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PMC:7556165 / 49779-52427 JSONTXT

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LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T162 426-433 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T163 657-664 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T164 1636-1647 Chemical denotes Pro-Pro-Ala http://purl.obolibrary.org/obo/CHEBI_162578
T165 1674-1685 Chemical denotes Gly-Val-Glu http://purl.obolibrary.org/obo/CHEBI_164159
T166 1686-1689 Chemical denotes Gly http://purl.obolibrary.org/obo/CHEBI_15428
T167 1916-1919 Chemical denotes Ile http://purl.obolibrary.org/obo/CHEBI_17191|http://purl.obolibrary.org/obo/CHEBI_30009

LitCovid-sample-PD-NCBITaxon

Id Subject Object Predicate Lexical cue ncbi_taxonomy_id
T282 36-46 Species denotes SARS-CoV-2 NCBItxid:2697049
T283 36-40 Species denotes SARS NCBItxid:694009
T284 112-122 Species denotes SARS-CoV-2 NCBItxid:2697049
T285 112-116 Species denotes SARS NCBItxid:694009
T286 786-794 Species denotes SARS-CoV NCBItxid:694009
T287 786-790 Species denotes SARS NCBItxid:694009
T288 808-818 Species denotes SARS-CoV-2 NCBItxid:2697049
T289 808-812 Species denotes SARS NCBItxid:694009
T290 883-893 Species denotes SARS-CoV-2 NCBItxid:2697049
T291 883-887 Species denotes SARS NCBItxid:694009
T292 953-961 Species denotes SARS-CoV NCBItxid:694009
T293 953-957 Species denotes SARS NCBItxid:694009
T294 1554-1564 Species denotes SARS-CoV-2 NCBItxid:2697049
T295 1554-1558 Species denotes SARS NCBItxid:694009
T296 1569-1577 Species denotes SARS-CoV NCBItxid:694009
T297 1569-1573 Species denotes SARS NCBItxid:694009
T298 1606-1614 Species denotes SARS-CoV NCBItxid:694009
T299 1606-1610 Species denotes SARS NCBItxid:694009
T300 1693-1703 Species denotes SARS-CoV-2 NCBItxid:2697049
T301 1693-1697 Species denotes SARS NCBItxid:694009
T302 1885-1895 Species denotes SARS-CoV-2 NCBItxid:2697049
T303 1885-1889 Species denotes SARS NCBItxid:694009
T304 1923-1927 Species denotes SARS NCBItxid:694009
T305 2262-2272 Species denotes SARS-CoV-2 NCBItxid:2697049
T306 2262-2266 Species denotes SARS NCBItxid:694009
T307 2289-2293 Species denotes SARS NCBItxid:694009
T308 2398-2408 Species denotes SARS-CoV-2 NCBItxid:2697049
T309 2398-2402 Species denotes SARS NCBItxid:694009

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T312 0-280 Sentence denotes In spite of the recent emergence of SARS-CoV-2, multiple authors have already highlighted the structure of ACE2/SARS-CoV-2 RBD complex by either X-ray (Lan et al., 2020; Shang et al., 2020b; Wang et al., 2020) or cryo-EM (Walls et al., 2020; Wrapp et al., 2020; Yan et al., 2020).
T313 281-391 Sentence denotes Pleasantly, all data converged to a consistent tridimensional arrangement of the receptor (Wang et al., 2020).
T314 392-509 Sentence denotes In the “closed” conformation of S protein, the RBD is buried at the interface between protomers (Walls et al., 2020).
T315 510-692 Sentence denotes Only in the “open” S conformation, RBD engages PD of ACE2 (Wrapp et al., 2020), and the complex may involve a dimeric ACE2 that accommodates two S protein trimers (Yan et al., 2020).
T316 693-882 Sentence denotes In keeping with their sequence similarity, strong structural homology was found between ACE2/SARS-CoV RBD and ACE2/SARS-CoV-2 RBD (Lan et al., 2020; Shang et al., 2020b; Wang et al., 2020).
T317 883-1071 Sentence denotes SARS-CoV-2 RBM spans from residue 438–506 of S sequence and, likewise SARS-CoV RBM, it approaches the outer surface of ACE2 by a gently concave surface with a ridge on one side (Figure 8).
T318 1072-1237 Sentence denotes The concave surface is made up by the two short β5 and β6 sheets of the external RBD subdomain, whereas the ridge contains the β5/β6 loop (loop 1: residues 474–489).
T319 1238-1339 Sentence denotes A second smaller loop (loop 2: residues 498–505) is visible on the other side of the concave surface.
T320 1340-1605 Sentence denotes Inspection of the complex structure and molecular dynamics (MD) highlighted that the motifs 453–456 (in β5), 484–489 (in the loop 1), and 500–505 (in the loop 2) are at the basis of the largest differences between SARS-CoV-2 and SARS-CoV RBM interactions with ACE2.
T321 1606-1860 Sentence denotes SARS-CoV RBM ridge contains a Pro-Pro-Ala motif that is replaced by Gly-Val-Glu-Gly in SARS-CoV-2 (residues 482–485), yielding a more compact loop able to engage more interactions with proximal ACE2 residues (e.g., Ser19 and Gln24) (Shang et al., 2020b).
T322 1861-2069 Sentence denotes Additionally, Phe486 of SARS-CoV-2 RBM (which replaces Ile of SARS) inserts into a hydrophobic pocket on the receptor surface, establishing strong aromatic interactions with Tyr83 of ACE2 (Wang et al., 2020).
T323 2070-2165 Sentence denotes Asn501 in loop 2 further engages recognized hotspots on the ACE2 surface (Shang et al., 2020b).
T324 2166-2317 Sentence denotes Consistently, MD studies confirmed that loop 1 and 2 are much more rigid in RBM-ACE2 complex of SARS-CoV-2 with respect to SARS (Brielle et al., 2020).
T325 2318-2438 Sentence denotes These subtle structural differences probably account for the higher affinity of SARS-CoV-2 for ACE2 (Wang et al., 2020).
T326 2439-2648 Sentence denotes Interestingly, MD simulations suggest that the difference in affinity is largely due to the solvation energy, emphasizing the relevant role of hydrophobic patches in RBM/ACE2 binding surface (He et al., 2020).

LitCovid-sample-Pubtator

Id Subject Object Predicate Lexical cue pubann:denotes
1050 642-649 Gene denotes mmodate Gene:43740571
1051 297-307 Gene denotes data conve Gene:43740571
1056 174-197 Chemical denotes g et al., 2020b; Wang e MESH:D005998
1057 223-229 Chemical denotes alls e MESH:D000409
1404 107-111 Gene denotes ACE2 Gene:59272
1405 563-567 Gene denotes ACE2 Gene:59272
1406 628-632 Gene denotes ACE2 Gene:59272
1407 781-785 Gene denotes ACE2 Gene:59272
1408 803-807 Gene denotes ACE2 Gene:59272
1409 1002-1006 Gene denotes ACE2 Gene:59272
1410 1444-1446 Gene denotes β5 Gene:28884
1411 1600-1604 Gene denotes ACE2 Gene:59272
1412 1800-1804 Gene denotes ACE2 Gene:59272
1413 2044-2048 Gene denotes ACE2 Gene:59272
1414 2130-2134 Gene denotes ACE2 Gene:59272
1415 2246-2250 Gene denotes ACE2 Gene:59272
1416 2413-2417 Gene denotes ACE2 Gene:59272
1417 2609-2613 Gene denotes ACE2 Gene:59272
1418 928-929 Gene denotes S Gene:43740568
1419 655-656 Gene denotes S Gene:43740568
1420 529-530 Gene denotes S Gene:43740568
1421 424-425 Gene denotes S Gene:43740568
1422 1127-1129 Gene denotes β6 Gene:28873
1423 1120-1122 Gene denotes β5 Gene:28884
1424 36-46 Species denotes SARS-CoV-2 Tax:2697049
1425 112-122 Species denotes SARS-CoV-2 Tax:2697049
1426 786-794 Species denotes SARS-CoV Tax:694009
1427 808-818 Species denotes SARS-CoV-2 Tax:2697049
1428 883-893 Species denotes SARS-CoV-2 Tax:2697049
1429 953-961 Species denotes SARS-CoV Tax:694009
1430 1554-1564 Species denotes SARS-CoV-2 Tax:2697049
1431 1569-1577 Species denotes SARS-CoV Tax:694009
1432 1606-1614 Species denotes SARS-CoV Tax:694009
1433 1693-1703 Species denotes SARS-CoV-2 Tax:2697049
1434 1885-1895 Species denotes SARS-CoV-2 Tax:2697049
1435 2262-2272 Species denotes SARS-CoV-2 Tax:2697049
1436 2398-2408 Species denotes SARS-CoV-2 Tax:2697049
1437 1636-1647 Chemical denotes Pro-Pro-Ala MESH:C027789
1438 1674-1689 Chemical denotes Gly-Val-Glu-Gly
1439 1821-1826 Chemical denotes Ser19
1440 1831-1836 Chemical denotes Gln24
1441 1875-1881 Chemical denotes Phe486
1442 2035-2040 Chemical denotes Tyr83
1443 2070-2076 Chemical denotes Asn501

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T5492 107-111 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T5493 123-126 Protein denotes RBD https://www.uniprot.org/uniprot/Q63492|https://www.uniprot.org/uniprot/Q63491|https://www.uniprot.org/uniprot/Q62815|https://www.uniprot.org/uniprot/Q62691|https://www.uniprot.org/uniprot/Q01542|https://www.uniprot.org/uniprot/P27732|https://www.uniprot.org/uniprot/O09024|https://www.uniprot.org/uniprot/O09023|https://www.uniprot.org/uniprot/O09022
T5502 424-433 Protein denotes S protein https://www.uniprot.org/uniprot/Q9UIP0|https://www.uniprot.org/uniprot/Q9UIN9|https://www.uniprot.org/uniprot/Q9UIN8|https://www.uniprot.org/uniprot/Q9UIN7|https://www.uniprot.org/uniprot/Q9UIN6|https://www.uniprot.org/uniprot/Q9UBH8|https://www.uniprot.org/uniprot/Q9NRH8|https://www.uniprot.org/uniprot/Q9NRH7|https://www.uniprot.org/uniprot/Q9NRH6|https://www.uniprot.org/uniprot/Q9NRH5|https://www.uniprot.org/uniprot/Q9NRH4|https://www.uniprot.org/uniprot/Q9NPG5|https://www.uniprot.org/uniprot/Q9NPE0|https://www.uniprot.org/uniprot/Q9NP52|https://www.uniprot.org/uniprot/Q95IF9|https://www.uniprot.org/uniprot/Q8N5P3|https://www.uniprot.org/uniprot/Q8IZU6|https://www.uniprot.org/uniprot/Q8IZU5|https://www.uniprot.org/uniprot/Q8IZU4|https://www.uniprot.org/uniprot/Q86Z04|https://www.uniprot.org/uniprot/Q7YR44|https://www.uniprot.org/uniprot/Q7LA71|https://www.uniprot.org/uniprot/Q7LA70|https://www.uniprot.org/uniprot/Q5STD2|https://www.uniprot.org/uniprot/Q5SQ85|https://www.uniprot.org/uniprot/Q1XI16|https://www.uniprot.org/uniprot/Q1XI12|https://www.uniprot.org/uniprot/Q15517|https://www.uniprot.org/uniprot/O43509|https://www.uniprot.org/uniprot/O19084|https://www.uniprot.org/uniprot/B0UYZ7|https://www.uniprot.org/uniprot/B0S7V2|https://www.uniprot.org/uniprot/A5A6L9
T5535 439-442 Protein denotes RBD https://www.uniprot.org/uniprot/Q63492|https://www.uniprot.org/uniprot/Q63491|https://www.uniprot.org/uniprot/Q62815|https://www.uniprot.org/uniprot/Q62691|https://www.uniprot.org/uniprot/Q01542|https://www.uniprot.org/uniprot/P27732|https://www.uniprot.org/uniprot/O09024|https://www.uniprot.org/uniprot/O09023|https://www.uniprot.org/uniprot/O09022
T5544 545-548 Protein denotes RBD https://www.uniprot.org/uniprot/Q63492|https://www.uniprot.org/uniprot/Q63491|https://www.uniprot.org/uniprot/Q62815|https://www.uniprot.org/uniprot/Q62691|https://www.uniprot.org/uniprot/Q01542|https://www.uniprot.org/uniprot/P27732|https://www.uniprot.org/uniprot/O09024|https://www.uniprot.org/uniprot/O09023|https://www.uniprot.org/uniprot/O09022
T5553 563-567 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T5554 628-632 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T5555 655-664 Protein denotes S protein https://www.uniprot.org/uniprot/Q9UIP0|https://www.uniprot.org/uniprot/Q9UIN9|https://www.uniprot.org/uniprot/Q9UIN8|https://www.uniprot.org/uniprot/Q9UIN7|https://www.uniprot.org/uniprot/Q9UIN6|https://www.uniprot.org/uniprot/Q9UBH8|https://www.uniprot.org/uniprot/Q9NRH8|https://www.uniprot.org/uniprot/Q9NRH7|https://www.uniprot.org/uniprot/Q9NRH6|https://www.uniprot.org/uniprot/Q9NRH5|https://www.uniprot.org/uniprot/Q9NRH4|https://www.uniprot.org/uniprot/Q9NPG5|https://www.uniprot.org/uniprot/Q9NPE0|https://www.uniprot.org/uniprot/Q9NP52|https://www.uniprot.org/uniprot/Q95IF9|https://www.uniprot.org/uniprot/Q8N5P3|https://www.uniprot.org/uniprot/Q8IZU6|https://www.uniprot.org/uniprot/Q8IZU5|https://www.uniprot.org/uniprot/Q8IZU4|https://www.uniprot.org/uniprot/Q86Z04|https://www.uniprot.org/uniprot/Q7YR44|https://www.uniprot.org/uniprot/Q7LA71|https://www.uniprot.org/uniprot/Q7LA70|https://www.uniprot.org/uniprot/Q5STD2|https://www.uniprot.org/uniprot/Q5SQ85|https://www.uniprot.org/uniprot/Q1XI16|https://www.uniprot.org/uniprot/Q1XI12|https://www.uniprot.org/uniprot/Q15517|https://www.uniprot.org/uniprot/O43509|https://www.uniprot.org/uniprot/O19084|https://www.uniprot.org/uniprot/B0UYZ7|https://www.uniprot.org/uniprot/B0S7V2|https://www.uniprot.org/uniprot/A5A6L9
T5588 781-785 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T5589 795-798 Protein denotes RBD https://www.uniprot.org/uniprot/Q63492|https://www.uniprot.org/uniprot/Q63491|https://www.uniprot.org/uniprot/Q62815|https://www.uniprot.org/uniprot/Q62691|https://www.uniprot.org/uniprot/Q01542|https://www.uniprot.org/uniprot/P27732|https://www.uniprot.org/uniprot/O09024|https://www.uniprot.org/uniprot/O09023|https://www.uniprot.org/uniprot/O09022
T5598 803-807 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T5599 819-822 Protein denotes RBD https://www.uniprot.org/uniprot/Q63492|https://www.uniprot.org/uniprot/Q63491|https://www.uniprot.org/uniprot/Q62815|https://www.uniprot.org/uniprot/Q62691|https://www.uniprot.org/uniprot/Q01542|https://www.uniprot.org/uniprot/P27732|https://www.uniprot.org/uniprot/O09024|https://www.uniprot.org/uniprot/O09023|https://www.uniprot.org/uniprot/O09022
T5608 1002-1006 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T5609 1153-1156 Protein denotes RBD https://www.uniprot.org/uniprot/Q63492|https://www.uniprot.org/uniprot/Q63491|https://www.uniprot.org/uniprot/Q62815|https://www.uniprot.org/uniprot/Q62691|https://www.uniprot.org/uniprot/Q01542|https://www.uniprot.org/uniprot/P27732|https://www.uniprot.org/uniprot/O09024|https://www.uniprot.org/uniprot/O09023|https://www.uniprot.org/uniprot/O09022
T5618 1600-1604 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T5619 1800-1804 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T5620 2044-2048 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T5621 2130-2134 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T5622 2246-2250 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T5623 2413-2417 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T5624 2609-2613 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T389 426-433 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T390 657-664 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T391 1042-1047 Body_part denotes ridge http://purl.org/sig/ont/fma/fma75035
T392 1180-1185 Body_part denotes ridge http://purl.org/sig/ont/fma/fma75035
T393 1619-1624 Body_part denotes ridge http://purl.org/sig/ont/fma/fma75035

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T254 36-46 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T255 36-40 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T256 112-122 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T257 112-116 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T258 786-794 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T259 786-790 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T260 808-818 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T261 808-812 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T262 883-893 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T263 883-887 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T264 928-938 Disease denotes S sequence http://purl.obolibrary.org/obo/MONDO_0007821
T265 953-961 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T266 953-957 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T267 1554-1564 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T268 1554-1558 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T269 1569-1577 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T270 1569-1573 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T271 1606-1614 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T272 1606-1610 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T273 1693-1703 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T274 1693-1697 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T275 1885-1895 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T276 1885-1889 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T277 1923-1927 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T278 2262-2272 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T279 2262-2266 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T280 2289-2293 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T281 2398-2408 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T282 2398-2402 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-sample-PD-MAT

Id Subject Object Predicate Lexical cue
T127 1791-1799 http://purl.obolibrary.org/obo/MAT_0000491 denotes proximal

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1404 107-111 Gene denotes ACE2 Gene:59272
1405 563-567 Gene denotes ACE2 Gene:59272
1406 628-632 Gene denotes ACE2 Gene:59272
1407 781-785 Gene denotes ACE2 Gene:59272
1408 803-807 Gene denotes ACE2 Gene:59272
1409 1002-1006 Gene denotes ACE2 Gene:59272
1410 1444-1446 Gene denotes β5 Gene:28884
1411 1600-1604 Gene denotes ACE2 Gene:59272
1412 1800-1804 Gene denotes ACE2 Gene:59272
1413 2044-2048 Gene denotes ACE2 Gene:59272
1414 2130-2134 Gene denotes ACE2 Gene:59272
1415 2246-2250 Gene denotes ACE2 Gene:59272
1416 2413-2417 Gene denotes ACE2 Gene:59272
1417 2609-2613 Gene denotes ACE2 Gene:59272
1418 928-929 Gene denotes S Gene:43740568
1419 655-656 Gene denotes S Gene:43740568
1420 529-530 Gene denotes S Gene:43740568
1421 424-425 Gene denotes S Gene:43740568
1422 1127-1129 Gene denotes β6 Gene:28873
1423 1120-1122 Gene denotes β5 Gene:28884
1424 36-46 Species denotes SARS-CoV-2 Tax:2697049
1425 112-122 Species denotes SARS-CoV-2 Tax:2697049
1426 786-794 Species denotes SARS-CoV Tax:694009
1427 808-818 Species denotes SARS-CoV-2 Tax:2697049
1428 883-893 Species denotes SARS-CoV-2 Tax:2697049
1429 953-961 Species denotes SARS-CoV Tax:694009
1430 1554-1564 Species denotes SARS-CoV-2 Tax:2697049
1431 1569-1577 Species denotes SARS-CoV Tax:694009
1432 1606-1614 Species denotes SARS-CoV Tax:694009
1433 1693-1703 Species denotes SARS-CoV-2 Tax:2697049
1434 1885-1895 Species denotes SARS-CoV-2 Tax:2697049
1435 2262-2272 Species denotes SARS-CoV-2 Tax:2697049
1436 2398-2408 Species denotes SARS-CoV-2 Tax:2697049
1437 1636-1647 Chemical denotes Pro-Pro-Ala MESH:C027789
1438 1674-1689 Chemical denotes Gly-Val-Glu-Gly
1439 1821-1826 Chemical denotes Ser19
1440 1831-1836 Chemical denotes Gln24
1441 1875-1881 Chemical denotes Phe486
1442 2035-2040 Chemical denotes Tyr83
1443 2070-2076 Chemical denotes Asn501

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T312 0-280 Sentence denotes In spite of the recent emergence of SARS-CoV-2, multiple authors have already highlighted the structure of ACE2/SARS-CoV-2 RBD complex by either X-ray (Lan et al., 2020; Shang et al., 2020b; Wang et al., 2020) or cryo-EM (Walls et al., 2020; Wrapp et al., 2020; Yan et al., 2020).
T313 281-391 Sentence denotes Pleasantly, all data converged to a consistent tridimensional arrangement of the receptor (Wang et al., 2020).
T314 392-509 Sentence denotes In the “closed” conformation of S protein, the RBD is buried at the interface between protomers (Walls et al., 2020).
T315 510-692 Sentence denotes Only in the “open” S conformation, RBD engages PD of ACE2 (Wrapp et al., 2020), and the complex may involve a dimeric ACE2 that accommodates two S protein trimers (Yan et al., 2020).
T316 693-882 Sentence denotes In keeping with their sequence similarity, strong structural homology was found between ACE2/SARS-CoV RBD and ACE2/SARS-CoV-2 RBD (Lan et al., 2020; Shang et al., 2020b; Wang et al., 2020).
T317 883-1071 Sentence denotes SARS-CoV-2 RBM spans from residue 438–506 of S sequence and, likewise SARS-CoV RBM, it approaches the outer surface of ACE2 by a gently concave surface with a ridge on one side (Figure 8).
T318 1072-1237 Sentence denotes The concave surface is made up by the two short β5 and β6 sheets of the external RBD subdomain, whereas the ridge contains the β5/β6 loop (loop 1: residues 474–489).
T319 1238-1339 Sentence denotes A second smaller loop (loop 2: residues 498–505) is visible on the other side of the concave surface.
T320 1340-1605 Sentence denotes Inspection of the complex structure and molecular dynamics (MD) highlighted that the motifs 453–456 (in β5), 484–489 (in the loop 1), and 500–505 (in the loop 2) are at the basis of the largest differences between SARS-CoV-2 and SARS-CoV RBM interactions with ACE2.
T321 1606-1860 Sentence denotes SARS-CoV RBM ridge contains a Pro-Pro-Ala motif that is replaced by Gly-Val-Glu-Gly in SARS-CoV-2 (residues 482–485), yielding a more compact loop able to engage more interactions with proximal ACE2 residues (e.g., Ser19 and Gln24) (Shang et al., 2020b).
T322 1861-2069 Sentence denotes Additionally, Phe486 of SARS-CoV-2 RBM (which replaces Ile of SARS) inserts into a hydrophobic pocket on the receptor surface, establishing strong aromatic interactions with Tyr83 of ACE2 (Wang et al., 2020).
T323 2070-2165 Sentence denotes Asn501 in loop 2 further engages recognized hotspots on the ACE2 surface (Shang et al., 2020b).
T324 2166-2317 Sentence denotes Consistently, MD studies confirmed that loop 1 and 2 are much more rigid in RBM-ACE2 complex of SARS-CoV-2 with respect to SARS (Brielle et al., 2020).
T325 2318-2438 Sentence denotes These subtle structural differences probably account for the higher affinity of SARS-CoV-2 for ACE2 (Wang et al., 2020).
T326 2439-2648 Sentence denotes Interestingly, MD simulations suggest that the difference in affinity is largely due to the solvation energy, emphasizing the relevant role of hydrophobic patches in RBM/ACE2 binding surface (He et al., 2020).