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PMC:7219429 / 17717-20735 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T99 22-29 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T100 48-60 Body_part denotes gangliosides http://purl.org/sig/ont/fma/fma82816
T101 66-71 Body_part denotes lipid http://purl.org/sig/ont/fma/fma67264
T102 151-162 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T103 169-176 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T104 235-247 Body_part denotes gangliosides http://purl.org/sig/ont/fma/fma82816
T105 418-430 Body_part denotes gangliosides http://purl.org/sig/ont/fma/fma82816
T106 595-602 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T107 662-672 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T108 695-702 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T109 804-809 Body_part denotes lipid http://purl.org/sig/ont/fma/fma67264
T110 912-924 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T111 946-957 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T112 1775-1782 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T113 1800-1805 Body_part denotes lipid http://purl.org/sig/ont/fma/fma67264
T114 1827-1839 Body_part denotes gangliosides http://purl.org/sig/ont/fma/fma82816
T115 2113-2120 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T116 2129-2139 Body_part denotes Amino acid http://purl.org/sig/ont/fma/fma82739
T117 2167-2178 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T118 2222-2229 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T119 2562-2572 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T120 2792-2797 Body_part denotes colon http://purl.org/sig/ont/fma/fma14543

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T13 2792-2797 Body_part denotes colon http://purl.obolibrary.org/obo/UBERON_0001155

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T61 5-13 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T62 578-586 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T63 895-898 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T65 1151-1159 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T66 1339-1347 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T67 1419-1422 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T69 1458-1466 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T70 1578-1582 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T71 1688-1696 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T72 2096-2099 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T74 2205-2213 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T75 2278-2286 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T76 2514-2522 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T77 2886-2889 Disease denotes PAM http://purl.obolibrary.org/obo/MONDO_0018959
T78 3002-3005 Disease denotes PAM http://purl.obolibrary.org/obo/MONDO_0018959

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T178 64-65 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T179 196-198 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T180 551-552 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T181 662-681 http://purl.obolibrary.org/obo/CHEBI_33708 denotes amino acid residues
T182 662-681 http://purl.obolibrary.org/obo/PR_000036907 denotes amino acid residues
T183 834-836 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T184 937-938 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T185 1241-1244 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T186 1315-1318 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T187 1508-1511 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T188 1512-1513 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T189 1552-1558 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T190 1564-1569 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T191 1618-1619 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T192 1719-1724 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T193 1747-1749 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T194 1798-1799 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T195 1940-1942 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T196 2066-2067 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T197 2390-2393 http://purl.obolibrary.org/obo/CLO_0001002 denotes 162
T198 2475-2480 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T199 2485-2491 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T200 2492-2499 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T201 2790-2791 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T202 2792-2797 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colon
T203 2907-2908 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T310 22-29 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T311 48-60 Chemical denotes gangliosides http://purl.obolibrary.org/obo/CHEBI_28892
T312 66-71 Chemical denotes lipid http://purl.obolibrary.org/obo/CHEBI_18059
T313 151-162 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T314 169-176 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T315 196-198 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T316 231-234 Chemical denotes GM1 http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110
T319 235-247 Chemical denotes gangliosides http://purl.obolibrary.org/obo/CHEBI_28892
T320 275-281 Chemical denotes lipids http://purl.obolibrary.org/obo/CHEBI_18059
T321 288-301 Chemical denotes sphingomyelin http://purl.obolibrary.org/obo/CHEBI_17636|http://purl.obolibrary.org/obo/CHEBI_64583
T323 306-317 Chemical denotes cholesterol http://purl.obolibrary.org/obo/CHEBI_16113
T324 418-430 Chemical denotes gangliosides http://purl.obolibrary.org/obo/CHEBI_28892
T325 445-456 Chemical denotes cholesterol http://purl.obolibrary.org/obo/CHEBI_16113
T326 461-474 Chemical denotes sphingomyelin http://purl.obolibrary.org/obo/CHEBI_17636|http://purl.obolibrary.org/obo/CHEBI_64583
T328 524-527 Chemical denotes GM1 http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110
T331 595-602 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T332 662-672 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T333 662-667 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T334 668-672 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T335 695-702 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T336 724-727 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T337 785-788 Chemical denotes GM1 http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110
T340 804-809 Chemical denotes lipid http://purl.obolibrary.org/obo/CHEBI_18059
T341 912-924 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T342 946-957 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T343 958-961 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T344 1747-1749 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T345 1765-1768 Chemical denotes GM1 http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110
T348 1775-1782 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T349 1800-1805 Chemical denotes lipid http://purl.obolibrary.org/obo/CHEBI_18059
T350 1823-1826 Chemical denotes GM1 http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110
T353 1827-1839 Chemical denotes gangliosides http://purl.obolibrary.org/obo/CHEBI_28892
T354 1863-1874 Chemical denotes cholesterol http://purl.obolibrary.org/obo/CHEBI_16113
T355 1876-1880 Chemical denotes chol http://purl.obolibrary.org/obo/CHEBI_16113
T356 1890-1903 Chemical denotes sphingomyelin http://purl.obolibrary.org/obo/CHEBI_17636|http://purl.obolibrary.org/obo/CHEBI_64583
T358 1905-1907 Chemical denotes SM http://purl.obolibrary.org/obo/CHEBI_17076|http://purl.obolibrary.org/obo/CHEBI_74817|http://purl.obolibrary.org/obo/CHEBI_17636
T361 1909-1915 Chemical denotes lipids http://purl.obolibrary.org/obo/CHEBI_18059
T362 1940-1942 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T363 2026-2037 Chemical denotes Cholesterol http://purl.obolibrary.org/obo/CHEBI_16113
T364 2042-2055 Chemical denotes sphingomyelin http://purl.obolibrary.org/obo/CHEBI_17636|http://purl.obolibrary.org/obo/CHEBI_64583
T366 2077-2080 Chemical denotes GM1 http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110
T369 2113-2120 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T370 2129-2139 Chemical denotes Amino acid http://purl.obolibrary.org/obo/CHEBI_33704
T371 2135-2139 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T372 2167-2178 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T373 2179-2182 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T374 2222-2229 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T375 2241-2246 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T376 2447-2452 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T377 2562-2572 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T378 2562-2567 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T379 2568-2572 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T380 2886-2889 Chemical denotes PAM http://purl.obolibrary.org/obo/CHEBI_51135|http://purl.obolibrary.org/obo/CHEBI_60882
T382 3002-3005 Chemical denotes PAM http://purl.obolibrary.org/obo/CHEBI_51135|http://purl.obolibrary.org/obo/CHEBI_60882

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T18 231-234 GlycoEpitope denotes GM1 http://www.glycoepitope.jp/epitopes/EP0050
T19 524-527 GlycoEpitope denotes GM1 http://www.glycoepitope.jp/epitopes/EP0050
T20 785-788 GlycoEpitope denotes GM1 http://www.glycoepitope.jp/epitopes/EP0050
T21 1765-1768 GlycoEpitope denotes GM1 http://www.glycoepitope.jp/epitopes/EP0050
T22 1823-1826 GlycoEpitope denotes GM1 http://www.glycoepitope.jp/epitopes/EP0050
T23 2077-2080 GlycoEpitope denotes GM1 http://www.glycoepitope.jp/epitopes/EP0050

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T132 0-83 Sentence denotes 3.3 SARS-CoV-2 spike protein interactions with gangliosides in a lipid raft domain
T133 84-324 Sentence denotes Based on recent in-silico data that led to the characterization of ganglioside-spike protein interactions [10], MD simulations were performed with GM1 gangliosides surrounded by typical raft lipids, i.e. sphingomyelin and cholesterol (Figs.
T134 325-335 Sentence denotes 5 and 6 ).
T135 336-436 Sentence denotes These new data confirmed and extended our previous results obtained with isolated gangliosides [10].
T136 437-612 Sentence denotes Indeed, cholesterol and sphingomyelin appeared to stabilize the typical chalice-shaped GM1 dimer, which serves as a landing platform for the SARS-CoV-2 spike protein (Fig. 6).
T137 613-849 Sentence denotes Moreover, the histograms of Fig. 5 show that all amino acid residues of the spike protein that are involved in ATM binding, including the QFN triad, are also essential for GM1 binding in the lipid raft environment (Table S1 and Fig. 5).
T138 850-1017 Sentence denotes Taken together, these data indicate that the NTD of the viral glycoprotein may display a common ganglioside/ATM binding site, in agreement with our working hypothesis.
T139 1018-1216 Sentence denotes Sequence alignments revealed that this common binding site, including the QFN triad, is totally conserved among clinical isolates of SARS-CoV-2 from various geographical origins worldwide (Fig. 7 ).
T140 1217-1399 Sentence denotes It is also conserved in bat RaTG13, which further illustrates the close relationship between this bat coronavirus and the SARS-CoV-2 strains that are currently circulating the world.
T141 1400-1488 Sentence denotes This region of the NTD should therefore be considered for SARS-CoV-2 vaccine strategies.
T142 1489-1739 Sentence denotes However, the motif has a different sequence signature in other animal- and human-related SARS coronaviruses (Fig. 7), indicating a recent evolution that may be linked to the higher contagiousness of SARS-CoV-2 compared with other human coronaviruses.
T143 1740-1818 Sentence denotes Fig. 6 MD simulations of GM1-spike protein interaction in a lipid raft domain.
T144 1819-1916 Sentence denotes Two GM1 gangliosides were merged with eight cholesterol (chol) and two sphingomyelin (SM) lipids.
T145 1917-1980 Sentence denotes After initial docking, MD simulations were performed for 50 ns.
T146 1981-2025 Sentence denotes Two distinct views of the complex are shown.
T147 2026-2121 Sentence denotes Cholesterol and sphingomyelin stabilize a dimer of GM1 clamped by the NTD of the spike protein.
T148 2122-2230 Sentence denotes Fig. 7 Amino acid sequence alignments of the ganglioside/ATM binding domain of the SARS-CoV-2 spike protein.
T149 2231-2395 Sentence denotes The first group of sequences includes clinical SARS-CoV-2 isolates from various geographical origins aligned with the reference sequence (6VSB_A, fragment 111-162).
T150 2396-2435 Sentence denotes The QFN triad is highlighted in yellow.
T151 2436-2525 Sentence denotes The second group of sequences includes human and animal viruses compared with SARS-CoV-2.
T152 2526-2668 Sentence denotes Deletions are highlighted in green, amino acid changes are highlighted in blue, conserved residues of the QFN triad are highlighted in yellow.
T153 2669-3018 Sentence denotes The degree of conservation observed in each column is symbolized by an asterisk (*) when the residue is fully conserved, a colon (:) for distinct residues with strongly similar properties (scoring > 0.5 in the Gonnet PAM 250 matrix), and a period (.) for distinct residues with weakly similar properties (scoring ≤ 0.5 in the Gonnet PAM 250 matrix).

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
440 16-21 Gene denotes spike Gene:43740568
441 5-15 Species denotes SARS-CoV-2 Tax:2697049
442 48-60 Chemical denotes gangliosides MESH:D005732
443 66-71 Chemical denotes lipid MESH:D008055
457 2107-2112 Gene denotes spike Gene:43740568
458 1765-1768 Chemical denotes GM1 MESH:D005677
459 1800-1805 Chemical denotes lipid MESH:D008055
460 1823-1826 Chemical denotes GM1 MESH:D005677
461 1827-1839 Chemical denotes gangliosides MESH:D005732
462 1863-1874 Chemical denotes cholesterol MESH:D002784
463 1876-1880 Chemical denotes chol MESH:D002784
464 1890-1903 Chemical denotes sphingomyelin MESH:D013109
465 1905-1907 Chemical denotes SM MESH:D013109
466 1909-1915 Chemical denotes lipids MESH:D008055
467 2026-2037 Chemical denotes Cholesterol MESH:D002784
468 2042-2055 Chemical denotes sphingomyelin MESH:D013109
469 2077-2080 Chemical denotes GM1 MESH:D005677
477 2216-2221 Gene denotes spike Gene:43740568
478 2205-2215 Species denotes SARS-CoV-2 Tax:2697049
479 2278-2288 Species denotes SARS-CoV-2 Tax:2697049
480 2475-2480 Species denotes human Tax:9606
481 2514-2524 Species denotes SARS-CoV-2 Tax:2697049
482 2167-2178 Chemical denotes ganglioside MESH:D005732
483 2632-2635 Chemical denotes QFN
510 589-594 Gene denotes spike Gene:43740568
511 689-694 Gene denotes spike Gene:43740568
512 163-168 Gene denotes spike Gene:43740568
513 578-588 Species denotes SARS-CoV-2 Tax:2697049
514 1151-1161 Species denotes SARS-CoV-2 Tax:2697049
515 1315-1330 Species denotes bat coronavirus Tax:1508220
516 1339-1349 Species denotes SARS-CoV-2 Tax:2697049
517 1458-1468 Species denotes SARS-CoV-2 Tax:2697049
518 1564-1569 Species denotes human Tax:9606
519 1578-1596 Species denotes SARS coronaviruses Tax:694009
520 1688-1698 Species denotes SARS-CoV-2 Tax:2697049
521 1719-1724 Species denotes human Tax:9606
522 1725-1738 Species denotes coronaviruses Tax:11118
523 151-162 Chemical denotes ganglioside MESH:D005732
524 231-247 Chemical denotes GM1 gangliosides MESH:D005677
525 275-281 Chemical denotes lipids MESH:D008055
526 288-301 Chemical denotes sphingomyelin MESH:D013109
527 306-317 Chemical denotes cholesterol MESH:D002784
528 418-430 Chemical denotes gangliosides MESH:D005732
529 445-456 Chemical denotes cholesterol MESH:D002784
530 461-474 Chemical denotes sphingomyelin MESH:D013109
531 524-527 Chemical denotes GM1 MESH:D005677
532 785-788 Chemical denotes GM1 MESH:D005677
533 804-809 Chemical denotes lipid MESH:D008055
534 946-957 Chemical denotes ganglioside MESH:D005732
535 958-961 Chemical denotes ATM MESH:D017963