LitCovid-sample-sentences  

PMC:7199903 / 1834-16161 JSONTXT 26 Projects

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Id Subject Object Predicate Lexical cue
T18 0-181 Sentence denotes Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative pathogen of coronavirus 2019 (COVID-19) (1, 2), induces fever, severe respiratory illness, and pneumonia.
T19 182-363 Sentence denotes SARS-CoV-2 uses an extensively glycosylated spike (S) protein that protrudes from the viral surface to bind to angiotensin-converting enzyme 2 (ACE2) to mediate host-cell entry (3).
T20 364-539 Sentence denotes The S protein is a trimeric class I fusion protein, composed of two functional subunits, responsible for receptor binding (S1 subunit) and membrane fusion (S2 subunit) (4, 5).
T21 540-672 Sentence denotes The surface of the envelope spike is dominated by host-derived glycans, with each trimer displaying 66 N-linked glycosylation sites.
T22 673-890 Sentence denotes The S protein is a key target in vaccine design efforts (6), and understanding the glycosylation of recombinant viral spikes can reveal fundamental features of viral biology and guide vaccine design strategies (7, 8).
T23 891-1037 Sentence denotes Viral glycosylation has wide-ranging roles in viral pathobiology, including mediating protein folding and stability and shaping viral tropism (9).
T24 1038-1181 Sentence denotes Glycosylation sites are under selective pressure as they facilitate immune evasion by shielding specific epitopes from antibody neutralization.
T25 1182-1327 Sentence denotes However, we note the low mutation rate of SARS-CoV-2 and that as yet, there have been no observed mutations to N-linked glycosylation sites (10).
T26 1328-1426 Sentence denotes Surfaces with an unusually high density of glycans can also enable immune recognition (9, 11, 12).
T27 1427-1552 Sentence denotes The role of glycosylation in camouflaging immunogenic protein epitopes has been studied for other coronaviruses (10, 13, 14).
T28 1553-1672 Sentence denotes Coronaviruses form virions by budding into the lumen of endoplasmic reticulum–Golgi intermediate compartments (15, 16).
T29 1673-1845 Sentence denotes However, observations of complex-type glycans on virally derived material suggests that the viral glycoproteins are subjected to Golgi-resident processing enzymes (13, 17).
T30 1846-1955 Sentence denotes High viral glycan density and local protein architecture can sterically impair the glycan maturation pathway.
T31 1956-2226 Sentence denotes Impaired glycan maturation resulting in the presence of oligomannose-type glycans can be a sensitive reporter of native-like protein architecture (8), and site-specific glycan analysis can be used to compare different immunogens and monitor manufacturing processes (18).
T32 2227-2335 Sentence denotes Additionally, glycosylation can influence the trafficking of recombinant immunogen to germinal centers (19).
T33 2336-2754 Sentence denotes To resolve the site-specific glycosylation of the SARS-CoV-2 S protein and visualize the distribution of glycoforms across the protein surface, we expressed and purified three biological replicates of recombinant soluble material in an identical manner to that which was used to obtain the high-resolution cryo–electron microscopy (cryo-EM) structure, albeit without a glycan-processing blockade using kifunensine (4).
T34 2755-2847 Sentence denotes This variant of the S protein contains all 22 glycans on the SARS-CoV-2 S protein (Fig. 1A).
T35 2848-3104 Sentence denotes Stabilization of the trimeric prefusion structure was achieved by using the 2P stabilizing mutations (20) at residues 986 and 987, a GSAS (Gly-Ser-Ala-Ser) substitution at the furin cleavage site (residues 682 to 685), and a C-terminal trimerization motif.
T36 3105-3177 Sentence denotes This helps to maintain quaternary architecture during glycan processing.
T37 3178-3377 Sentence denotes Before analysis, supernatant containing the recombinant SARS-CoV-2 S was purified by size exclusion chromatography to ensure that only native-like trimeric protein was analyzed (Fig. 1B and fig. S1).
T38 3378-3480 Sentence denotes The trimeric conformation of the purified material was validated by using negative-stain EM (Fig. 1C).
T39 3481-3548 Sentence denotes Fig. 1 Expression and validation of the SARS-CoV-2 S glycoprotein.
T40 3549-3611 Sentence denotes (A) Schematic representation of the SARS-CoV-2 S glycoprotein.
T41 3612-3754 Sentence denotes The positions of N-linked glycosylation sequons (N-X-S/T, where X ≠ P) are shown as branches (N, Asn; X, any residue; S, Ser; T, Thr; P, Pro).
T42 3755-4124 Sentence denotes Protein domains are illustrated: N-terminal domain (NTD), receptor binding domain (RBD), fusion peptide (FP), heptad repeat 1 (HR1), central helix (CH), connector domain (CD), and transmembrane domain (TM). (B) SDS–polyacrylamide gel electrophoresis analysis of the SARS-CoV-2 S protein (indicated by the arrowhead) expressed in human embryonic kidney (HEK) 293F cells.
T43 4125-4368 Sentence denotes Lane 1: filtered supernatant from transfected cells; lane 2: flow-through from StrepTactin resin; lane 3: wash from StrepTactin resin; lane 4: elution from StrepTactin resin. (C) Negative-stain EM 2D class averages of the SARS-CoV-2 S protein.
T44 4369-4555 Sentence denotes 2D class averages of the SARS-CoV-2 S protein are shown, confirming that the protein adopts the trimeric prefusion conformation matching the material used to determine the structure (4).
T45 4556-4709 Sentence denotes To determine the site-specific glycosylation of SARS-CoV-2 S, we used trypsin, chymotrypsin, and α-lytic protease to generate three glycopeptide samples.
T46 4710-4811 Sentence denotes These proteases were selected to generate glycopeptides that contain a single N-linked glycan sequon.
T47 4812-4974 Sentence denotes The glycopeptides were analyzed by liquid chromatography–mass spectrometry, and the glycan compositions were determined for all 22 N-linked glycan sites (Fig. 2).
T48 4975-5187 Sentence denotes To convey the main processing features at each site, the abundances of each glycan are summed into oligomannose-type, hybrid-type, and categories of complex-type glycosylation based on branching and fucosylation.
T49 5188-5305 Sentence denotes The detailed, expanded graphs showing the diverse range of glycan compositions are presented in table S1 and fig. S2.
T50 5306-5384 Sentence denotes Fig. 2 Site-specific N-linked glycosylation of the SARS-CoV-2 S glycoprotein.
T51 5385-5555 Sentence denotes The schematic illustrates the color code for the principal glycan types that can arise along the maturation pathway from oligomannose- to hybrid- to complex-type glycans.
T52 5556-5732 Sentence denotes The graphs summarize quantitative mass spectrometric analysis of the glycan population present at individual N-linked glycosylation sites simplified into categories of glycans.
T53 5733-6049 Sentence denotes The oligomannose-type glycan series (M9 to M5; Man9GlcNAc2 to Man5GlcNAc2) is colored green, afucosylated and fucosylated hybrid-type glycans (hybrid and F hybrid) are dashed pink, and complex glycans are grouped according to the number of antennae and presence of core fucosylation (A1 to FA4) and are colored pink.
T54 6050-6112 Sentence denotes Unoccupancy of an N-linked glycan site is represented in gray.
T55 6113-6174 Sentence denotes The pie charts summarize the quantification of these glycans.
T56 6175-6340 Sentence denotes Glycan sites are colored according to oligomannose-type glycan content, with the glycan sites labeled in green (80 to 100%), orange (30 to 79%), and pink (0 to 29%).
T57 6341-6475 Sentence denotes An extended version of the site-specific analysis showing the heterogeneity within each category can be found in table S1 and fig. S2.
T58 6476-6613 Sentence denotes The bar graphs represent the mean quantities of three biological replicates, with error bars representing the standard error of the mean.
T59 6614-6689 Sentence denotes Two sites on SARS-CoV-2 S are principally oligomannose-type: N234 and N709.
T60 6690-7082 Sentence denotes The predominant oligomannose-type glycan structure observed across the protein, with the exception of N234, is Man5GlcNAc2 (Man, mannose; GlcNAc, N-acetylglucosamine), which demonstrates that these sites are largely accessible to α-1,2-mannosidases but are poor substrates for GlcNAcT-I, which is the gateway enzyme in the formation of hybrid- and complex-type glycans in the Golgi apparatus.
T61 7083-7209 Sentence denotes The stage at which processing is impeded is a signature related to the density and presentation of glycans on the viral spike.
T62 7210-7356 Sentence denotes For example, the more densely glycosylated spikes of HIV-1 Env and Lassa virus (LASV) GPC exhibit numerous sites dominated by Man9GlcNAc2 (21–24).
T63 7357-7479 Sentence denotes A mixture of oligomannose- and complex-type glycans can be found at sites N61, N122, N603, N717, N801, and N1074 (Fig. 2).
T64 7480-7680 Sentence denotes Of the 22 sites on the S protein, 8 contain substantial populations of oligomannose-type glycans, highlighting how the processing of the SARS-CoV-2 S glycans is divergent from host glycoproteins (25).
T65 7681-7753 Sentence denotes The remaining 14 sites are dominated by processed, complex-type glycans.
T66 7754-7928 Sentence denotes Although unoccupied glycosylation sites were detected on SARS-CoV-2 S, when quantified they were revealed to form a very minor component of the total peptide pool (table S2).
T67 7929-8094 Sentence denotes In HIV-1 immunogen research, the holes generated by unoccupied glycan sites have been shown to be immunogenic and potentially give rise to distracting epitopes (26).
T68 8095-8259 Sentence denotes The high occupancy of N-linked glycan sequons of SARS-CoV-2 S indicates that recombinant immunogens will not require further optimization to enhance site occupancy.
T69 8260-8509 Sentence denotes Using the cryo-EM structure of the trimeric SARS-CoV-2 S protein [Protein Data Bank (PDB) ID 6VSB] (4), we mapped the glycosylation status of the coronavirus spike mimetic onto the experimentally determined three-dimensional (3D) structure (Fig. 3).
T70 8510-8665 Sentence denotes This combined mass spectrometric and cryo-EM analysis reveals how the N-linked glycans occlude distinct regions across the surface of the SARS-CoV-2 spike.
T71 8666-8731 Sentence denotes Fig. 3 Structure-based mapping of SARS-CoV-2 S N-linked glycans.
T72 8732-8945 Sentence denotes Representative glycans are modeled onto the prefusion structure of the trimeric SARS-CoV-2 S glycoprotein (PDB ID 6VSB) (4), with one RBD in the “up” conformation and the other two RBDs in the “down” conformation.
T73 8946-9026 Sentence denotes The glycans are colored according to oligomannose content as defined by the key.
T74 9027-9085 Sentence denotes ACE2 receptor binding sites are highlighted in light blue.
T75 9086-9205 Sentence denotes The S1 and S2 subunits are rendered with translucent surface representation, colored light and dark gray, respectively.
T76 9206-9376 Sentence denotes The flexible loops on which the N74 and N149 glycan sites reside are represented as gray dashed lines, with glycan sites on the loops mapped at their approximate regions.
T77 9377-9583 Sentence denotes Shielding of the receptor binding sites on the SARS-CoV-2 spike by proximal glycosylation sites (N165, N234, N343) can be observed, especially when the receptor binding domain is in the “down” conformation.
T78 9584-9785 Sentence denotes The shielding of receptor binding sites by glycans is a common feature of viral glycoproteins, as observed on SARS-CoV-1 S (10, 13), HIV-1 Env (27), influenza hemagglutinin (28, 29), and LASV GPC (24).
T79 9786-10076 Sentence denotes Given the functional constraints of receptor binding sites and the resulting low mutation rates of these residues, there is likely selective pressure to use N-linked glycans to camouflage one of the most conserved and potentially vulnerable areas of their respective glycoproteins (30, 31).
T80 10077-10164 Sentence denotes We note the dispersion of oligomannose-type glycans across both the S1 and S2 subunits.
T81 10165-10362 Sentence denotes This is in contrast to other viral glycoproteins; for example, the dense glycan clusters in several strains of HIV-1 Env induce oligomannose-type glycans that are recognized by antibodies (32, 33).
T82 10363-10586 Sentence denotes In SARS-CoV-2 S, the oligomannose-type structures are likely protected by the protein component, as exemplified by the N234 glycan, which is partially sandwiched between the N-terminal and receptor binding domains (Fig. 3).
T83 10587-10786 Sentence denotes We characterized the N-linked glycans on extended flexible loop structures (N74 and N149) and at the membrane-proximal C terminus (N1158, N1173, N1194) that were not resolved in the cryo-EM maps (4).
T84 10787-10892 Sentence denotes These were determined to be complex-type glycans, consistent with steric accessibility of these residues.
T85 10893-11052 Sentence denotes Whereas the oligomannose-type glycan content (28%) (table S2) is above that observed on typical host glycoproteins, it is lower than other viral glycoproteins.
T86 11053-11193 Sentence denotes For example, one of the most densely glycosylated viral spike proteins is HIV-1 Env, which exhibits ~60% oligomannose-type glycans (21, 34).
T87 11194-11456 Sentence denotes This suggests that the SARS-CoV-2 S protein is less densely glycosylated and that the glycans form less of a shield compared with other viral glycoproteins, including HIV-1 Env and LASV GPC, which may be beneficial for the elicitation of neutralizing antibodies.
T88 11457-11696 Sentence denotes Additionally, the processing of complex-type glycans is an important consideration in immunogen engineering, especially considering that epitopes of neutralizing antibodies against SARS-CoV-2 S can contain fucosylated glycans at N343 (35).
T89 11697-11848 Sentence denotes Across the 22 N-linked glycosylation sites, 52% are fucosylated and 15% of the glycans contain at least one sialic acid residue (table S2 and fig. S3).
T90 11849-11955 Sentence denotes Our analysis reveals that N343 is highly fucosylated with 98% of detected glycans bearing fucose residues.
T91 11956-12042 Sentence denotes Glycan modifications can be heavily influenced by the cellular expression system used.
T92 12043-12360 Sentence denotes We have previously demonstrated for HIV-1 Env glycosylation that the processing of complex-type glycans is driven by the producer cell but that the levels of oligomannose-type glycans were largely independent of the expression system and are much more closely related to the protein structure and glycan density (36).
T93 12361-12516 Sentence denotes Highly dense glycan shields, such as those observed on LASV GPC and HIV-1 Env, feature so-called mannose clusters (22, 24) on the protein surface (Fig. 4).
T94 12517-12731 Sentence denotes Whereas small mannose-type clusters have been characterized on the S1 subunit of Middle East respiratory syndrome (MERS)–CoV S (10), no such phenomenon has been observed for the SARS-CoV-1 or SARS-CoV-2 S proteins.
T95 12732-12956 Sentence denotes The site-specific glycosylation analysis reported here suggests that the glycan shield of SARS-CoV-2 S is consistent with other coronaviruses and similarly exhibits numerous vulnerabilities throughout the glycan shield (10).
T96 12957-13194 Sentence denotes Last, we detected trace levels of O-linked glycosylation at Thr323/Ser325 (T323/S325), with over 99% of these sites unmodified (fig. S4), suggesting that O-linked glycosylation of this region is minimal when the structure is native-like.
T97 13195-13243 Sentence denotes Fig. 4 Underprocessing of viral glycan shields.
T98 13244-13351 Sentence denotes From left to right, MERS-CoV S (10), SARS-CoV-1 S (10), SARS-CoV-2 S, LASV GPC (24), and HIV-1 Env (8, 21).
T99 13352-13444 Sentence denotes Site-specific N-linked glycan oligomannose quantifications are colored according to the key.
T100 13445-13620 Sentence denotes All glycoproteins were expressed as soluble trimers in HEK 293F cells apart from LASV GPC, which was derived from virus-like particles from Madin-Darby canine kidney II cells.
T101 13621-13776 Sentence denotes Our glycosylation analysis of SARS-CoV-2 offers a detailed benchmark of site-specific glycan signatures characteristic of a natively folded trimeric spike.
T102 13777-14036 Sentence denotes As an increasing number of glycoprotein-based vaccine candidates are being developed, their detailed glycan analysis offers a route for comparing immunogen integrity and will also be important to monitor as manufacturing processes are scaled for clinical use.
T103 14037-14164 Sentence denotes Glycan profiling will therefore also be an important measure of antigen quality in the manufacture of serological testing kits.
T104 14165-14327 Sentence denotes Last, with the advent of nucleotide-based vaccines, it will be important to understand how those delivery mechanisms affect immunogen processing and presentation.