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.