We present ONIOM calculations using density functional theory (DFT) as the high and AM1 as the medium level that explore the abilities of different hexapeptide sequences to terminate the growth of a model for the tau-amyloid implicated in Alzheimer’s disease. We delineate and explore several design principles (H-bonding in the side chains, using antiparallel interactions on the growing edge of a parallel sheet, using all-D residues to form rippled interactions at the edge of the sheet, and replacing the H-bond donor N−H’s that inhibit further growth) that can be used individually and in combination to design such peptides that will have a greater affinity for binding to the parallel β-sheet of acetyl-VQIVYK-NHCH3 than the natural sequence and will prevent another strand from binding to the sheet, thus providing a cap to the growing sheet that arrests further growth. We found peptides in which the Q is replaced by an acetyllysine (aK) residue to be particularly promising candidates, particularly if the reverse sequence (KYVIaKV) is used to form an antiparallel interaction with the sheet.
Plumley, Joshua A.; Ali-Torres, Jorge; Pohl, Gabor; and Dannenberg, J. J., "Capping Amyloid β‑Sheets of the Tau-Amyloid Structure VQIVYK with Hexapeptides Designed To Arrest Growth. An ONIOM and Density Functional Theory Study" (2014). CUNY Academic Works.