LitCovid-sample-sentences  

PMC:7443692 / 9723-13789 JSONTXT 12 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T50 0-506 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 507-635 Sentence denotes In addition, proteolytic digestions followed by proteomic analyses confirmed that the proteins were highly purified (Table S12).
T52 636-835 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 836-1064 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 1065-1312 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 1313-1646 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 1647-1866 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 1867-2108 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 2109-2230 Sentence denotes Both expression systems produced a similar amount of S regardless of which expression construct was utilized (Figure S4).
T59 2231-2436 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 2437-2550 Sentence denotes Figure 1 Expression and Characterization of SARS-CoV-2 Spike Glycoprotein Trimer Immunogen and Soluble Human ACE2
T61 2551-2614 Sentence denotes (A) Sequences of SARS-CoV-2 S immunogen and soluble human ACE2.
T62 2615-2721 Sentence denotes The N-terminal pyroglutamines for both mature protein monomers are bolded, underlined, and shown in green.
T63 2722-2808 Sentence denotes The canonical N-linked glycosylation sequons are bolded, underlined, and shown in red.
T64 2809-3018 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 3019-3049 Sentence denotes MWM, molecular weight markers.
T66 3050-3219 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 3220-3312 Sentence denotes This spectrum defines the N terminus of the mature protein monomer as (pyro-)glutamine 0014.
T68 3313-3474 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 3475-3511 Sentence denotes This complex glycan occurs at N0017.
T70 3512-3631 Sentence denotes Note, that as expected, the cysteine is carbamidomethylated, and the mass accuracy of the assigned peptide is 0.98 ppm.
T71 3632-3744 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 3745-3898 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 3899-4066 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.