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PMC:7081066 / 7095-10023 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id tao:has_standard_notation
216 23-28 Gene denotes Spike Gene:43740568
217 29-33 Gene denotes ACE2 Gene:59272
249 74-79 Gene denotes spike Gene:43740568
250 266-270 Gene denotes ACE2 Gene:59272
251 1206-1210 Gene denotes ACE2 Gene:59272
252 1579-1583 Gene denotes ACE2 Gene:59272
253 2143-2148 Gene denotes spike Gene:43740568
254 2454-2458 Gene denotes ACE2 Gene:59272
255 2914-2919 Gene denotes spike Gene:43740568
256 91-99 Species denotes SARS-CoV Tax:694009
257 127-130 Species denotes CoV Tax:11118
258 164-167 Species denotes CoV Tax:11118
259 171-190 Species denotes Rhinolophus sinicus Tax:89399
260 196-206 Species denotes SARS-CoV-2 Tax:2697049
261 260-265 Species denotes human Tax:9606
262 630-640 Species denotes SARS-CoV-2 Tax:2697049
263 645-653 Species denotes SARS-CoV Tax:694009
264 816-824 Species denotes SARS-CoV Tax:694009
265 967-977 Species denotes SARS-CoV-2 Tax:2697049
266 1055-1060 Species denotes human Tax:9606
267 1111-1119 Species denotes SARS-CoV Tax:694009
268 1200-1205 Species denotes human Tax:9606
269 1300-1305 Species denotes human Tax:9606
270 1345-1355 Species denotes SARS-CoV-2 Tax:2697049
271 1450-1460 Species denotes SARS-CoV-2 Tax:2697049
272 1957-1962 Species denotes human Tax:9606
273 2187-2195 Species denotes SARS-CoV Tax:694009
274 2348-2358 Species denotes SARS-CoV-2 Tax:2697049
275 2655-2665 Species denotes SARS-CoV-2 Tax:2697049
276 2702-2710 Species denotes SARS-CoV Tax:694009
277 880-889 Disease denotes infection MESH:D007239
278 1307-1312 Mutation denotes K479N p.K479N
279 1317-1322 Mutation denotes S487T p.S487T

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T40 80-87 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T41 2149-2156 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T42 2531-2538 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T43 2539-2546 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T44 2920-2927 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T35 91-99 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T36 196-204 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T37 630-638 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 645-653 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 816-824 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 880-889 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T41 967-975 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T42 1111-1119 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 1345-1353 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T44 1450-1458 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 2187-2195 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T46 2348-2356 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 2655-2663 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 2702-2710 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T42 260-265 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T43 482-483 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 800-807 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T45 1055-1060 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T46 1200-1205 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T47 1266-1267 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T48 1300-1305 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T49 1324-1326 http://purl.obolibrary.org/obo/CLO_0001022 denotes Li
T50 1324-1326 http://purl.obolibrary.org/obo/CLO_0007314 denotes Li
T51 1627-1628 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T52 1827-1828 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T53 1957-1962 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T54 1973-1980 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T55 2003-2006 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T56 2007-2012 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T50 80-87 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T51 484-488 Chemical denotes beta http://purl.obolibrary.org/obo/CHEBI_10545
T52 934-936 Chemical denotes Lu http://purl.obolibrary.org/obo/CHEBI_33382
T53 1221-1223 Chemical denotes Lu http://purl.obolibrary.org/obo/CHEBI_33382
T54 1324-1326 Chemical denotes Li http://purl.obolibrary.org/obo/CHEBI_30145
T55 2149-2156 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T56 2531-2538 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T57 2539-2546 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T58 2920-2927 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T60 0-43 Sentence denotes Structural analysis of Spike-ACE2 complexes
T61 44-285 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 286-358 Sentence denotes The interaction pattern between the three viral spikes is quite similar.
T63 359-586 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 587-808 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 809-954 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 955-1107 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 1108-1241 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 1242-1337 Sentence denotes These residues suffered a punctual mutation from civet to human, K479N and S487T (Li, 2013[5]).
T69 1338-1428 Sentence denotes In the SARS-CoV-2, the residues corresponding to N479 correspond to Q493 and T487 to N501.
T70 1429-1541 Sentence denotes These changes in the SARS-CoV-2 represent energetically favorable changes for the interaction with the receptor.
T71 1542-1703 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 1704-1708 Sentence denotes 1)).
T73 1709-1898 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 1899-2013 Sentence denotes Our models showed that these capping loops appear in both human-infecting viruses but are absent in the bat virus.
T75 2014-2183 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 2184-2420 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 2421-2493 Sentence denotes The counter-pairs located in the ACE2 receptor are shown in Table 1(Tab.
T78 2494-2497 Sentence denotes 1).
T79 2498-2569 Sentence denotes Altogether, the higher number of protein-protein contacts (Table 2(Tab.
T80 2570-2741 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 2742-2746 Sentence denotes 3)).
T82 2747-2928 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 950-951 26206723 denotes 6
32210742-26206723-29811236 1237-1238 26206723 denotes 6
32210742-23994189-29811237 1333-1334 23994189 denotes 5

2_test

Id Subject Object Predicate Lexical cue
32210742-26206723-29811235 950-951 26206723 denotes 6
32210742-26206723-29811236 1237-1238 26206723 denotes 6
32210742-23994189-29811237 1333-1334 23994189 denotes 5