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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T49","span":{"begin":1554,"end":1562},"obj":"Body_part"},{"id":"T50","span":{"begin":2640,"end":2650},"obj":"Body_part"}],"attributes":[{"id":"A49","pred":"fma_id","subj":"T49","obj":"http://purl.org/sig/ont/fma/fma13478"},{"id":"A50","pred":"fma_id","subj":"T50","obj":"http://purl.org/sig/ont/fma/fma82739"}],"text":"Structural Dynamics\nTo compute the RMSD of systems, the rotational and translational movements were removed by first fitting the Cα atoms of the RBD to the crystal structure and then computing the RMSD with respect to the Cα atoms of RBD in each system.\nFigure 3 shows the RMSD plot in the RBD of SARS-COV, nCOV-2019, and some of its variants. Comparison of the RMSD of SARS and nCOV-2019 RBD shows that SARS-COV has a larger RMSD throughout the 500 ns simulation. In nCOV-2019, the RMSD is very stable with a value of about 1.5 Å, whereas in SARS-COV, the RMSD increases up to ∼4 Å after 100 ns and then fluctuates between 3 and 4 Å. The change in RMSD of SARS is partially related to the motion in the C-terminal which is a flexible loop.\nFigure 3 Cα RMSD plots for nCOV-2019 and SARS-COV and a few nCOV-2019 mutations. The RMSD plots for the nCOV-2019 mutants show similar behaviors to nCOV-2019-wt. In most of the variants, the RMSD is very stable during the 300 ns simulation which shows the great tolerance of the interface for mutations. However, a few mutations showed some RMSD variance. In mutation Y489A, the RMSD increases from 1.37 ± 0.21 Å to1.88 ± 0.16 Å after 2000 ns. Mutation Y505A resulted in an increase in RMSD up to 100 ns to a value to 1.98 ± 0.20 Å and decreased afterward. The RMSD for mutation N487A shows an increasing behavior with a value of 2.10 ± 0.23 Å. Mutations N439K, V483A, and V483F showed a stable RMSD of ∼1.5 Å. For mutations T478I, G476S, S494P, and A475V, the RMSD increases up to ∼2 Å. These variations in the backbone RMSD show the involvement of these residues in the complex stability. RMSD plots for other mutations are shown in Figure S1.\nSince the extended loop (residues 449 to 510 shown in Figure 1B from α4 to α5) of the RBD makes all contacts with ACE2, the RMSD was computed by also fitting to the Cα atoms of this region (Figure S2). The extended loop in nCOV-2019 is very stable with less deviation (RMSD = 0.86 ± 0.017 Å) from the crystal structure compared to SARS-COV having an RMSD of 2.79 ± 0.05 Å. Few of the mutants show an increase in the loop RMSD during the simulation. In mutants N487A and Y449A the loop RMSD jumps to a value of about 1.95 ± 0.12 Å and 1.94 ± 0.24 Å, respectively, after about 200 ns of simulation. Mutants G447A and E484A show a loop RMSD values of 2.22 ± 0.03 Å and 1.96 ± 0.02 Å during the last 100 ns of simulation. Other mutants showed a stable extended loop (observed in loop RMSD) during simulation. The stability of extended loop for mutant systems confirms the high tolerance of this region of RBD.\nTo characterize the dynamic behavior for each amino acid in the RBD, we analyzed the root mean square fluctuation (RMSF) of all systems. The RMSF plots for nCOV-2019, SARS-COV, and four other mutations are shown in Figure 4. nCOV-2019 shows less fluctuations compared to SARS-COV. L3 in nCOV-2019 corresponding to residues 476 to 487 (shown in red in Figure 4) has smaller RMSF (1.5 Å) than SARS-COV L3 residues 463 to 474. L1 in both nCOV-2019 and SARS-COV (green) has small fluctuation (less than 1.5 Å). Moreover, the C-terminal residues of SARS-COV show high fluctuation (Figure 4 shown in orange). Few mutants show higher fluctuation in the L1. Mutants Y505A and S494A had a RMSF of 2.5 Å and mutation N487A had a RMSF of about 4 Å in the L1. Mutation Y449A has a higher RMSF of about 3 Å in the L3. Mutants G496A, E484A, and G447A show a high fluctuation of about 4.5 Å in the L3. The RMSF of other variants is shown in Figure S3.\nFigure 4 RMSF plots for nCOV-2019-wt, SARS-COV, Y505A, N487A, G496A, and E484A. The red shaded region shows the fluctuation in L1 and the green shaded region shows the fluctuation in L3. The orange shaded region in SARS-COV shows the fluctuation in the C-terminal. For comparison, the RMSF of nCOV-2019-wt is shown as cyan in other plots."}

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T76","span":{"begin":132,"end":137},"obj":"Chemical"},{"id":"T77","span":{"begin":225,"end":230},"obj":"Chemical"},{"id":"T78","span":{"begin":1856,"end":1861},"obj":"Chemical"},{"id":"T79","span":{"begin":1885,"end":1887},"obj":"Chemical"},{"id":"T80","span":{"begin":2640,"end":2650},"obj":"Chemical"},{"id":"T81","span":{"begin":2640,"end":2645},"obj":"Chemical"},{"id":"T82","span":{"begin":2646,"end":2650},"obj":"Chemical"},{"id":"T83","span":{"begin":3527,"end":3529},"obj":"Chemical"}],"attributes":[{"id":"A76","pred":"chebi_id","subj":"T76","obj":"http://purl.obolibrary.org/obo/CHEBI_33250"},{"id":"A77","pred":"chebi_id","subj":"T77","obj":"http://purl.obolibrary.org/obo/CHEBI_33250"},{"id":"A78","pred":"chebi_id","subj":"T78","obj":"http://purl.obolibrary.org/obo/CHEBI_33250"},{"id":"A79","pred":"chebi_id","subj":"T79","obj":"http://purl.obolibrary.org/obo/CHEBI_29387"},{"id":"A80","pred":"chebi_id","subj":"T80","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A81","pred":"chebi_id","subj":"T81","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A82","pred":"chebi_id","subj":"T82","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A83","pred":"chebi_id","subj":"T83","obj":"http://purl.obolibrary.org/obo/CHEBI_29388"}],"text":"Structural Dynamics\nTo compute the RMSD of systems, the rotational and translational movements were removed by first fitting the Cα atoms of the RBD to the crystal structure and then computing the RMSD with respect to the Cα atoms of RBD in each system.\nFigure 3 shows the RMSD plot in the RBD of SARS-COV, nCOV-2019, and some of its variants. Comparison of the RMSD of SARS and nCOV-2019 RBD shows that SARS-COV has a larger RMSD throughout the 500 ns simulation. In nCOV-2019, the RMSD is very stable with a value of about 1.5 Å, whereas in SARS-COV, the RMSD increases up to ∼4 Å after 100 ns and then fluctuates between 3 and 4 Å. The change in RMSD of SARS is partially related to the motion in the C-terminal which is a flexible loop.\nFigure 3 Cα RMSD plots for nCOV-2019 and SARS-COV and a few nCOV-2019 mutations. The RMSD plots for the nCOV-2019 mutants show similar behaviors to nCOV-2019-wt. In most of the variants, the RMSD is very stable during the 300 ns simulation which shows the great tolerance of the interface for mutations. However, a few mutations showed some RMSD variance. In mutation Y489A, the RMSD increases from 1.37 ± 0.21 Å to1.88 ± 0.16 Å after 2000 ns. Mutation Y505A resulted in an increase in RMSD up to 100 ns to a value to 1.98 ± 0.20 Å and decreased afterward. The RMSD for mutation N487A shows an increasing behavior with a value of 2.10 ± 0.23 Å. Mutations N439K, V483A, and V483F showed a stable RMSD of ∼1.5 Å. For mutations T478I, G476S, S494P, and A475V, the RMSD increases up to ∼2 Å. These variations in the backbone RMSD show the involvement of these residues in the complex stability. RMSD plots for other mutations are shown in Figure S1.\nSince the extended loop (residues 449 to 510 shown in Figure 1B from α4 to α5) of the RBD makes all contacts with ACE2, the RMSD was computed by also fitting to the Cα atoms of this region (Figure S2). The extended loop in nCOV-2019 is very stable with less deviation (RMSD = 0.86 ± 0.017 Å) from the crystal structure compared to SARS-COV having an RMSD of 2.79 ± 0.05 Å. Few of the mutants show an increase in the loop RMSD during the simulation. In mutants N487A and Y449A the loop RMSD jumps to a value of about 1.95 ± 0.12 Å and 1.94 ± 0.24 Å, respectively, after about 200 ns of simulation. Mutants G447A and E484A show a loop RMSD values of 2.22 ± 0.03 Å and 1.96 ± 0.02 Å during the last 100 ns of simulation. Other mutants showed a stable extended loop (observed in loop RMSD) during simulation. The stability of extended loop for mutant systems confirms the high tolerance of this region of RBD.\nTo characterize the dynamic behavior for each amino acid in the RBD, we analyzed the root mean square fluctuation (RMSF) of all systems. The RMSF plots for nCOV-2019, SARS-COV, and four other mutations are shown in Figure 4. nCOV-2019 shows less fluctuations compared to SARS-COV. L3 in nCOV-2019 corresponding to residues 476 to 487 (shown in red in Figure 4) has smaller RMSF (1.5 Å) than SARS-COV L3 residues 463 to 474. L1 in both nCOV-2019 and SARS-COV (green) has small fluctuation (less than 1.5 Å). Moreover, the C-terminal residues of SARS-COV show high fluctuation (Figure 4 shown in orange). Few mutants show higher fluctuation in the L1. Mutants Y505A and S494A had a RMSF of 2.5 Å and mutation N487A had a RMSF of about 4 Å in the L1. Mutation Y449A has a higher RMSF of about 3 Å in the L3. Mutants G496A, E484A, and G447A show a high fluctuation of about 4.5 Å in the L3. The RMSF of other variants is shown in Figure S3.\nFigure 4 RMSF plots for nCOV-2019-wt, SARS-COV, Y505A, N487A, G496A, and E484A. The red shaded region shows the fluctuation in L1 and the green shaded region shows the fluctuation in L3. The orange shaded region in SARS-COV shows the fluctuation in the C-terminal. For comparison, the RMSF of nCOV-2019-wt is shown as cyan in other plots."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T6","span":{"begin":71,"end":84},"obj":"http://purl.obolibrary.org/obo/GO_0006412"},{"id":"T7","span":{"begin":877,"end":886},"obj":"http://purl.obolibrary.org/obo/GO_0007610"},{"id":"T8","span":{"begin":1347,"end":1355},"obj":"http://purl.obolibrary.org/obo/GO_0007610"},{"id":"T9","span":{"begin":2622,"end":2630},"obj":"http://purl.obolibrary.org/obo/GO_0007610"}],"text":"Structural Dynamics\nTo compute the RMSD of systems, the rotational and translational movements were removed by first fitting the Cα atoms of the RBD to the crystal structure and then computing the RMSD with respect to the Cα atoms of RBD in each system.\nFigure 3 shows the RMSD plot in the RBD of SARS-COV, nCOV-2019, and some of its variants. Comparison of the RMSD of SARS and nCOV-2019 RBD shows that SARS-COV has a larger RMSD throughout the 500 ns simulation. In nCOV-2019, the RMSD is very stable with a value of about 1.5 Å, whereas in SARS-COV, the RMSD increases up to ∼4 Å after 100 ns and then fluctuates between 3 and 4 Å. The change in RMSD of SARS is partially related to the motion in the C-terminal which is a flexible loop.\nFigure 3 Cα RMSD plots for nCOV-2019 and SARS-COV and a few nCOV-2019 mutations. The RMSD plots for the nCOV-2019 mutants show similar behaviors to nCOV-2019-wt. In most of the variants, the RMSD is very stable during the 300 ns simulation which shows the great tolerance of the interface for mutations. However, a few mutations showed some RMSD variance. In mutation Y489A, the RMSD increases from 1.37 ± 0.21 Å to1.88 ± 0.16 Å after 2000 ns. Mutation Y505A resulted in an increase in RMSD up to 100 ns to a value to 1.98 ± 0.20 Å and decreased afterward. The RMSD for mutation N487A shows an increasing behavior with a value of 2.10 ± 0.23 Å. Mutations N439K, V483A, and V483F showed a stable RMSD of ∼1.5 Å. For mutations T478I, G476S, S494P, and A475V, the RMSD increases up to ∼2 Å. These variations in the backbone RMSD show the involvement of these residues in the complex stability. RMSD plots for other mutations are shown in Figure S1.\nSince the extended loop (residues 449 to 510 shown in Figure 1B from α4 to α5) of the RBD makes all contacts with ACE2, the RMSD was computed by also fitting to the Cα atoms of this region (Figure S2). The extended loop in nCOV-2019 is very stable with less deviation (RMSD = 0.86 ± 0.017 Å) from the crystal structure compared to SARS-COV having an RMSD of 2.79 ± 0.05 Å. Few of the mutants show an increase in the loop RMSD during the simulation. In mutants N487A and Y449A the loop RMSD jumps to a value of about 1.95 ± 0.12 Å and 1.94 ± 0.24 Å, respectively, after about 200 ns of simulation. Mutants G447A and E484A show a loop RMSD values of 2.22 ± 0.03 Å and 1.96 ± 0.02 Å during the last 100 ns of simulation. Other mutants showed a stable extended loop (observed in loop RMSD) during simulation. The stability of extended loop for mutant systems confirms the high tolerance of this region of RBD.\nTo characterize the dynamic behavior for each amino acid in the RBD, we analyzed the root mean square fluctuation (RMSF) of all systems. The RMSF plots for nCOV-2019, SARS-COV, and four other mutations are shown in Figure 4. nCOV-2019 shows less fluctuations compared to SARS-COV. L3 in nCOV-2019 corresponding to residues 476 to 487 (shown in red in Figure 4) has smaller RMSF (1.5 Å) than SARS-COV L3 residues 463 to 474. L1 in both nCOV-2019 and SARS-COV (green) has small fluctuation (less than 1.5 Å). Moreover, the C-terminal residues of SARS-COV show high fluctuation (Figure 4 shown in orange). Few mutants show higher fluctuation in the L1. Mutants Y505A and S494A had a RMSF of 2.5 Å and mutation N487A had a RMSF of about 4 Å in the L1. Mutation Y449A has a higher RMSF of about 3 Å in the L3. Mutants G496A, E484A, and G447A show a high fluctuation of about 4.5 Å in the L3. The RMSF of other variants is shown in Figure S3.\nFigure 4 RMSF plots for nCOV-2019-wt, SARS-COV, Y505A, N487A, G496A, and E484A. The red shaded region shows the fluctuation in L1 and the green shaded region shows the fluctuation in L3. The orange shaded region in SARS-COV shows the fluctuation in the C-terminal. For comparison, the RMSF of nCOV-2019-wt is shown as cyan in other plots."}

LitCovid-sentences

LitCovid-PubTator