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71 results for “spike protein”
The use of nanobodies in a sensitive ELISA test for SARS-CoV-2 Spike 1 protein
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SARS-CoV-2 spike protein ELISA calculations and summary data
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F I G U R E 1 in Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS- CoV-2
F I G U R E 1 Structural diagrams of spike glycoproteins of SARS‐CoV, MERS‐CoV, and SARS‐CoV‐2. All spike proteins of coronaviruses contain S1 subunit and S2 subunit, which were divided by the S cleavage sites. FP, fusion peptide; HR, heptad repeat 1 and heptad repeat 2; RBD, receptor‐binding domain, contains core binding motif in the external subdomain; SP, signal peptide
F I G U R E 2 in Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS- CoV-2
F I G U R E 2 Phylogenetic analysis of sequences of coronavirus spike glycoproteins. The sequences of spike glycoproteins of SARS‐CoV‐2, bat SARS‐like CoV, pangolin SARS‐like CoV, and SARS‐CoV were analyzed. The red stars indicate pangolin SARS‐like CoV and bat SARS‐like CoV. Host flags are marked after the clusters. SARS‐CoV‐2, severe respiratory syndrome coronavirus‐2
Computational epitope map of SARS-CoV-2 spike protein
<p>Dataset accompanying the publication "Map of SARS-CoV-2 spike epitopes not shielded byglycans" published in XYZ.</p> <p> </p> <p>The dataset contains:</p> <p>1. raw epitope screening scores (README file attached in the archive)</p> <p>2. structure and GROMACS topology and input files for two systems:</p> <p> - 4x SARS-CoV-2 spike protein, glycosylated<br> - 4x SARS-CoV-2 spike protein, non-glycosylated</p> <p> </p>
Impact of New Variants on SARS-CoV-2 Infectivity and Neutralization: A Molecular Assessment of the Alterations in the Spike-Host Protein Interactions
<p>MD simulation trajectories and structural models from the work which first appeared on bioRxiv (https://doi.org/10.1101/2021.01.10.426143), later ssrn (<a href="https://dx.doi.org/10.2139/ssrn.3907841">http://dx.doi.org/10.2139/ssrn.3907841</a>), and finally accepted for publication by Iscience.</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run1_WT_RBD_ACE2.zip">Run1_WT_RBD_ACE2.zip</a></p> <p>Description: A compressed (zipped) folder contains three independent MD trajectories of WT RBD-ACE2 complex.</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run2_N501Y_RBD_ACE2.zip">Run2_N501Y_RBD_ACE2.zip</a></p> <p>Description: A compressed folder contains three independent MD trajectories of Alpha RBD-ACE2 complex.</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run3_Beta_RBD_ACE2.zip">Run3_Beta_RBD_ACE2.zip</a></p> <p>Description: A compressed folder contains three independent MD trajectories of Beta RBD-ACE2 complex.</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run4_Delta_RBD_ACE2.zip">Run4_Delta_RBD_ACE2.zip</a></p> <p>Description: A compressed folder contains three independent MD trajectories of Delta RBD-ACE2 complex</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Run5_UK2_E484K_N501Y_ACE2.zip">Run5_UK2_E484K_N501Y_ACE2.zip</a></p> <p>Description: A compressed folder contains three independent MD trajectories of UK2 RBD-ACE2 complex</p> <p>File Name: <a href="https://zenodo.org/api/files/d5ac679d-c267-4e55-8f63-0abdaa41d067/Structural_model_PDBs.zip">Structural_model_PDBs.zip</a></p> <p>Description: A compressed folder contains eight pdb files of those structural models plotted in Figs 1, 3, 5, 6, 7 and S1.</p>
Cleavage of SARS-CoV-2 spike protein mutants
<p class="MsoNormal"><span>Several SARS-CoV-2 variants emerged that harbor mutations in the surface unit of the viral spike (S) protein that enhance infectivity and transmissibility. Here, we analyzed whether ten naturally-occurring mutations found within the extended loop harboring the S1/S2 cleavage site of the S protein, a determinant of SARS-CoV-2 cell tropism and pathogenicity, impact S protein processing and function. None of the mutations increased but several decreased S protein cleavage at the S1/S2 site, including S686G and P681H, the latter of which is found in variants of concern B.1.1.7 (Alpha variant) and B.1.1.529 (Omicron variant). None of the mutations reduced ACE2 binding and cell-cell fusion although several modulated the efficiency of host cell entry. The effects of mutation S686G on viral entry were cell-type dependent and could be linked to the availability of cathepsin L for S protein activation. These results show that polymorphisms at the S1/S2 site can modulate S protein processing and host cell entry. </span></p>
The Spike Protein of SARS-CoV-2 Impairs Lipid Metabolism and Increases Susceptibility to Lipotoxicity: Implication for a Role of Nrf2
<p>Original figures for the following publication: </p> <p>The Spike Protein of SARS-CoV-2 Impairs Lipid Metabolism and Increases Susceptibility to Lipotoxicity: Implication for a Role of Nrf2</p> <table align="left"> <tbody> <tr> <td> <p><em>Cells </em><strong>2022</strong>, <em>11</em>, x. https://doi.org/10.3390/xxxxx</p> </td> </tr> </tbody> </table>
Mutations of the Spike protein
<p>Test file for Aquaria</p>
Assessment of the Humoral Immune Response to the SARS-CoV-2 Spike Protein Receptor Binding Motif
<p><strong>Figure S1.</strong> Purification of human antibodies against the RBM region of the SARS-CoV-2 spike protein using a recombinant RBM Sepharose 4B affinity column (3 x 1 cm, inner diameter) (A) and SDS-PAGE (10%) analysis of the eluate (1) alongside a standard low molecular weight marker (Sigma Chemical Co, Saint Louis, Mo, U.S.A.) stained with Coomassie Blue. <strong>Table S1</strong>: Microscale thermophoresis (MST) traces of anti-RBM antibodies binding to different concentrations of S1WT (red) and S2WT (green) peptides by MST. Relative fluorescence (RF) between the bound and unbound state was determined over a time of 21s with 20s MST-on time for evaluation. The blue bar indicates the ΔRF before the temperature gradient was applied, whereas the red bar shows the ΔRF during the thermophoresis. For interaction experi ments, the amount of NT.647-labeled antibodies was kept constant, while the concentration of unlabeled peptides varied from 0.5 µg/mL–0.12 ng/mL. The assay was performed in PBS containing 0.05% Tween 20 and after a short incubation period, the samples were analyzed in standard glass MST NT.115 capillaries. <strong>Table S2:</strong> One-dose regime AstraZeneca-Oxford vaccinated serum information. <strong>Table S3</strong>: Heterologous booster dose vaccinated serum information.</p>
Safety and Immunogenicity of an Intranasal RSV Vaccine Expressing SARS-CoV-2 Spike Protein (COVID-19 Vaccine) in Adults
ClinicalTrials.gov study NCT04798001. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Phase II Clinical Trial of Recombinant SARS-CoV-2 Spike Protein Vaccine (CHO Cell) for the Prevention of COVID-19
ClinicalTrials.gov study NCT04990544. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Phase 1 Study of Intranasal PIV5 COVID-19 Vaccine Expressing SARS-CoV-2 Spike Protein in Healthy Adults and Adolescents
ClinicalTrials.gov study NCT04954287. IPD Sharing: YES. Countries: 1. Publications: 1.
A Study Assessing the Safety, Tolerability, Immunogenicity of COVID-19 Vaccine Candidate PRIME-2-CoV_Beta, Orf Virus Expressing SARS-CoV_2 Spike and Nucleocapsid Proteins
ClinicalTrials.gov study NCT05367843. IPD Sharing: Not stated. Countries: 2. Publications: 1.
Phase I Clinical Trial of Recombinant SARS-CoV-2 Spike Protein Vaccine (CHO Cell) for the Prevention of COVID-19
ClinicalTrials.gov study NCT04982068. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Cleavage of SARS-CoV-2 spike protein mutants
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Plasmodium infection is associated with cross-reactive antibodies to carbohydrate epitopes on the SARS-CoV-2 Spike protein
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Supplementary Structural Models (SARS-CoV-2 Spike-RBD:ACE2 complex and TMPRSS2) - SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals
<p>Structural Models (PDB) of SARS-CoV-2 Spike RBD bound to ACE2 receptors of 215 animals.</p> <p>Structural model of Human TMPRSS2.</p> <p>Modelled using the FunMod pipeline and referenced in the preprint</p> <p><a href="https://www.biorxiv.org/content/10.1101/2020.05.01.072371v5">SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals</a></p> <p> </p>
Supervised molecular dynamics for exploring the druggability of the SARS-CoV-2 spike protein (Topology and .xtc files)
<p>ABSTRACT. The recent outbreak of the respiratory syndrome-related coronavirus (SARS-CoV-2) is stimulating an unprecedented scientific campaign to alleviate the burden of the coronavirus disease (COVID-19). One line of research has focused on targeting SARS-CoV-2 proteins fundamental for its replication by repurposing drugs approved for other diseases. The first interaction between the virus and the host cell is mediated by the spike protein on the virus surface and the human angiotensin-converting enzyme (ACE2). Small molecules able to bind the receptor-binding domain (RBD) of the spike protein and disrupt the binding to ACE2 would offer an important tool for slowing, or even preventing, the infection. Here, we screened 2421 approved small molecules<em> in </em>silico and validated the docking outcomes through extensive molecular dynamics simulations. Out of six drugs characterized as putative RBD binders, the cephalosporin antibiotic cefsulodin was further assessed for its effect on the binding between the RBD and ACE2, suggesting the importance of considering the dynamic formation of the heterodimer when judging any potential candidate.</p>
CORVax12: SARS-CoV-2 Spike (S) Protein Plasmid DNA Vaccine Trial for COVID-19 (SARS-CoV-2)
ClinicalTrials.gov study NCT04627675. IPD Sharing: NO. Countries: 1. Publications: 0.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.