Figure 5
The representative structure of each cluster is the peptide conformation with the least distance from the centroid of its population.
(a) Representative structures from the largest clusters of the eIF4E:sTIP-04 complex MD simulations and the sTIP-04 solution simulation were overlaid. Both the bound and unbound structures of sTIP-04 show high structural similarity. (b) The similarity in the conformations is shown by a large population showing small a small deviation of the RMSD values between the two clusters. (c) Crystal structure of sTIP-04 peptide in complex with eIF4E (4BEA). The 2Fo-Fc electron density map (blue) for sTIP-04 is shown at 1.5 sigma. (d) The N-terminal of the eIF4GD5S peptide (yellow) has a very high structural similarity to sTIP-04 (blue), but its conformation begins to diverge from that of the stapled peptide at position L10. This results in displacement of residues G11 and F12 with respect to their sTIP-04 counterparts. This displacement occurs due to unwinding of the C-terminal helical turn, which occurs in order to accommodate the interactions of F8 and F12 with each other and with the surface of eIF4E. sTIP-04 residues are labelled in italics whilst eIF4GD5S are not.
