FIGURE SUMMARY
Title

Insights into structure and dynamics of extracellular domain of Toll-like receptor 5 in Cirrhinus mrigala (mrigala): A molecular dynamics simulation approach

Authors
Rout, A.K., Acharya, V., Maharana, D., Dehury, B., Udgata, S.R., Jena, R., Behera, B., Parida, P.K., Behera, B.K.
Source
Full text @ PLoS One
Fig 1

Evolutionary relationship of taxa using TLR5 from <italic>Cirrhinus mrigala</italic> and other closely related organisms using NJ method.

The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) was displayed. Evolutionary analyses were conducted on MEGA 6.0.
Fig 2

Sequence-structure alignment, modeling, and validation of the modelled <italic>Cm</italic>TLR5.

(A) Target-template alignment of CmTLR5 with the close structural homolog 3V47 using Multalin and ESPript. (B) The architecture of the modelled CmTLR5 protein displaying the sixteen LRRs and variable loops. (C) Structural superimposed view of the modeled CmTLR5 concerning the template i.e. TLR5 from zebrafish. (D) Ramachandran plot of the modeled CmTLR5 was obtained using PROCHECK. (E) Evaluation of the modeled CmTLR5 through z-score using ProSA-web.
Fig 3

Intrinsic dynamic stability of the modeled ECD of <italic>Cm</italic>TLR5, <italic>Cm</italic>TLR5-flagellin and <italic>Dr</italic>TLR5-flagellin complex during all-atoms MD simulation of 200 ns.

(A) The backbone RMSD of three MD systems over the time scale of 200 ns (Blue: CmTLR5, Maroon: DrTLR5-flagellin and Cyan: CmTLR5-flagellin complex). (B) Radius of gyration (Rg) plot showing the compactness of trajectory of the three systems over the time scale of 200 ns. (C) Variation of intermolecular Hydrogen-bonds forming strong intermolecular contacts of flagellin with DrTLR5 and CmTLR5 during 200 ns MD simulation (D).
Fig 4

Residual flexibility and principal component analysis of <italic>Cm</italic>TLR5 alone during the last 100 ns of MD.

(A) The residual flexibility is measured by RMSF of Cα-atoms of the CmTLR5. (B) B-factor analysis of the MD simulated CmTLR5. (C) Porcupine plot displaying the movement of CmTLR5 by analyzing the PC1 from PCA. (D) Porcupine plot displaying the movement of CmTLR5 by analyzing the PC2 from PCA.
Fig 5

Structural imposed views of the top two cluster representatives (cluster 1: Green and cluster 2: Blue) obtained from clustering analysis using the snapshots from last 100 ns trajectory (A) and the evolution of secondary structure elements of CmTLR5 over time scale of 200 ns (B).

Fig 6

PCA of <italic>Cm</italic>TLR5-flagellin and <italic>Dr</italic>TLR5-flagellin complexes with using the last 100 ns MD trajectories.

(A) Eigenvalues of the few first 20 PCs in TLR5 (alone), CmTLR5-flagellin and DrTLR5-flagellin complexes (B) Projection of the motion of the structures of the main-chain atoms in phase space along the first two principal components (PC1 vs. PC2) constructed from the 100 ns MD trajectory of all the systems. (C) The Porcupine plot of the first two PCs displaying the movement of the DrTLR5-flagellin complex. (D) The Porcupine plot of the first two PCs displaying the movement of the CmTLR5-flagellin complex. The arrows show the tendency of movement.
Fig 7

Per residue decomposition analysis displaying the contribution of each residue towards binding free energy in DrTLR5-Flagellin and CmTLR5-Flagellin complex systems.

Fig 8

Protein-protein interaction involving TLR5 and Flagellin obtained from the top-ranked cluster from MD simulations.

(A) Inter-molecular contact analysis of CmTLR5 with flagellin (B) Interactions analysis of DrTLR5 with flagellin. The hydrogen bonds are shown in blue line while other hydrophobic non-bonded contacts are displayed in red dashed lines.
Fig 9

Inter-atomic distance profile of the important hydrogen bond forming amino acid pairs in CmTLR5-flagellin complex using the MD trajectory.

Fig 10

Inter-atomic distance profile of the important hydrogen bond forming amino acid pairs in DrTLR5-flagellin complex using the 200 ns MD trajectory.

Acknowledgments
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