Fig.7. Molecular docking
(A) Structure of hesperetin. (B)
Structure of m7GTP. (C) Structure of eIF4E in open
(grey, PDB ID – 3TF2) and close (green, PDB ID – 1IPC) conformations.
The flexible loop regions of eIF4E in close conformation are highlighted
in orange and red. Both eIF4E structures were aligned using Pymol
software version 0.99rc6. The bottom loop region of eIF4E (red) in both
conformations may be seen moving by 6.4 Å in a zoomed image.(D-G). Docking results and Ligplot analysis of
m7GTP and hesperetin docked to eIF4E. m7GTP (D) and
hesperetin (E) binding to the cap-binding pocket of
eIF4E. Major eIF4E residues interacting with m7GTP can be seen in the
respective zoomed view. Ligplot interaction analysis of the docked
complexes of m7GTP-eIF4E (F) and hesperetin-eIF4E (G)is shown.
Fig. 8. Output of normal mode analysis (NMA) study of
apo-eIF4E, m7GTP-eIF4E complex and hesperetin-eIF4E complex by iMODS
server
(A) NMA mobility with affine arrows (large, colored) and
arrow fields (small). (B) Main chain deformability.
(C) B-factor values. (D) Eigenvalue
plot. (E) Normal mode variance plot. The blue bars
indicate the variance of individual modes while the teal bars indicate
cumulative variance. (F ) Co-variance map. The
correlated, uncorrelated and anti-correlated motions are represented by
red, white and blue color respectively. (G) Elastic
network model. The dark color represents stiffer springs.