Capping Amyloid β‑Sheets of the Tau-Amyloid Structure VQIVYK with Hexapeptides Designed To Arrest Growth. An ONIOM and Density Functional Theory Study

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...

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Bibliographic Details
Published in:The journal of physical chemistry. B 2014-03, Vol.118 (12), p.3326-3334
Main Authors: Plumley, Joshua A, Ali-Torres, Jorge, Pohl, Gabor, Dannenberg, J. J
Format: Article
Language:English
Subjects:
Affinity
Alzheimer's disease
Amyloid beta-Peptides - chemistry
Binding
Capping
Density functional theory
Humans
Hydrogen Bonding
Models, Chemical
Nickel base alloys
Peptides
Protein Structure, Secondary
Quantum Theory
Residues
Strands
Superalloys
tau Proteins - chemistry
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Summary: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.
ISSN:1520-6106
1520-5207
DOI:10.1021/jp501890p