LitCovid-sample-sentences  

PMC:7443692 / 9613-13789 JSONTXT 12 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T49 0-109 Sentence denotes Expression, Purification, and Characterization of SARS-CoV-2 Spike Glycoprotein Trimer and Soluble Human ACE2
T50 110-616 Sentence denotes A trimer-stabilized, soluble variant of the SARS-CoV-2 S that contains 22 canonical N-linked glycosylation sequons per protomer and a soluble version of human ACE2 that contains six, lacking the most C-terminal seventh, canonical N-linked glycosylation sequons (Figure 1 A) were purified from the media of transfected HEK293 cells, and the quaternary structure confirmed by negative EM staining for the S trimer (Figure 1B) and purity examined by SDS-PAGE Coomassie G-250 stained gels for both (Figure 1C).
T51 617-745 Sentence denotes In addition, proteolytic digestions followed by proteomic analyses confirmed that the proteins were highly purified (Table S12).
T52 746-945 Sentence denotes Finally, the N terminus of both the mature S and the soluble mature ACE2 were empirically determined via proteolytic digestions and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses.
T53 946-1174 Sentence denotes These results confirmed that both the secreted, mature forms of S protein and ACE2 begin with an N-terminal glutamine that has undergone condensation to form pyroglutamine at residues 14 and 18, respectively (Figures 1D and S1).
T54 1175-1422 Sentence denotes The N-terminal peptide observed for S also contains a glycan at Asn-0017 (Figure 1D), and mass spectrometry analysis of non-reducing proteolytic digestions confirmed that Cys-0015 of S is in a disulfide linkage with Cys-0136 (Figure S2; Table S2).
T55 1423-1756 Sentence denotes Given that SignalP (Almagro Armenteros et al., 2019) predicts signal sequence cleavage between Cys-0015 and Val-0016 but we observed cleavage between Ser-0013 and Gln-0014, we examined the possibility that an in-frame upstream methionine to the proposed start methionine (Figure 1A) might be used to initiate translation (Figure S3).
T56 1757-1976 Sentence denotes If one examines the predicted signal sequence cleavage using the in-frame Met that is encoded nine amino acids upstream, SignalP now predicts cleavage between the Ser and Gln that we observed in our studies (Figure S3).
T57 1977-2218 Sentence denotes To examine whether this impacted S expression, we expressed constructs that contained or did not contain the upstream 27 nucleotides in a pseudovirus (VSV) system expressing SARS-CoV-2 S (Figure S4) and in our HEK293 system (data not shown).
T58 2219-2340 Sentence denotes Both expression systems produced a similar amount of S regardless of which expression construct was utilized (Figure S4).
T59 2341-2546 Sentence denotes Thus, while the translation initiation start site has still not been fully defined, allowing for earlier translation in expression construct design did not have a significant impact on the generation of S.
T60 2547-2660 Sentence denotes Figure 1 Expression and Characterization of SARS-CoV-2 Spike Glycoprotein Trimer Immunogen and Soluble Human ACE2
T61 2661-2724 Sentence denotes (A) Sequences of SARS-CoV-2 S immunogen and soluble human ACE2.
T62 2725-2831 Sentence denotes The N-terminal pyroglutamines for both mature protein monomers are bolded, underlined, and shown in green.
T63 2832-2918 Sentence denotes The canonical N-linked glycosylation sequons are bolded, underlined, and shown in red.
T64 2919-3128 Sentence denotes (B and C) Negative stain electron microscopy of the purified trimer (B) and Coomassie G-250-stained reducing SDS-PAGE gels (C) confirmed purity of the SARS-CoV-2 S protein trimer and of the soluble human ACE2.
T65 3129-3159 Sentence denotes MWM, molecular weight markers.
T66 3160-3329 Sentence denotes (D) A representative Step-HCD fragmentation spectrum from mass-spectrometry analysis of a tryptic digest of S annotated manually based on search results from pGlyco 2.2.
T67 3330-3422 Sentence denotes This spectrum defines the N terminus of the mature protein monomer as (pyro-)glutamine 0014.
T68 3423-3584 Sentence denotes A representative N-glycan consistent with this annotation and our glycomics data (Figure 2) is overlaid by using the Symbol Nomenclature For Glycans (SNFG) code.
T69 3585-3621 Sentence denotes This complex glycan occurs at N0017.
T70 3622-3741 Sentence denotes Note, that as expected, the cysteine is carbamidomethylated, and the mass accuracy of the assigned peptide is 0.98 ppm.
T71 3742-3854 Sentence denotes On the sequence of the N-terminal peptide and in the spectrum, the assigned b (blue) and y (red) ions are shown.
T72 3855-4008 Sentence denotes In the spectrum, purple highlights glycan oxonium ions and green marks intact peptide fragment ions with various partial glycan sequences still attached.
T73 4009-4176 Sentence denotes Note that the green-labeled ions allow for limited topology to be extracted including defining that the fucose is on the core and not the antennae of the glycopeptide.