LitCovid-sample-sentences  

PMC:7253482 / 17528-20451 JSONTXT 23 Projects

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Id Subject Object Predicate Lexical cue
T102 0-56 Sentence denotes Visualising the HIV-1 and SARS glycan shields by cryo-EM
T103 57-258 Sentence denotes HIV-1 Env is a prototypic viral class I fusion protein that exhibits extensive surface glycosylation, resulting in an effective glycan shield to aid evasion from the host adaptive immune response21,31.
T104 259-419 Sentence denotes In order to visualize the structure of the respective glycan “shields” of HIV-1 and SARS coronavirus we used single-particle cryo-electron microscopy (cryo-EM).
T105 420-574 Sentence denotes The results for HIV-1 Env were reproduced directly from Berndsen et al.51 while the previously published SARS 2P dataset52 was reprocessed for this study.
T106 575-771 Sentence denotes Although cryo-EM datasets of fully glycosylated MERS S41 and chimpanzee simian immunodeficiency virus (SIVcpz)53 are also available, only the HIV and SARS data were of sufficient quality (Fig. 5).
T107 772-947 Sentence denotes We recently showed51 that dynamics in surface exposed glycans HIV-1 Env leads to an extensive network of interactions that drive higher-order structuring in the glycan shield.
T108 948-1101 Sentence denotes This structure defines diffuse boundaries between buried and exposed surface protein surface, which can serve to define potential sites of vulnerability.
T109 1102-1282 Sentence denotes Cryo-EM captures the ensemble-average structure of biomolecules and therefore glycan dynamics results in blurred density at the resolutions necessary for building atomic structure.
T110 1283-1536 Sentence denotes However, we showed how a simple combination of low-pass filtering and auto-thresholding, as well as 3D variability analysis, can reveal the previously hidden structure of the SARS glycan shield and compare it with the HIV-1 Env glycan shield51 (Fig. 5).
T111 1537-1855 Sentence denotes We observe the nearly all-encompassing glycan density on HIV-1 Env and evidence for extensive glycan–glycan interactions, especially in the oligomannose patch regions, whereas the glycans on SARS S appear more isolated and lack the wide-ranging glycan networks that are the hallmark of an effective glycan shield54,55.
T112 1856-2307 Sentence denotes The 3D variability maps are more sensitive to low intensity signal and reveal additional glycan–glycan interactions in both maps, however the S1 receptor-binding domains in the SARS dataset were shown to exist in both up and down conformations52, leading to poor resolution and significant 2D-variability which is convolved with the variability coming from glycans and limits the interpretability of glycan shielding effects in this region of the map.
T113 2308-2383 Sentence denotes Fig. 5 Comparative cryo-EM analysis of SARS S and HIV-1 Env glycan shields.
T114 2384-2397 Sentence denotes a Left panel:
T115 2398-2606 Sentence denotes Sharpened 3.2-Å-resolution C3-symmetric cryo-EM map of SARS S 2P ectodomain52 visualized at a high contour level with disordered S1 receptor-binding and N-terminal domains extending out from the central core.
T116 2607-2620 Sentence denotes Middle panel:
T117 2621-2760 Sentence denotes Low-pass filtered (lpf) cryo-EM map of the glycoprotein visualised at a low contour level along with a simulated peptide-only map overlaid.
T118 2761-2923 Sentence denotes Right panel: SPARX 3D variability map51. b Same as in (a) but for HIV-1 Env BG505 SOSIP.664 construct in complex with three copies of RM20A3 base-specific Fabs51.