Scaffolds 1OZJ and 1RK9 have shapes complementary to EGFR domain II.

<p>(A) The inactivated EGFR monomer exists in equilibrium between the tethered and untethered conformations. The binding of EGF (pink) stabilizes the untethered monomers, which exposes the dimerization arm of domain II (green) and activates EGFR to form homodimers at the domain II dimeric interface (domain I, blue; domain II, green; domain III, yellow; domain IV, gray). For clarity, domain II on the right-hand EGFR in the homodimer is shown in orange. (B) EGFR activation can be blocked by binding domain II, which is exposed in the untethered conformation, with the designed scaffold (magenta), which sterically interferes with EGFR dimerization. (C) The docking conformation of 1OZJ–EGFR, which was selected from the virtual screening procedure (left), and the enlarged 1OZJ structure (magenta). (D) The docking conformation of 1RK9–EGFR, which was selected from the virtual screening procedure (left), and the enlarged 1RK9 structure (magenta). Energetically unfavorable residues that were selected for optimization are depicted in blue. (E–F) Amino acid sequences for 1OZJ and 1RK9, respectively. The blue residues represent amino acid residues that were energetically unfavorable for EGFR complex formation. (G–H) The complex formation energy of the scaffold interface residues upon the formation of the 1OZJ–EGFR and 1RK9–EGFR docking complexes, respectively. The blue bars depict the energetically unfavorable residues that were selected for optimization. The horizontal axis shows each amino acid in the scaffold interface, and the vertical axis represents the energy contribution (delta G) to the complex formation.