LitCovid-sentences  

PMC:7245302 / 40073-43357 JSONTXT 9 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T302 0-35 Sentence denotes 3.11 Molecular Dynamics Simulation
T303 36-397 Sentence denotes The stability and dynamics of the designed vaccine construct ensemble docked to innate immune receptors were disclosed through 100-ns of MD production run and interpreted through the root mean square deviation (RMSD) [81], root mean square fluctuation (RMSF) 82, the radius of gyration (Rg) [83] and beta factor (β-factor) [84] assays as depicted in Figure 10 .
T304 398-527 Sentence denotes Fig. 10 MD trajectories based calculation of Cα RMSD (top left), RMSD (top right), Rg (bottom left), and β-factor (bottom right).
T305 528-638 Sentence denotes The average Cα atomic distance over 10,000 frames of TLR3-MEPVC and TLR4-MEPVC was decoded through RMSD assay.
T306 639-771 Sentence denotes An average RMSD of 3.44 Å (maximum, 6.30 Å) and 3.36 Å (maximum, 5.22 Å) were estimated for TLR3-MEPVC and TLR4-MEPVC, respectively.
T307 772-1002 Sentence denotes The TLR3 and TLR4 receptors are observed more compact than the MEPVC and as a result, continuous movements of the vaccine construct through its length are noticed at the exposed regions though rooted stable at the docked position.
T308 1003-1090 Sentence denotes This seems to be responsible for bringing small structural deviation as probed by RMSD.
T309 1091-1248 Sentence denotes Visual inspection of the trajectories illustrated no major global and local secondary structure conformation changes in the receptor TLR3 and TLR4 structure.
T310 1249-1356 Sentence denotes The MEPVC movements with respect to the TLR3 are shown at different snapshots as illustrated in Figure 11 .
T311 1357-1519 Sentence denotes The MEPVC seems responsible for the deviations in the receptor TLR4 at positions Glu1-Ser79, Hie540-Asn614, Gln1144-Gln1209, Gln1347-Pro1371, and Lys1489-Lys1491.
T312 1520-1711 Sentence denotes Continuous flexibility of the loops of MEPVC exposed region is observed and is highly flexible responsible for the movements of the MEPVC at the docked site though rooted stably (Figure 12 ).
T313 1712-1789 Sentence denotes Fig. 11 Binding mode of MEPVC at different snapshots at the TLR3 docked side.
T314 1790-1867 Sentence denotes Fig. 12 Binding mode of MEPVC at different snapshots at the TLR4 docked side.
T315 1868-2061 Sentence denotes The second statistical parameter computed for both complexes was the root mean square fluctuations (RMSF) that demonstrate average dynamical residue fluctuations over a specific length of time.
T316 2062-2184 Sentence denotes The mean RMSF concluded for TLR3-MEPVC system is 2.1 Å whereas, an average RMSF of 2.03 Å for TLR4-MEPVC was demonstrated.
T317 2185-2298 Sentence denotes Majority of the receptors residues are showing less variability and are satisfactory stable with mean RMSF < 3 Å.
T318 2299-2431 Sentence denotes The residues range mentioned above were reported to have higher RMSF values and revealed fluctuating throughout the simulation time.
T319 2432-2523 Sentence denotes These fluctuations are in all likelihood as an outcome of the moving adjuvant of the MEPVC.
T320 2524-2636 Sentence denotes This is supported by the fact that the mean RMSF of the MEPVC is comparatively very high than that of receptors.
T321 2637-2743 Sentence denotes The RMSF of MEPVC in TLR3-MEPVC and TLR4-MEPVC is 1.86 Å (maximum, 10.16 Å) and 7.45 Ǻ (maximum, 13.04 Ǻ).
T322 2744-2954 Sentence denotes The receptors stability in both complexes is reaffirmed by radius of gyration (Rg) analysis that depicted stable plot with mean value of 33.97 Å (maximum, 35.62 Å) and 41.01 Ǻ (maximum, 41.65 Ǻ) for TLR4-MEPVC.
T323 2955-3078 Sentence denotes The Rg findings are coherent with that of RMSD in interpreting systems stable behavior and compact nature of the receptors.
T324 3079-3183 Sentence denotes Lastly, thermal beta factor (β-factor) indicated the same pattern of residues dynamics as shown by RMSF.
T325 3184-3284 Sentence denotes An average β-factor derived from TLR3-MEPVC and TLR4-MEPVC is 121.34 Ų and 123.47 Ų, respectively.