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12 results for “Spike glycoprotein”
X-ray diffraction data for SARS-CoV2 spike glycoprotein N-terminal heptad repeat domain + SARS-CoV2(QEYKKEKE)
<p>X-ray diffraction dataset for SARS-CoV2 spike glycoprotein N-terminal heptad repeat domain + SARS-CoV2(QEYKKEKE) collected at the AMX beamline (17-ID-1) at the National Synchrotron Lightsource II, Brookhaven National Laboratory, Upton, NY, USA.</p> <p>Final XDS.INP file generated by autoPROC.</p> <p>Serialized request document for vector collection from LSDC.</p> <p>KB mirrors</p> <p>Detector: EigerX9M (Si)</p> <p>Approx. photon flux at 13475eV: 4E12 ph/s</p> <p>Approx. beam size: 5 x 7 um</p>
Simple structural views of the SARS spike glycoprotein complex with human angiotensin-converting enzyme 2 (ACE2)
<p>A set of 5 screenshots of UnityMol running the first example system. Three screenshots are from a multi-user virtual reality session with 3 participants, two screenshots illustrate a custom menu to drive the example more efficiently and make it simple for the end user.</p>
Uncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein
<p>The COVID-19 pandemic has prompted a rapid response in vaccine and drug development targeting SARS-CoV-2. Herein, we modelled a complete membrane-embedded SARS-CoV-2 spike (S) protein and used molecular dynamics (MD) simulations in the presence of benzene probes designed to enhance discovery of cryptic, potentially druggable pockets. This approach recapitulated lipid binding sites previously characterized by cryo-electron microscopy, and uncovered a novel cryptic pocket with promising druggable properties located underneath the 617-628 loop, which was shown to be involved in modulating the stability of cleaved S protein trimers a well as the formation of S protein multimers on the viral surface. A multi-conformational behaviour of this loop in simulations was validated using hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments, supportive of opening and closing dynamics. The pocket is the site of multiple mutations associated with increased transmissibility and severity of infection found in SARS-CoV-2 variants of concern including D614G. Collectively, this work highlights the utility of the benzene mapping approach in uncovering potential druggable sites on the surface of SARS-CoV-2 targets.</p> <p> </p>
(VIDEOS) Glycosylation as a key for enhancing drug recognition into spike glycoprotein of SARS-CoV-2.
<ul> <li>S1_movie_1. Movie of MD1 trajectory showing the Interaction of ligand TCMDC-124223 (roto-translate phenomenon) on RBD in absence of glycosylations within 50ns of simulation.</li> <li>S2_movie_2. Movie of MD4 trajectory showing the Interaction of ligand TCMDC-133766 (induced fit phenomenon) on the cryptic pocket of NTD in presence of glycosylations within 50ns of simulation.</li> <li>S3_movie_3. Movie of MD2 trajectory showing the Interaction of ligand TCMDC-124223 on RBD in presence of glycosylations within 50ns of simulation.</li> <li>S4_movie_4. Movie of MD3 trajectory showing the Interaction of ligand TCMDC-133766 on the cryptic pocket of NTD in absence of glycosylations within 50ns of simulation.</li> <li>S1_movie_1_v2. Movie of MD1 trajectory showing the Interaction of ligand TCMDC-124223 (roto-translate phenomenon) on RBD in absence of glycosylations within 300ns of simulation.</li> <li>S2_movie_2_v2. Movie of MD4 trajectory showing the Interaction of ligand TCMDC-133766 (induced fit phenomenon) on the cryptic pocket of NTD in presence of glycosylations within 300ns of simulation.</li> <li>S3_movie_3_v2. Movie of MD2 trajectory showing the Interaction of ligand TCMDC-124223 on RBD in presence of glycosylations within 300ns of simulation.</li> <li>S4_movie_4_v2. Movie of MD3 trajectory showing the Interaction of ligand TCMDC-133766 on the cryptic pocket of NTD in absence of glycosylations within 300ns of simulation.</li> </ul>
Figure 4 from: Padilla-Sanchez V (2020) In silico analysis of SARS-CoV-2 spike glycoprotein and insights into antibody binding. Research Ideas and Outcomes 6: e55281. https://doi.org/10.3897/rio.6.e55281
Figure 4 Docking energies and interface score charts. A shows the Rosetta Dock results, binding energies from PDBEPISA server in B shows good results for ΔG. Developability of this antibody shows all green flags in C.
Figure 3 from: Padilla-Sanchez V (2020) In silico analysis of SARS-CoV-2 spike glycoprotein and insights into antibody binding. Research Ideas and Outcomes 6: e55281. https://doi.org/10.3897/rio.6.e55281
Figure 3 Docking interface between the modified 80R antibody and the RBD of the SARS-CoV-2 spike protein. The model shows the structural interface with the 80R antibody above and the RBD below. The seven substitutions in 80R are shown in magenta and RBD residues are shown in cyan. Notice how the substitutions in 80R allow new aromatic-aromatic interactions that improve binding to the RBD and are not present in wild type 80R. E484 is shown pointing towards the beta strand of 80R and a glycine substitution was therefore introduced to avoid clashes.
Figure 6 from: Padilla-Sanchez V (2020) In silico analysis of SARS-CoV-2 spike glycoprotein and insights into antibody binding. Research Ideas and Outcomes 6: e55281. https://doi.org/10.3897/rio.6.e55281
Figure 6 m396 mutations docking results. A shows Rosetta Dock funnels for the original partners SARS-CoV and m396, SARS-CoV-2 and m396 and the SARS-CoV-2 and mutated m396. Notice how the binding is improved to the level of the original partners. B shows the ΔG energies again notice the improvement of binding when the mutations are introduced. Finally, C shows the developability flags with only one warning that is not that far from green flag.
Figure 5 from: Padilla-Sanchez V (2020) In silico analysis of SARS-CoV-2 spike glycoprotein and insights into antibody binding. Research Ideas and Outcomes 6: e55281. https://doi.org/10.3897/rio.6.e55281
Figure 5 Docking interface between the modified m396 antibody and SARS-CoV-2 spike protein RBD. In magenta is m396 mutant and in cyan SARS-CoV-2 RBD. These five mutations introduce many electrostatic interactions between the partners therefore stabilizing very much the binding.
Figure 2 from: Padilla-Sanchez V (2020) In silico analysis of SARS-CoV-2 spike glycoprotein and insights into antibody binding. Research Ideas and Outcomes 6: e55281. https://doi.org/10.3897/rio.6.e55281
Figure 2 Structural analysis of SARS-CoV spike glycoprotein. In A the SARS-CoV spike protein (PDB ID: 6ACG) is shown bound to ACE2 (brown) and 80R antibody (cyan), superimposed on the same binding site. In B the spike protein is shown bound only to the 80R antibody (PDB ID: 2GHW), with the structural model of the RBD of the SARS-CoV-2 spike protein (magenta) containing the missing loops. This homology model served as the basis for the docking experiments. In C it is shown a spike colored by subunit and showing the glycans. There are only two possible glycans in RBD region at 331 and 343 and neither of these sites affect the 80R binding.
Figure 1 from: Padilla-Sanchez V (2020) In silico analysis of SARS-CoV-2 spike glycoprotein and insights into antibody binding. Research Ideas and Outcomes 6: e55281. https://doi.org/10.3897/rio.6.e55281
Figure 1 Structural model of SARS-CoV-2 infection. This structural model was built with UCSF Chimera using high-performance computers (Bridges Large and Frontera). The model shows 16 viruses, with the spike proteins shown in green (PDB ID: 6VSB) and an actual lipid bilayer membrane, with ACE2 dimers shown in magenta. All these structures are at atomic resolution. The length of the membrane is approximately 1 micrometer.
Differential effect of SARS-CoV-2 spike glycoprotein 1 on human bronchial and alveolar lung mucosa models: Implications on pathogenicity.
GEO Series GSE185657. Homo sapiens. 24 samples. Type: Expression profiling by high throughput sequencing.
Cytotoxic T cells targeting spike glycoprotein are associated with hybrid immunity to SARS-CoV-2
GEO Series GSE223236. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
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