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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T56","span":{"begin":3470,"end":3480},"obj":"Body_part"},{"id":"T57","span":{"begin":4140,"end":4147},"obj":"Body_part"},{"id":"T58","span":{"begin":4767,"end":4774},"obj":"Body_part"}],"attributes":[{"id":"A56","pred":"fma_id","subj":"T56","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A57","pred":"fma_id","subj":"T57","obj":"http://purl.org/sig/ont/fma/fma82749"},{"id":"A58","pred":"fma_id","subj":"T58","obj":"http://purl.org/sig/ont/fma/fma82749"}],"text":"Hydrogen Bond, Salt-Bridge, and Hydrophobic Contact Analysis\nImportant 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.\nTable 1 H-Bonds and Salt-Bridges between nCOV-2019 and ACE2 and SARS-COV and ACE2 that Persist for \u003e30%a\n# nCOV-2019 ACE2 % occupancy SARS-COV ACE2 % occupancy\n1 G502 K353 89 Y436 D38 96\n2 Q493 E35 83 R426 E329 87\n3 N487 Y83 80 T486 D355 83\n4 Q498 D38 73 G488 K353 80\n5 K417 D30 55 N479 K31 52\n6 T500 D355 53 Y440 H34 47\n7 Y505 E37 52 \n8 Q498 K353 49 \n9 Y449 D38 45 \n10 G496 K353 37 \n11 Q493 K31 32 \na Salt bridge is shown as bold. The evolution of the coronavirus from SARS-COV to nCOV-2019 has reshaped the interfacial hydrogen bonds with ACE2. G502 in nCOV-2019 has a persistent H-bond with residue K353 on ACE2. This residue was G488 in SARS-COV, which also makes the H-bond with K353 on ACE2. Q493 in nCOV-2019 makes H-bond with E35 and another H-bond with K31 on ACE2. This residue was an N479 in SARS-COV, which only makes one H-bond with K31 on ACE2. An important mutation from SARS-COV to nCOV-2019 is residue Q498, which was Y484 in SARS-COV. Q498 makes two H-bonds with residues D38 and K353 on ACE2, whereas Y484 in SARS-COV does not make any H-bonds. 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. This residue is V404 in SARS-COV which is not able to make any salt-bridge and does not make H-bond with ACE2. 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. A salt bridge between R426 on RBD and E329 on ACE2 stabilizes the complex in SARS-COV/ACE2. This residue is N439 in nCOV-2019 which is unable to make salt-bridge with ACE2 residue E329. 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. Y436 in SARS-COV and Y449 in nCOV-2019 both make H-bonds with D38 on ACE2. The unchanged T486 in SARS-COV corresponds to T500 in nCOV-2019, both of which make consistent H-bonds with ACE2 residue D355.\nHydrophobic interactions also play an important role in stabilizing the RBD/ACE2 complex in nCOV-2019. An important interaction between nCOV-2019 RBD and ACE2 is the π-stacking interaction between F486 (RBD) and Y83 (ACE2). This interaction helps in stabilizing L3 in nCOV-2019 compared to SARS-COV where this residue is L472. 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. Other interfacial residues in nCOV-2019 RBD that participate in the hydrophobic interaction with ACE2 are L455, F456, Y473, A475, and Y489. It is interesting to note that all these residues except Y489 have mutated from SARS-COV. 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). 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. 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. The H-bonds between RBD of nCOV-2019 and SARS-COV are shown in Figure 9A. The structural details discussed here are in agreement with other structural studies of the nCOV-2019 RBD/ACE2 complex.4,53\nH-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. Few of the alanine substitutions increase the number of interfacial H-bonds between nCOV-2019 RBD and ACE2. Interestingly, the ala-substitution at Y489A increased the number of H-bonds in the wild-type complex. 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. 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. However, few mutations decrease the number of H-bonds from the wild-type complex. Alanine substitution at residue G502 has a significant effect on the network of H-bonds between nCOV-2019 and SARS-COV. This residue locates at the end of L4 loop near two other important residues Q498 and T500. This mutation breaks the H-bonds at these residues. Mutation K417A decreases the number of H-bonds to only 5 where the H-bond at residue Q498 is broken. This indicates the delicate nature of the H-bond from residue Q498 which can easily be broken upon ala-substitution at other residues. Furthermore, mutation N487 also decreases the number of H-bonds by breaking the H-bond at Q498."}

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