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PMC:7605337 / 41468-43354 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T59 758-765 Body_part denotes Alanine http://purl.org/sig/ont/fma/fma82749
T60 1472-1479 Body_part denotes Alanine http://purl.org/sig/ont/fma/fma82749
T61 1763-1770 Body_part denotes Alanine http://purl.org/sig/ont/fma/fma82749

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T283 32-41 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T284 43-47 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T285 126-135 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T286 190-194 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T287 278-287 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T288 350-359 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T289 565-574 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T290 645-649 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T291 1045-1054 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T292 1089-1093 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T293 1161-1170 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T294 1557-1561 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T295 1748-1752 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T252 143-144 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T253 167-168 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T254 179-180 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T255 203-204 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T256 231-234 http://purl.obolibrary.org/obo/CLO_0001302 denotes 3–4
T257 235-236 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T258 344-345 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T259 402-405 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2 Å
T260 613-614 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T261 679-680 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T262 707-709 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T263 707-709 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T264 835-836 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T265 894-897 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2 Å
T266 1130-1131 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T267 1206-1207 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T268 1512-1513 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T269 1710-1711 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T270 1858-1859 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T128 707-709 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T129 758-765 Chemical denotes Alanine http://purl.obolibrary.org/obo/CHEBI_16449
T130 1472-1479 Chemical denotes Alanine http://purl.obolibrary.org/obo/CHEBI_16449
T131 1763-1770 Chemical denotes Alanine http://purl.obolibrary.org/obo/CHEBI_16449

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T13 944-952 http://purl.obolibrary.org/obo/GO_0007610 denotes behavior

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T283 0-259 Sentence denotes Changes in the RBD structure of nCOV-2019, SARS-COV, and mutants from their crystal structure were analyzed by RMSD and RMSF. nCOV-2019 showed a stable structure with a RMSD =1.5 Å, whereas SARS-COV had a larger RMSD value between 3–4 Å during the simulation.
T284 260-334 Sentence denotes Most mutations of nCOV-2019 maintained similar stability to the wild-type.
T285 335-466 Sentence denotes However, a few nCOV-2019 mutations resulted in larger deviations (>2 Å), i.e., Y489A, F456A, Y505A, N487A, K417A, Y473A, and Y449A.
T286 467-711 Sentence denotes We further investigated the structure of the extended loop domain (Figure 1B) and discovered that nCOV-2019 is stable with an RMSD of less than 1 Å, whereas the extended loop in SARS-COV shows an RMSD of about 3 Å during simulation (Figure S2).
T287 712-757 Sentence denotes Some mutants showed high RMSD in this region.
T288 758-837 Sentence denotes Alanine-substitution at residue N487 increased the extended loop RMSD to 2.5 Å.
T289 838-931 Sentence denotes Other mutations that increased the extended loop RMSD (>2 Å) include Y449A, G477A, and E484A.
T290 932-1022 Sentence denotes The dynamic behavior of RBD was further investigated by analyzing the RMSF of all systems.
T291 1023-1098 Sentence denotes As shown in Figure 4, nCOV-2019 shows less fluctuation in L3 than SARS-COV.
T292 1099-1324 Sentence denotes This is due to the presence of a four-residue motif (GQTQ) in nCOV-2019 L3, which forces the loop to adopt a compact structure by making two H-bonds (G485-C488 and Q474-G476) and thereby reducing the fluctuations in the loop.
T293 1325-1471 Sentence denotes Residues F486 and N487 play major roles in stabilizing the recognition loop by making π-stacking and H-bond interactions with residue Y83 on ACE2.
T294 1472-1531 Sentence denotes Alanine substitution at N487 introduced a large RMSF to L1.
T295 1532-1886 Sentence denotes Mutation L472 to F486 in SARS-COV was shown to favor binding by −1.2 ± 0.2 kcal/mol using FEP.26 In addition, this mutation was shown to be among the five mutations that produce a super affinity ACE2 binder based on SARS-COV RBD.6 Alanine mutations at residues Y449, G447, and E484 increased the motion in L3 characterized by a large RMSF in this region.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1038 1466-1470 Gene denotes ACE2 Gene:59272
1039 1727-1731 Gene denotes ACE2 Gene:59272
1040 32-36 Species denotes nCOV Tax:2697049
1041 43-51 Species denotes SARS-COV Tax:694009
1042 126-130 Species denotes nCOV Tax:2697049
1043 190-198 Species denotes SARS-COV Tax:694009
1044 278-282 Species denotes nCOV Tax:2697049
1045 350-354 Species denotes nCOV Tax:2697049
1046 565-569 Species denotes nCOV Tax:2697049
1047 645-653 Species denotes SARS-COV Tax:694009
1048 1045-1049 Species denotes nCOV Tax:2697049
1049 1089-1097 Species denotes SARS-COV Tax:694009
1050 1161-1165 Species denotes nCOV Tax:2697049
1051 1557-1565 Species denotes SARS-COV Tax:694009
1052 1748-1756 Species denotes SARS-COV Tax:694009
1053 758-765 Chemical denotes Alanine MESH:D000409
1054 790-794 Chemical denotes N487
1055 1334-1338 Chemical denotes F486
1056 1343-1347 Chemical denotes N487
1057 1459-1462 Chemical denotes Y83
1058 1472-1479 Chemical denotes Alanine MESH:D000409
1059 1763-1770 Chemical denotes Alanine MESH:D000409