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PMC:7081066 / 7139-10023 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id tao:has_standard_notation
249 30-35 Gene denotes spike Gene:43740568
250 222-226 Gene denotes ACE2 Gene:59272
251 1162-1166 Gene denotes ACE2 Gene:59272
252 1535-1539 Gene denotes ACE2 Gene:59272
253 2099-2104 Gene denotes spike Gene:43740568
254 2410-2414 Gene denotes ACE2 Gene:59272
255 2870-2875 Gene denotes spike Gene:43740568
256 47-55 Species denotes SARS-CoV Tax:694009
257 83-86 Species denotes CoV Tax:11118
258 120-123 Species denotes CoV Tax:11118
259 127-146 Species denotes Rhinolophus sinicus Tax:89399
260 152-162 Species denotes SARS-CoV-2 Tax:2697049
261 216-221 Species denotes human Tax:9606
262 586-596 Species denotes SARS-CoV-2 Tax:2697049
263 601-609 Species denotes SARS-CoV Tax:694009
264 772-780 Species denotes SARS-CoV Tax:694009
265 923-933 Species denotes SARS-CoV-2 Tax:2697049
266 1011-1016 Species denotes human Tax:9606
267 1067-1075 Species denotes SARS-CoV Tax:694009
268 1156-1161 Species denotes human Tax:9606
269 1256-1261 Species denotes human Tax:9606
270 1301-1311 Species denotes SARS-CoV-2 Tax:2697049
271 1406-1416 Species denotes SARS-CoV-2 Tax:2697049
272 1913-1918 Species denotes human Tax:9606
273 2143-2151 Species denotes SARS-CoV Tax:694009
274 2304-2314 Species denotes SARS-CoV-2 Tax:2697049
275 2611-2621 Species denotes SARS-CoV-2 Tax:2697049
276 2658-2666 Species denotes SARS-CoV Tax:694009
277 836-845 Disease denotes infection MESH:D007239
278 1263-1268 Mutation denotes K479N p.K479N
279 1273-1278 Mutation denotes S487T p.S487T

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T40 36-43 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T41 2105-2112 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T42 2487-2494 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T43 2495-2502 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T44 2876-2883 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T35 47-55 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T36 152-160 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T37 586-594 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 601-609 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 772-780 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 836-845 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T41 923-931 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T42 1067-1075 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 1301-1309 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T44 1406-1414 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 2143-2151 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T46 2304-2312 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 2611-2619 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 2658-2666 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T42 216-221 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T43 438-439 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 756-763 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T45 1011-1016 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T46 1156-1161 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T47 1222-1223 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T48 1256-1261 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T49 1280-1282 http://purl.obolibrary.org/obo/CLO_0001022 denotes Li
T50 1280-1282 http://purl.obolibrary.org/obo/CLO_0007314 denotes Li
T51 1583-1584 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T52 1783-1784 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T53 1913-1918 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T54 1929-1936 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T55 1959-1962 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T56 1963-1968 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T50 36-43 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T51 440-444 Chemical denotes beta http://purl.obolibrary.org/obo/CHEBI_10545
T52 890-892 Chemical denotes Lu http://purl.obolibrary.org/obo/CHEBI_33382
T53 1177-1179 Chemical denotes Lu http://purl.obolibrary.org/obo/CHEBI_33382
T54 1280-1282 Chemical denotes Li http://purl.obolibrary.org/obo/CHEBI_30145
T55 2105-2112 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T56 2487-2494 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T57 2495-2502 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T58 2876-2883 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T61 0-241 Sentence denotes The crystal structures of the spike protein of SARS-CoV and homology models of Bat-CoV (accession number MG772933), Bat-CoV of Rhinolophus sinicus, and SARS-CoV-2 interacting with the putative binding domain site in human ACE2 were analyzed.
T62 242-314 Sentence denotes The interaction pattern between the three viral spikes is quite similar.
T63 315-542 Sentence denotes The main region of interaction with the putative cellular receptor counter-part is formed by fifteen residues ordered into a beta-sheet conformation surrounded by two capping loops (Figure 3(Fig. 3) and Supplementary Figure 1).
T64 543-764 Sentence denotes Interestingly, sequence comparison between SARS-CoV-2 and SARS-CoV revealed that the residues present in the receptor-interacting motive are highly conserved with 70 % identity, sharing nine residues between both viruses.
T65 765-910 Sentence denotes In the SARS-CoV RBD are present residues that allowed the interspecies infection, known as Y442, L472, N479, D480, and T487 (Lu et al., 2015[6]).
T66 911-1063 Sentence denotes However, in SARS-CoV-2, slight modification of some residues could improve the interaction with the human cellular receptor: L455, F486, Q493, and N501.
T67 1064-1197 Sentence denotes In SARS-CoV, two main residues (479 and 487) have been associated to the recognition of the human ACE2 receptor (Lu et al., 2015[6]).
T68 1198-1293 Sentence denotes These residues suffered a punctual mutation from civet to human, K479N and S487T (Li, 2013[5]).
T69 1294-1384 Sentence denotes In the SARS-CoV-2, the residues corresponding to N479 correspond to Q493 and T487 to N501.
T70 1385-1497 Sentence denotes These changes in the SARS-CoV-2 represent energetically favorable changes for the interaction with the receptor.
T71 1498-1659 Sentence denotes The local environment present in the ACE2 receptor allows these mutations to produce a significant number of electrostatic stabilizing interactions (Table 1(Tab.
T72 1660-1664 Sentence denotes 1)).
T73 1665-1854 Sentence denotes Furthermore, as mentioned previously, the presence of the two capping loops in the binding domain is likely producing a stabilization effect over the interaction with the cellular receptor.
T74 1855-1969 Sentence denotes Our models showed that these capping loops appear in both human-infecting viruses but are absent in the bat virus.
T75 1970-2139 Sentence denotes The data showed here strongly suggest that these capping loops produce an increase in the electrostatic interactions between the spike protein and the cellular receptor.
T76 2140-2376 Sentence denotes In SARS-CoV, the residues present in these capping loops showing direct interaction with the receptor are R426, S432, T433, Y436, P462, D463, S472, and N473 and in SARS-CoV-2 are V445, Y449, Y473, Q474, A475, E484, G485, F486, and N487.
T77 2377-2449 Sentence denotes The counter-pairs located in the ACE2 receptor are shown in Table 1(Tab.
T78 2450-2453 Sentence denotes 1).
T79 2454-2525 Sentence denotes Altogether, the higher number of protein-protein contacts (Table 2(Tab.
T80 2526-2697 Sentence denotes 2)) and the longer capping loops could explain the increase in binding affinities in SARS-CoV-2 (-15.7 Kcal/mol) in comparison with SARS-CoV (-14.1 Kcal/mol) (Table 3(Tab.
T81 2698-2702 Sentence denotes 3)).
T82 2703-2884 Sentence denotes Thus, these loops could play an important role together with the punctual mutations being an interesting clue to determine the host receptor specificity for the viral spike protein.

MyTest

Id Subject Object Predicate Lexical cue
32210742-26206723-29811235 906-907 26206723 denotes 6
32210742-26206723-29811236 1193-1194 26206723 denotes 6
32210742-23994189-29811237 1289-1290 23994189 denotes 5

2_test

Id Subject Object Predicate Lexical cue
32210742-26206723-29811235 906-907 26206723 denotes 6
32210742-26206723-29811236 1193-1194 26206723 denotes 6
32210742-23994189-29811237 1289-1290 23994189 denotes 5