LitCovid-sentences  

PMC:7605337 / 23862-26557 JSONTXT 7 Projects

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Id Subject Object Predicate Lexical cue
T141 0-12 Sentence denotes PCA and aFEL
T142 13-113 Sentence denotes To identify the dominant motions in the nCOV-2019, SARS-COV, and all the mutants, PCA was performed.
T143 114-319 Sentence denotes Most of the combined motions were captured by the first ten eigenvectors generated from the last 400 ns for SARS-COV, nCOV-2019, and extended mutant systems and the last 200 ns for other nCOV-2019 mutants.
T144 320-434 Sentence denotes The percentage of the motions captured by the first three eigenvectors was 51% for nCOV-2019 and 68% for SARS-COV.
T145 435-528 Sentence denotes In all mutations, more than 50% of the motions were captured by the first three eigenvectors.
T146 529-689 Sentence denotes The first few PC’s describe the highest motions in a protein which are related to a functional motion such as binding or unbinding of protein from the receptor.
T147 690-889 Sentence denotes The first three eigenvectors were used to calculate the aFEL using the last 400 ns of simulation for nCOV-2019 and SARS-COV as shown in Figure 5, which displays the variance in conformational motion.
T148 890-988 Sentence denotes SARS-COV showed two distinct low free energy states shown as blue separated by a metastable state.
T149 989-1090 Sentence denotes There is a clear separation between the two regions by a free energy barrier of about 6–7.5 kcal/mol.
T150 1091-1206 Sentence denotes These two states correspond to the loop motions in the L3 as well as the motion in C-terminal residues of SARS-COV.
T151 1207-1355 Sentence denotes The L3 motion in nCOV-2019 is stabilized by the H-bond between N487 on RBD and Y83 on ACE2 as well as a π-stacking interaction between F486 and Y83.
T152 1356-1552 Sentence denotes It is evident that the nCOV-2019 RBD is more stable than SASR-COV RBD and exists in one conformation whereas the SARS-COV interface fluctuates and the aFEL is separated into two different regions.
T153 1553-1774 Sentence denotes The first two eigenvectors were used to calculate and plot the aFEL as a function of first two principal components using the last 200 ns of the simulation for mutant systems. aFEL for other systems is shown in Figure S4.
T154 1775-1934 Sentence denotes Figure 5 Mapping of the principal components of the RBD for the aFEL from the last 400 ns of simulations for SARS-COV (top row) and nCOV-2019-wt (bottom row).
T155 1935-1993 Sentence denotes The color bar is relative to the lowest free energy state.
T156 1994-2272 Sentence denotes In each system, the first eigenvector was used to construct the porcupine plots to visualize the most dominant movements (Figure S5). nCOV-2019 showed a small motion in L3 and the core region and the extended loop region are very rigid showing small cones in the porcupine plot.
T157 2273-2378 Sentence denotes The core structure of the RBD remains dormant as the cones are blue in most of the regions (Figure S5-A).
T158 2379-2448 Sentence denotes In SARS-COV, the C-terminal region shows large motions (Figure S5-B).
T159 2449-2506 Sentence denotes Mutation N487A showed a large motion in L1 (Figure S5-C).
T160 2507-2585 Sentence denotes Mutations Y449A, G447A, and E484A demonstrate large motions in L3 (Figure S5).
T161 2586-2695 Sentence denotes Overall, these plots show the involvement of these residues in the dynamic stability of the RBD/ACE2 complex.