LitCovid-sentences  

PMC:7605337 / 35128-40490 JSONTXT 6 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T223 0-60 Sentence denotes Hydrogen Bond, Salt-Bridge, and Hydrophobic Contact Analysis
T224 61-365 Sentence denotes Important hydrogen bonds (H-bonds) and salt bridges between nCOV-2019 RBD or SARS-COV RBD and ACE2 for the last 400 ns of trajectory are shown in Table 1. nCOV-2019 RBD makes 10 H-bonds/1 salt bridge with ACE2, whereas SARS-COV makes only 5 H-bonds/1 salt bridge with ACE2 with more than 30% persistence.
T225 366-471 Sentence denotes Table 1 H-Bonds and Salt-Bridges between nCOV-2019 and ACE2 and SARS-COV and ACE2 that Persist for >30%a
T226 472-532 Sentence denotes # nCOV-2019 ACE2 % occupancy SARS-COV ACE2 % occupancy
T227 533-565 Sentence denotes 1 G502 K353 89 Y436 D38 96
T228 566-601 Sentence denotes 2 Q493 E35 83 R426 E329 87
T229 602-634 Sentence denotes 3 N487 Y83 80 T486 D355 83
T230 635-667 Sentence denotes 4 Q498 D38 73 G488 K353 80
T231 668-702 Sentence denotes 5 K417 D30 55 N479 K31 52
T232 703-735 Sentence denotes 6 T500 D355 53 Y440 H34 47
T233 736-761 Sentence denotes 7 Y505 E37 52      
T234 762-788 Sentence denotes 8 Q498 K353 49      
T235 789-814 Sentence denotes 9 Y449 D38 45      
T236 815-842 Sentence denotes 10 G496 K353 37      
T237 843-869 Sentence denotes 11 Q493 K31 32      
T238 870-902 Sentence denotes a Salt bridge is shown as bold.
T239 903-1017 Sentence denotes The evolution of the coronavirus from SARS-COV to nCOV-2019 has reshaped the interfacial hydrogen bonds with ACE2.
T240 1018-1086 Sentence denotes G502 in nCOV-2019 has a persistent H-bond with residue K353 on ACE2.
T241 1087-1168 Sentence denotes This residue was G488 in SARS-COV, which also makes the H-bond with K353 on ACE2.
T242 1169-1245 Sentence denotes Q493 in nCOV-2019 makes H-bond with E35 and another H-bond with K31 on ACE2.
T243 1246-1329 Sentence denotes This residue was an N479 in SARS-COV, which only makes one H-bond with K31 on ACE2.
T244 1330-1423 Sentence denotes An important mutation from SARS-COV to nCOV-2019 is residue Q498, which was Y484 in SARS-COV.
T245 1424-1534 Sentence denotes Q498 makes two H-bonds with residues D38 and K353 on ACE2, whereas Y484 in SARS-COV does not make any H-bonds.
T246 1535-1679 Sentence denotes Importantly, a salt bridge between K417 and D30 in the nCOV-2019/ACE2 complex contributes to the total binding energy by −12.34 ± 0.23 kcal/mol.
T247 1680-1790 Sentence denotes This residue is V404 in SARS-COV which is not able to make any salt-bridge and does not make H-bond with ACE2.
T248 1791-1936 Sentence denotes Gao et al.27 used a FEP approach and showed that mutation V404 to K417 lowers the binding energy of nCOV-2019 RBD to ACE2 by −2.2 ± 0.9 kcal/mol.
T249 1937-2028 Sentence denotes A salt bridge between R426 on RBD and E329 on ACE2 stabilizes the complex in SARS-COV/ACE2.
T250 2029-2122 Sentence denotes This residue is N439 in nCOV-2019 which is unable to make salt-bridge with ACE2 residue E329.
T251 2123-2294 Sentence denotes One of the most observed mutations in nCOV-2019 according to the GISAID database is N439K which recovers some of the electrostatic interactions with ACE2 at this position.
T252 2295-2369 Sentence denotes Y436 in SARS-COV and Y449 in nCOV-2019 both make H-bonds with D38 on ACE2.
T253 2370-2496 Sentence denotes The unchanged T486 in SARS-COV corresponds to T500 in nCOV-2019, both of which make consistent H-bonds with ACE2 residue D355.
T254 2497-2599 Sentence denotes Hydrophobic interactions also play an important role in stabilizing the RBD/ACE2 complex in nCOV-2019.
T255 2600-2720 Sentence denotes An important interaction between nCOV-2019 RBD and ACE2 is the π-stacking interaction between F486 (RBD) and Y83 (ACE2).
T256 2721-2823 Sentence denotes This interaction helps in stabilizing L3 in nCOV-2019 compared to SARS-COV where this residue is L472.
T257 2824-2970 Sentence denotes It was observed by Gao et al.26 that mutation L472 to F486 in nCOV-2019 results in a net change in the binding free energy of −1.2 ± 0.2 kcal/mol.
T258 2971-3110 Sentence denotes Other interfacial residues in nCOV-2019 RBD that participate in the hydrophobic interaction with ACE2 are L455, F456, Y473, A475, and Y489.
T259 3111-3200 Sentence denotes It is interesting to note that all these residues except Y489 have mutated from SARS-COV.
T260 3201-3453 Sentence denotes Spinello and co-workers30 performed long-timescale (1μs) simulation of nCOV-2019/ACE2 and SARS-COV ACE2 and found that L3 in nCOV-2019 is more stable due to presence of the β6 strand and existence of two H-bonds in L3 (H-bonds G485-C488 and Q474-G476).
T261 3454-3629 Sentence denotes Importantly, an amino acid insertion in L3 makes this loop longer than L3 in SARS-COV and enables it to act like a recognition loop and make more persistent H-bonds with ACE2.
T262 3630-3790 Sentence denotes L455 in nCOV-2019 RBD is important for hydrophobic interaction with ACE2 and mutation L455A lowers the vdw contribution of binding affinity by about 5 kcal/mol.
T263 3791-3864 Sentence denotes The H-bonds between RBD of nCOV-2019 and SARS-COV are shown in Figure 9A.
T264 3865-3988 Sentence denotes The structural details discussed here are in agreement with other structural studies of the nCOV-2019 RBD/ACE2 complex.4,53
T265 3989-4128 Sentence denotes H-bond analysis was also performed for the mutant systems and the results for H-bonds with more than 40% consistency are shown in Table S3.
T266 4129-4236 Sentence denotes Few of the alanine substitutions increase the number of interfacial H-bonds between nCOV-2019 RBD and ACE2.
T267 4237-4339 Sentence denotes Interestingly, the ala-substitution at Y489A increased the number of H-bonds in the wild-type complex.
T268 4340-4516 Sentence denotes Mutation in some of the residues having consistent H-bonds in the wild type complex such as Q498A and Q493A, stunningly maintain the number of H-bonds in the wild-type complex.
T269 4517-4684 Sentence denotes This indicates that the plasticity in the network of H-bonds in RBM of nCOV-2019 can reshape the network and strengthen other H-bonds upon mutation in these locations.
T270 4685-4766 Sentence denotes However, few mutations decrease the number of H-bonds from the wild-type complex.
T271 4767-4886 Sentence denotes Alanine substitution at residue G502 has a significant effect on the network of H-bonds between nCOV-2019 and SARS-COV.
T272 4887-4978 Sentence denotes This residue locates at the end of L4 loop near two other important residues Q498 and T500.
T273 4979-5030 Sentence denotes This mutation breaks the H-bonds at these residues.
T274 5031-5131 Sentence denotes Mutation K417A decreases the number of H-bonds to only 5 where the H-bond at residue Q498 is broken.
T275 5132-5266 Sentence denotes This indicates the delicate nature of the H-bond from residue Q498 which can easily be broken upon ala-substitution at other residues.
T276 5267-5362 Sentence denotes Furthermore, mutation N487 also decreases the number of H-bonds by breaking the H-bond at Q498.