

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Snyder, Melissa, Angela Dispenzieri, S. Vincent Rajkumar, Robert Kyle, Joanne Benson, and Jerry A. Katzmann. "The Biologic and Analytic Variability of Serum Protein Electrophoresis M-Spike, Nephelometric Ig Quantitation, Serum FLC Quantitation, and Urine M-Spike in Monoclonal Gammopathies." Blood 114, no. 22 (2009): 1803. http://dx.doi.org/10.1182/blood.v114.22.1803.1803.

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Abstract Abstract 1803 Poster Board I-829 Background Plasma cell proliferative disorders are monitored by a variety of methods. Serum protein electrophoresis (SPEP) and/or urine PEP M-spike quantitation are commonly assessed in patients with monoclonal gammopathy of undetermined significance (MGUS), smoldering multiple myeloma (SMM), and multiple myeloma (MM) to determine disease progression, response, or relapse. Serum immunoglobin (Ig) concentrations can be quantitated when the M-spike is large or if the migration is obscured within the SPEP beta fraction. Serum FLC quantitation provides a r

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Sipala, Federica, Gianfranco Cavallaro, Giuseppe Forte, et al. "Different In Silico Approaches Using Heterocyclic Derivatives against the Binding between Different Lineages of SARS-CoV-2 and ACE2." Molecules 28, no. 9 (2023): 3908. http://dx.doi.org/10.3390/molecules28093908.

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Over the last few years, the study of the SARS-CoV-2 spike protein and its mutations has become essential in understanding how it interacts with human host receptors. Since the crystallized structure of the spike protein bound to the angiotensin-converting enzyme 2 (ACE2) receptor was released (PDB code 6M0J), in silico studies have been performed to understand the interactions between these two proteins. Specifically, in this study, heterocyclic compounds with different chemical characteristics were examined to highlight the possibility of interaction with the spike protein and the disruption

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Wang, H., J. M. Clarke, T. N. McCaig, and R. M. DePauw. "Physiology of genetic improvements in yield and grain protein of Canadian Western Amber Durum wheat." Canadian Journal of Plant Science 89, no. 3 (2009): 497–500. http://dx.doi.org/10.4141/cjps08196.

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Two relatively new Canada Western Amber Durum (CWAD) (Triticum turgidum L. var durum) cultivars used different strategies to increase yield and maintain high grain protein relative to older cultivars. AC Navigator (semi-dwarf) increased kernel weight and spikes per plant. AC Avonlea (conventional height) reduced height and increased spike size. AC Avonlea remobilized more nitrogen (N) to the grain than AC Navigator, which could be attributed to its large spike sink.Key words: Triticum turgidum, yield, protein, spike size, nitrogen uptake and remobilization

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Mushebenge, Aganze Gloire-Aimé, Samuel Chima Ugbaja, Nonkululeko Avril Mbatha, Rene B. Khan, and Hezekiel M. Kumalo. "A Comprehensive Analysis of Structural and Functional Changes Induced by SARS-CoV-2 Spike Protein Mutations." COVID 3, no. 9 (2023): 1454–72. http://dx.doi.org/10.3390/covid3090100.

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The emergence of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has sparked intense research on its spike protein, which is essential for viral entrance into host cells. Viral reproduction and transmission, host immune response regulation, receptor recognition and host cell entrance mechanisms, as well as structural and functional effects have all been linked to mutations in the spike protein. Spike protein mutations can also result in immune evasion mechanisms that impair vaccine effectiveness and escape, and they are linked to illness severity and clinical consequences. Numerou

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Cia, Gabriel, Fabrizio Pucci, and Marianne Rooman. "Analysis of the Neutralizing Activity of Antibodies Targeting Open or Closed SARS-CoV-2 Spike Protein Conformations." International Journal of Molecular Sciences 23, no. 4 (2022): 2078. http://dx.doi.org/10.3390/ijms23042078.

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SARS-CoV-2 infection elicits a polyclonal neutralizing antibody (nAb) response that primarily targets the spike protein, but it is still unclear which nAbs are immunodominant and what distinguishes them from subdominant nAbs. This information would however be crucial to predict the evolutionary trajectory of the virus and design future vaccines. To shed light on this issue, we gathered 83 structures of nAbs in complex with spike protein domains. We analyzed in silico the ability of these nAbs to bind the full spike protein trimer in open and closed conformations, and predicted the change in bi

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Ouyang, Weiming, Tao Xie, Hui Fang, et al. "Variable Induction of Pro-Inflammatory Cytokines by Commercial SARS CoV-2 Spike Protein Reagents: Potential Impacts of LPS on In Vitro Modeling and Pathogenic Mechanisms In Vivo." International Journal of Molecular Sciences 22, no. 14 (2021): 7540. http://dx.doi.org/10.3390/ijms22147540.

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Proinflammatory cytokine production following infection with severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) is associated with poor clinical outcomes. Like SARS CoV-1, SARS CoV-2 enters host cells via its spike protein, which attaches to angiotensin-converting enzyme 2 (ACE2). As SARS CoV-1 spike protein is reported to induce cytokine production, we hypothesized that this pathway could be a shared mechanism underlying pathogenic immune responses. We herein compared the capabilities of Middle East Respiratory Syndrome (MERS), SARS CoV-1 and SARS CoV-2 spike proteins to induce cyto

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Pillay, Tahir S. "Gene of the month: the 2019-nCoV/SARS-CoV-2 novel coronavirus spike protein." Journal of Clinical Pathology 73, no. 7 (2020): 366–69. http://dx.doi.org/10.1136/jclinpath-2020-206658.

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The year 2020 has seen a major and sustained outbreak of a novel betacoronavirus (severe acute respiratory syndrome (SARS)-coronavirus (CoV)-2) infection that causes fever, severe respiratory illness and pneumonia, a disease called COVID-19. At the time of writing, the death toll was greater than 120 000 worldwide with more than 2 million documented infections. The genome of the CoV encodes a number of structural proteins that facilitate cellular entry and assembly of virions, of which the spike protein S appears to be critical for cellular entry. The spike protein guides the virus to attach t

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Tooba, Qamar, Yadav Ruchi, and Srivastava Prachi. "Targeting Surface Glycoproteins of Sars-Cov-2 for Drug Repurposing: State of the Art and Future Opportunities." International Journal of Innovative Science and Research Technology 8, no. 1 (2023): 573–81. https://doi.org/10.5281/zenodo.7578035.

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- SARS (Severe Acute Respiratory Syndrome) virus is analogous to SARS-CoV-2. Both viruses share the same beta corona virus genus (lineage B). One of the crucial step for disease progression caused by novel SARS-CoV-2 involves the entry of virus into the cell. The virus entry inside the host cell is facilitated by the release of spike fusion peptide that is formed by cleavage of spike protein by the host protease. The receptor binding domain similarity of both SARS-CoV-2, delineates that ACE2 receptor is shared by both these viruses. In this research we have studied the structural similarity of

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Suresh, Sri Jayalakshmi, and Yuichiro Justin Suzuki. "SARS-CoV-2 Spike Protein and Lung Vascular Cells." Journal of Respiration 1, no. 1 (2020): 40–48. http://dx.doi.org/10.3390/jor1010004.

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing the current pandemic of coronavirus disease 2019 (COVID-19), and COVID-19 vaccines focus on its spike protein. However, in addition to facilitating the membrane fusion and viral entry, the SARS-CoV-2 spike protein promotes cell growth signaling in human lung vascular cells, and patients who have died of COVID-19 have thickened pulmonary vascular walls, linking the spike protein to a fatal disease, pulmonary arterial hypertension (PAH). In addition to SARS-CoV spike proteins, gp120, the viral membrane fusion protein of huma

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Li, Fang. "Structure, Function, and Evolution of Coronavirus Spike Proteins." Annual review of virology 3, no. 1 (2016): 237–61. https://doi.org/10.5281/zenodo.13533083.

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(Uploaded by Plazi for the Bat Literature Project) The coronavirus spike protein is a multifunctional molecular machine that mediates coronavirus entry into host cells. It first binds to a receptor on the host cell surface through its S1 subunit and then fuses viral and host membranes through its S2 subunit. Two domains in S1 from different coronaviruses recognize a variety of host receptors, leading to viral attachment. The spike protein exists in two structurally distinct conformations, prefusion and postfusion. The transition from prefusion to postfusion conformation of the spike protein mu

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Li, Fang. "Structure, Function, and Evolution of Coronavirus Spike Proteins." Annual review of virology 3, no. 1 (2016): 237–61. https://doi.org/10.5281/zenodo.13533083.

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(Uploaded by Plazi for the Bat Literature Project) The coronavirus spike protein is a multifunctional molecular machine that mediates coronavirus entry into host cells. It first binds to a receptor on the host cell surface through its S1 subunit and then fuses viral and host membranes through its S2 subunit. Two domains in S1 from different coronaviruses recognize a variety of host receptors, leading to viral attachment. The spike protein exists in two structurally distinct conformations, prefusion and postfusion. The transition from prefusion to postfusion conformation of the spike protein mu

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Kielian, M., and A. Helenius. "pH-induced alterations in the fusogenic spike protein of Semliki Forest virus." Journal of Cell Biology 101, no. 6 (1985): 2284–91. http://dx.doi.org/10.1083/jcb.101.6.2284.

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The spike glycoproteins of Semliki Forest virus mediate membrane fusion between the viral envelope and cholesterol-containing target membranes under conditions of mildly acidic pH (pH less than 6.2). The fusion reaction is critical for the infectious cycle, catalyzing virus penetration from the acidic endosome compartment. To define the role of the viral spike glycoproteins in the fusion reaction, conformational changes in the spikes at acid pH were studied using protease digestion and binding assays to liposomes and nonionic detergent. A method was also developed to prepare fragments of both

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Snozek, Christine LH, Amy K. Saenger, Philip R. Greipp, et al. "Comparison of Bromcresol Green and Agarose Protein Electrophoresis for Quantitation of Serum Albumin in Multiple Myeloma." Clinical Chemistry 53, no. 6 (2007): 1099–103. http://dx.doi.org/10.1373/clinchem.2007.088252.

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Abstract Background: The International Staging System for multiple myeloma has increased the importance of accurate measurement of serum albumin. Two common albumin assays, bromcresol green (BCG) and agarose gel protein electrophoresis (PEL), frequently yield discordant results, creating confusion regarding which assay is superior for use in myeloma. Methods: We measured albumin by BCG on a Roche Modular system, by PEL with a Helena SPIFE SPE Vis agarose gel, and by immunonephelometry performed on a Dade Behring BNII nephelometer. BCG and PEL were used to measure albumin in 5777 patient sample

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Matthews, Alicia M., Thomas G. Biel, Uriel Ortega-Rodriguez, et al. "SARS-CoV-2 spike protein variant binding affinity to an angiotensin-converting enzyme 2 fusion glycoproteins." PLOS ONE 17, no. 12 (2022): e0278294. http://dx.doi.org/10.1371/journal.pone.0278294.

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Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of the Coronavirus disease 2019 (Covid-19) pandemic, continues to evolve and circulate globally. Current prophylactic and therapeutic countermeasures against Covid-19 infection include vaccines, small molecule drugs, and neutralizing monoclonal antibodies. SARS-CoV-2 infection is mainly mediated by the viral spike glycoprotein binding to angiotensin converting enzyme 2 (ACE2) on host cells for viral entry. As emerging mutations in the spike protein evade efficacy of spike-targeted countermeasures, a potential str

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Jana, Sirsendu, Michael R. Heaven, and Abdu I. Alayash. "Cell-Free Hemoglobin Does Not Attenuate the Effects of SARS-CoV-2 Spike Protein S1 Subunit in Pulmonary Endothelial Cells." International Journal of Molecular Sciences 22, no. 16 (2021): 9041. http://dx.doi.org/10.3390/ijms22169041.

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SARS-CoV-2 primarily infects epithelial airway cells that express the host entry receptor angiotensin-converting enzyme 2 (ACE2), which binds to the S1 spike protein on the surface of the virus. To delineate the impact of S1 spike protein interaction with the ACE2 receptor, we incubated the S1 spike protein with human pulmonary arterial endothelial cells (HPAEC). HPAEC treatment with the S1 spike protein caused disruption of endothelial barrier function, increased levels of numerous inflammatory molecules (VCAM-1, ICAM-1, IL-1β, CCL5, CXCL10), elevated mitochondrial reactive oxygen species (RO

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Vettori, Marco, Francesco Dima, Brandon Michael Henry, et al. "Effects of Different Types of Recombinant SARS-CoV-2 Spike Protein on Circulating Monocytes’ Structure." International Journal of Molecular Sciences 24, no. 11 (2023): 9373. http://dx.doi.org/10.3390/ijms24119373.

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This study investigated the biological effects on circulating monocytes after challenge with SARS-CoV-2 recombinant spike protein. Whole blood collected from seven ostensibly healthy healthcare workers was incubated for 15 min with 2 and 20 ng/mL final concentration of recombinant spike protein of Ancestral, Alpha, Delta, and Omicron variants. Samples were analyzed with Sysmex XN and DI-60 analyzers. Cellular complexity (i.e., the presence of granules, vacuoles and other cytoplasmic inclusions) increased in all samples challenged with the recombinant spike protein of the Ancestral, Alpha, and

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Qian, Zhaohui, Xiuyuan Ou, Luiz Gustavo Bentim Góes, et al. "Identification of the Receptor-Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1." Journal of Virology 89, no. 17 (2015): 8816–27. http://dx.doi.org/10.1128/jvi.03737-14.

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ABSTRACTCoronavirus spike (S) glycoproteins mediate receptor binding, membrane fusion, and virus entry and determine host range. Murine betacoronavirus (β-CoV) in group A uses the N-terminal domain (NTD) of S protein to bind to its receptor, whereas the β-CoVs severe acute respiratory syndrome CoV in group B and Middle East respiratory syndrome CoV in group C and several α-CoVs use the downstream C domain in their S proteins to recognize their receptor proteins. To identify the receptor-binding domain in the spike of human β-CoV HKU1 in group A, we generated and mapped a panel of monoclonal an

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Petersen, Jennifer D., Jianming Lu, Wendy Fitzgerald, et al. "Unique Aggregation of Retroviral Particles Pseudotyped with the Delta Variant SARS-CoV-2 Spike Protein." Viruses 14, no. 5 (2022): 1024. http://dx.doi.org/10.3390/v14051024.

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Individuals infected with the SARS-CoV-2 Delta variant, lineage B.1.617.2, exhibit faster initial infection with a higher viral load than prior variants, and pseudotyped viral particles bearing the SARS-CoV-2 Delta variant spike protein induce a faster initial infection rate of target cells compared to those bearing other SARS-CoV-2 variant spikes. Here, we show that pseudotyped viral particles bearing the Delta variant spike form unique aggregates, as evidenced by negative stain and cryogenic electron microscopy (EM), flow cytometry, and nanoparticle tracking analysis. Viral particles pseudot

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Shukla, Nidhi, Sarah M. Roelle, John C. Snell, Olivia DelSignore, Anna M. Bruchez, and Kenneth A. Matreyek. "Pseudotyped virus infection of multiplexed ACE2 libraries reveals SARS-CoV-2 variant shifts in receptor usage." PLOS Pathogens 20, no. 5 (2024): e1012044. http://dx.doi.org/10.1371/journal.ppat.1012044.

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Pairwise compatibility between virus and host proteins can dictate the outcome of infection. During transmission, both inter- and intraspecies variabilities in receptor protein sequences can impact cell susceptibility. Many viruses possess mutable viral entry proteins and the patterns of host compatibility can shift as the viral protein sequence changes. This combinatorial sequence space between virus and host is poorly understood, as traditional experimental approaches lack the throughput to simultaneously test all possible combinations of protein sequences. Here, we created a pseudotyped vir

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D, Haile, R. Nigussie-Dechassa, W. Abdo, and F. Girma. "Seeding rate and genotype effects on agronomic performance and grain protein content of durum wheat (Triticum turgidum L. Durum) in south-eastern Ethiopia." African Journal of Food, Agriculture, Nutrition and Development 13, no. 58 (2013): 7693–710. http://dx.doi.org/10.18697/ajfand.58.10555.

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The use of optimum seeding rate for the genotype may enhance productivity and grain protein content of durum wheat. Therefore, an experiment was conducted at two locations in south-eastern Ethiopia during the main cropping season of 2008 with the objective of elucidating the effects of seeding rate and genotype on agronomic performance and grain protein content of the crop. The experiment consisted of factorial arrangements of four improved durum wheat genotypes and five seeding rates, which were laid out as a randomized complete block design with three replicates. Seeding rates significantly

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Parrott, Megan M., Sarah A. Sitarski, Randy J. Arnold, Lora K. Picton, R. Blake Hill, and Suchetana Mukhopadhyay. "Role of Conserved Cysteines in the Alphavirus E3 Protein." Journal of Virology 83, no. 6 (2008): 2584–91. http://dx.doi.org/10.1128/jvi.02158-08.

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ABSTRACT Alphavirus particles are covered by 80 glycoprotein spikes that are essential for viral entry. Spikes consist of the E2 receptor binding protein and the E1 fusion protein. Spike assembly occurs in the endoplasmic reticulum, where E1 associates with pE2, a precursor containing E3 and E2 proteins. E3 is a small, cysteine-rich, extracellular glycoprotein that mediates proper folding of pE2 and its subsequent association with E1. In addition, cleavage of E3 from the assembled spike is required to make the virus particles efficiently fusion competent. We have found that the E3 protein in S

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Mizuno, Yuya, Wataru Nakasone, Morikazu Nakamura, and Joji M. Otaki. "In Silico and In Vitro Evaluation of the Molecular Mimicry of the SARS-CoV-2 Spike Protein by Common Short Constituent Sequences (cSCSs) in the Human Proteome: Toward Safer Epitope Design for Vaccine Development." Vaccines 12, no. 5 (2024): 539. http://dx.doi.org/10.3390/vaccines12050539.

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Spike protein sequences in SARS-CoV-2 have been employed for vaccine epitopes, but many short constituent sequences (SCSs) in the spike protein are present in the human proteome, suggesting that some anti-spike antibodies induced by infection or vaccination may be autoantibodies against human proteins. To evaluate this possibility of “molecular mimicry” in silico and in vitro, we exhaustively identified common SCSs (cSCSs) found both in spike and human proteins bioinformatically. The commonality of SCSs between the two systems seemed to be coincidental, and only some cSCSs were likely to be re

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Ye, Qiushi, He Wang, Fanding Xu, et al. "Co-Mutations and Possible Variation Tendency of the Spike RBD and Membrane Protein in SARS-CoV-2 by Machine Learning." International Journal of Molecular Sciences 25, no. 9 (2024): 4662. http://dx.doi.org/10.3390/ijms25094662.

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Since the onset of the coronavirus disease 2019 (COVID-19) pandemic, SARS-CoV-2 variants capable of breakthrough infections have attracted global attention. These variants have significant mutations in the receptor-binding domain (RBD) of the spike protein and the membrane (M) protein, which may imply an enhanced ability to evade immune responses. In this study, an examination of co-mutations within the spike RBD and their potential correlation with mutations in the M protein was conducted. The EVmutation method was utilized to analyze the distribution of the mutations to elucidate the relatio

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Lee, Yung-Kuo, Wen-Chiu Chang, Ekambaranellore Prakash, et al. "Carbohydrate Ligands for COVID-19 Spike Proteins." Viruses 14, no. 2 (2022): 330. http://dx.doi.org/10.3390/v14020330.

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An outbreak of SARS-CoV-2 coronavirus (COVID-19) first detected in Wuhan, China, has created a public health emergency all over the world. The pandemic has caused more than 340 million confirmed cases and 5.57 million deaths as of 23 January 2022. Although carbohydrates have been found to play a role in coronavirus binding and infection, the role of cell surface glycans in SARS-CoV-2 infection and pathogenesis is still not understood. Herein, we report that the SARS-CoV-2 spike protein S1 subunit binds specifically to blood group A and B antigens, and that the spike protein S2 subunit has a bi

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Lungu, Claudiu N., and Mihai V. Putz. "SARS-CoV-2 Spike Protein Interaction Space." International Journal of Molecular Sciences 24, no. 15 (2023): 12058. http://dx.doi.org/10.3390/ijms241512058.

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a +sense single-strand RNA virus. The virus has four major surface proteins: spike (S), envelope (E), membrane (M), and nucleocapsid (N), respectively. The constitutive proteins present a high grade of symmetry. Identifying a binding site is difficult. The virion is approximately 50–200 nm in diameter. Angiotensin-converting enzyme 2 (ACE2) acts as the cell receptor for the virus. SARS-CoV-2 has an increased affinity to human ACE2 compared with the original SAR strain. Topological space, and its symmetry, is a critical component i

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Choi, Kwang-Eun, Jeong-Min Kim, JeeEun Rhee, Ae Kyung Park, Eun-Jin Kim, and Nam Sook Kang. "Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2." International Journal of Molecular Sciences 22, no. 16 (2021): 8714. http://dx.doi.org/10.3390/ijms22168714.

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) affects the COVID-19 pandemic in the world. The spike protein of the various proteins encoded in SARS-CoV-2 binds to human ACE2, fuses, and enters human cells in the respiratory system. Spike protein, however, is highly variable, and many variants were identified continuously. In this study, Korean mutants for spike protein (D614G and D614A-C terminal domain, L455F and F456L-RBD, and Q787H-S2 domain) were investigated in patients. Because RBD in spike protein is related to direct interaction with ACE2, almost all researches were focu

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Zhang, Xiaoyu, Haiyan Jia, Tian Li, et al. "TaCol-B5 modifies spike architecture and enhances grain yield in wheat." Science 376, no. 6589 (2022): 180–83. http://dx.doi.org/10.1126/science.abm0717.

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Spike architecture influences grain yield in wheat. We report the map-based cloning of a gene determining the number of spikelet nodes per spike in common wheat. The cloned gene is named TaCOL-B5 and encodes a CONSTANS-like protein that is orthologous to COL5 in plant species. Constitutive overexpression of the dominant TaCol-B5 allele but without the region encoding B-boxes in a common wheat cultivar increases the number of spikelet nodes per spike and produces more tillers and spikes, thereby enhancing grain yield in transgenic plants under field conditions. Allelic variation in TaCOL-B5 res

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Luzak, Boguslawa, Marcin Rozalski, Tomasz Przygodzki, et al. "SARS-CoV-2 Spike Protein and Neutralizing Anti-Spike Protein Antibodies Modulate Blood Platelet Function." International Journal of Molecular Sciences 24, no. 6 (2023): 5312. http://dx.doi.org/10.3390/ijms24065312.

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Several studies report elevated blood platelet activation and altered platelet count in COVID-19 patients, but the role of the SARS-CoV-2 spike protein in this process remains intriguing. Additionally, there is no data that anti-SARS-CoV-2 neutralizing antibodies (nAb) may attenuate spike protein activity toward blood platelets. Our results indicate that under in vitro conditions, the spike protein increased the collagen-stimulated aggregation of isolated platelets and induced the binding of vWF to platelets in ristocetin-treated blood. The spike protein also significantly reduced collagen- or

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Ahmad, Maira, Sehrish Rashid, and Taseer Ahmad. "Spike protein of SARS-COV-2 as a potential target for phytochemical constituents: A literature review." Journal of Shifa Tameer-e-Millat University 4, no. 2 (2021): 124–30. http://dx.doi.org/10.32593/jstmu/vol4.iss2.169.

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SARS-CoV-2 belongs to well-known SARS Coronaviridae family. One of the main structural proteins of SARS-CoV-2 is the spike protein that is present around the surface of a viral cell and plays an essential role in viral attachment, fusion and invasion in host cell. Once a virus invades a cell, it replicates and infects other cells. The fundamental role of spike protein in the progression of viral infection has led to an increased interest in exploring agents that target the viral spike protein for effective control of CoVID-19. The related data from published articles reviewed and numerous phyt

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Fakih, Taufik Muhammad, and Mentari Luthfika Dewi. "Analysis of SARS-CoV-2 Spike Protein as The Key Target in the Development of Antiviral Candidates for COVID-19 through Computational Study." Journal of Tropical Pharmacy and Chemistry 5, no. 4 (2021): 347–52. http://dx.doi.org/10.25026/jtpc.v5i4.254.

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The recent public health crisis is threatening the world with the emergence of the spread of the new coronavirus 2019 (2019-nCoV) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This virus originates from bats and is transmitted to humans through unknown intermediate animals in Wuhan, China in December 2019. Advances in technology have opened opportunities to find candidates for natural compounds capable of preventing and controlling COVID-19 infection through inhibition of spike proteins of SARS-CoV-2. This research aims to identify, evaluate, and explore the structure of spi

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Gowthaman, Ragul, Johnathan D. Guest, Rui Yin, Jared Adolf-Bryfogle, William R. Schief, and Brian G. Pierce. "CoV3D: a database of high resolution coronavirus protein structures." Nucleic Acids Research 49, no. D1 (2020): D282—D287. http://dx.doi.org/10.1093/nar/gkaa731.

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Abstract SARS-CoV-2, the etiologic agent of COVID-19, exemplifies the general threat to global health posed by coronaviruses. The urgent need for effective vaccines and therapies is leading to a rapid rise in the number of high resolution structures of SARS-CoV-2 proteins that collectively reveal a map of virus vulnerabilities. To assist structure-based design of vaccines and therapeutics against SARS-CoV-2 and other coronaviruses, we have developed CoV3D, a database and resource for coronavirus protein structures, which is updated on a weekly basis. CoV3D provides users with comprehensive set

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Verkhivker, Gennady. "Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability." International Journal of Molecular Sciences 23, no. 3 (2022): 1646. http://dx.doi.org/10.3390/ijms23031646.

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Structural and functional studies of the SARS-CoV-2 spike proteins have recently determined distinct functional states of the B.1.1.7 and B.1.351 spike variants, providing a molecular framework for understanding the mechanisms that link the effect of mutations with the enhanced virus infectivity and transmissibility. A detailed dynamic and energetic analysis of these variants was undertaken in the present work to quantify the effects of different mutations on functional conformational changes and stability of the SARS-CoV-2 spike protein. We employed the efficient and accurate coarse-grained (

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Evdokimova, O. V., A. E. Akhremchuk, L. N. Valentovich, O. E. Soboleva, and S. V. Gubkin. "THE RECOMBINANT BACTERIA LACTOCOCCUS LACTIS EXPRESSING SARS-COV-2 SPIKE PROTEIN OR ITS RECEPTOR-BINDING DOMAIN ELICITS AN IMMUNE RESPONSE FOLLOWING ORAL IMMUNISATION OF RATS." Eurasian Journal of Applied Biotechnology, no. 3S (September 12, 2024): 29. http://dx.doi.org/10.11134/btp.3s.2024.17.

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Mucosal delivery of antigens represents an effective strategy for the development of vaccines to control diseases with the upper respiratory and/or gastrointestinal tracts as the main routes of transmission. Lactic acid bacteria (LAB) are food-grade bacteria used for the expression of target antigens in the development of mucosal vaccines. Over the last two decades, research on the use of LAB has focused on the construction of genetically modified strains. Current study aimed to develop and examine the recombinant Lactococcus lactis strains, expressing SARS-CoV-2 spike (S) protein or the recep

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Semmarath, Warathit, Punnida Arjsri, Kamonwan Srisawad, Sonthaya Umsumarng, and Pornngarm Dejkriengkraikul. "Luteolin-Rich Extract from Harrisonia perforata (Blanco) Merr. Root Alleviates SARS-CoV-2 Spike Protein-Stimulated Lung Inflammation via Inhibition of MAPK/NLRP3 Inflammasome Signaling Pathways." Life 15, no. 7 (2025): 1077. https://doi.org/10.3390/life15071077.

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The COVID-19-related long-standing effect or Post-Acute Sequelae of COVID-19 (PASC) is often associated with NLRP3 inflammasome activation in pulmonary inflammation elicited by SARS-CoV-2 spike proteins. Spike proteins engage toll-like receptors (TLRs) in respiratory epithelial cells, leading to excessive cytokine production. Given the need for effective therapeutic strategies to mitigate spike protein-stimulated lung inflammation, we examined the anti-inflammatory properties of luteolin and ethanolic extract from Harrisonia perforata (Blanco) Merr. root. The ethanolic extract of H. perforata

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Yoder, Joshua D., Shane D. Trask, Phuoc T. Vo, et al. "VP5* Rearranges when Rotavirus Uncoats." Journal of Virology 83, no. 21 (2009): 11372–77. http://dx.doi.org/10.1128/jvi.01228-09.

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ABSTRACT Trypsin primes rotavirus for efficient infectivity by cleaving the spike protein, VP4, into VP8* and VP5*. A recombinant VP5* fragment has a trimeric, folded-back structure. Comparison of this structure with virion spikes suggests that a rearrangement, analogous to those of enveloped virus fusion proteins, may mediate membrane penetration by rotavirus during entry. To detect this inferred rearrangement of virion-associated authentic VP5*, we raised conformation-specific monoclonal antibodies against the recombinant VP5* fragment in its putative post-membrane penetration conformation.

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Al-Hamidawi, Ibtisam F. R., and Ali H. Noaema. "Effect of Seeding Rates and Genetic Compositions on some Growth and Yield Traits of European Rye (Secale cereale L.)." IOP Conference Series: Earth and Environmental Science 1371, no. 5 (2024): 052006. http://dx.doi.org/10.1088/1755-1315/1371/5/052006.

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Abstract The experiment was carried out at Agricultural Experiment Station 2, Agriculture College, Muthanna University, in Al-Bander area during the agricultural season 2022-2023, to study the effect of four seeding rates (80 s1, 100 s2, 120s3, 140 s4) kg ha-1 on some yield and quality traits of three newly introduced genetic compositions of Rye (Krzuca v1, Daukowskie zlote v2, Horyzo v3). The experiment was conducted using a completely randomized block design according to the split-plot design with three replications. The seeding rates occupied the main plots and the genetic compositions in t

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Hulswit, R. J. G., Haan C. a. M. de, and B.-J. Bosch. "Coronavirus Spike Protein and Tropism Changes." Advances in Virus Research 96 (June 12, 2016): 29–57. https://doi.org/10.5281/zenodo.13536812.

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(Uploaded by Plazi for the Bat Literature Project) Coronaviruses (CoVs) have a remarkable potential to change tropism. This is particularly illustrated over the last 15 years by the emergence of two zoonotic CoVs, the severe acute respiratory syndrome (SARS)- and Middle East respiratory syndrome (MERS)-CoV. Due to their inherent genetic variability, it is inevitable that new cross-species transmission events of these enveloped, positive-stranded RNA viruses will occur. Research into these medical and veterinary important pathogens-sparked by the SARS and MERS outbreaks-revealed important princ

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Hulswit, R. J. G., Haan C. a. M. de, and B.-J. Bosch. "Coronavirus Spike Protein and Tropism Changes." Advances in Virus Research 96 (June 7, 2016): 29–57. https://doi.org/10.5281/zenodo.13536812.

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(Uploaded by Plazi for the Bat Literature Project) Coronaviruses (CoVs) have a remarkable potential to change tropism. This is particularly illustrated over the last 15 years by the emergence of two zoonotic CoVs, the severe acute respiratory syndrome (SARS)- and Middle East respiratory syndrome (MERS)-CoV. Due to their inherent genetic variability, it is inevitable that new cross-species transmission events of these enveloped, positive-stranded RNA viruses will occur. Research into these medical and veterinary important pathogens-sparked by the SARS and MERS outbreaks-revealed important princ

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Zeng, Lianjie, Yitan Lu, Wenying Yan, and Yang Yang. "A Protein Co-Conservation Network Model Characterizes Mutation Effects on SARS-CoV-2 Spike Protein." International Journal of Molecular Sciences 24, no. 4 (2023): 3255. http://dx.doi.org/10.3390/ijms24043255.

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The emergence of numerous variants of SARS-CoV-2 has presented challenges to the global efforts to control the COVID-19 pandemic. The major mutation is in the SARS-CoV-2 viral envelope spike protein that is responsible for virus attachment to the host, and is the main target for host antibodies. It is critically important to study the biological effects of the mutations to understand the mechanisms of how mutations alter viral functions. Here, we propose a protein co-conservation weighted network (PCCN) model only based on the protein sequence to characterize the mutation sites by topological

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