Figure 7
Features of the primary amino acid sequence of Aβ1–42. A: Prediction of the intrinsically unstructured amino acid region of Aβ1–42 by the ANCHOR server. ANCHOR identifies segments in a generally disordered region that cannot form sufficient numbers of favorable intrachain interactions. The amino acid residues from Asp1–Val18 exhibited unstructured characteristics. B: A1 monomer model of the Protein Data Bank (PDB) file of Aβ1–42 (2BEG), split by the Molegro Virtual Docker (MVD). C: Dimer (A-B1) of the A1 and B1 monomer of 2BEG. The dimer was formed by feeding the A1 and B1 monomers to RosettaDock. D: Validation graph of dimer (A1-B1) formation by RosettaDock. A hallmark of a successful dimer run is an energetic “funnel” of low-energy structures clustered around a single position. E,G: Grid-based pocketness cluster of the A1 monomer (E) and dimer (A1-B1) (G) by GHECOM. F,H: Contributions of amino acids of the A1 monomer (F) and A1–B1 dimer (H) to cluster pocketness. The line shows the value of pocketness [%] for each residue. A residue in a deeper and larger pocket has a larger value of pocketness. The color of the pocketness bar indicates the cluster number of pockets. I,J: The views were generated in Jmol viewer after the docking of asiaticoside onto the (A1) monomer and dimer (A1–B1) to demonstrate that the ligand (asiaticoside) truly bound with the pockets and/or binding sites.