UC Irvine

While amyloid plaques and fibrils are a visible hallmark of Alzheimer's disease, smaller assemblies of Aβ, termed oligomers, are now widely thought to be the Aβ species that cause neurodegeneration. Since the structures of the oligomers are not known and not well understood, determination of the structure of amyloid oligomers is one of the most important problems in structural biology. The Nowick group uses chemical model systems to study β-sheet structures and interactions, and these systems can also be used to stabilize oligomers for structural studies. This dissertation describes chemical model systems to elucidate different amyloid oligomer assemblies using an amyloidogenic sequence from Aβ and to gain a structure-based understanding of how natural Aβ may form toxic oligomers.

Chapter 1 describes the use of chemical model systems in the research group in helping us understand the types of supramolecular interactions in protein quaternary structure and in amyloids. The model systems are macrocyclic β-sheet peptides that contain artificial turn and template units that mimic β-sheet structure and interactions. Studies of the macrocyclic β-sheet peptides by X-ray crystallography illustrate the importance of edge-to-edge hydrogen bonding interactions and the face-to-face hydrophobic interactions between proteins and amyloid peptides. The macrocycles were used in inhibition studies against amyloid aggregation assays.

Chapter 2 describes the X-ray crystallographic structures of oligomers of a new chemical model system of a macrocyclic β-sheet peptide that incorporates an amyloidogenic sequence Aβ15-23 from the Aβ peptide. In the solid state structure, the macrocycle folds well as an artificial β-sheet and forms a cruciform tetramer that are made up of antiparallel, hydrogen-bonded dimers. The cruciform tetramers assemble into triangular dodecamers, and the triangular dodecamers further assemble into a lattice. The lattice features a hexagonal cavity, which can be thought of as a porelike assembly, and may disrupt cell membranes by serving as a channel for water or metal cations. The cruciform tetramers also organize into a linear assembly through the lattice. The self-association of the β-sheet macrocycle seen in the crystal structure provides clues into the self-assembly mechanism of amyloid oligomers. Chapter 2 culminates with the use of the crystal structure to model similar oligomer structures using the linear sequence of Aβ (Ac-QKLVFFAED-NHMe, Ac-Aβ15-23-NHMe); the modeling suggests that natural Aβ can form similar structures.

Chapter 3 complements the work conducted in Chapter 2 and describes a series of macrocyclic β-sheet peptides that differs in the solution structure vs. the solid-state structure. In the study, the macrocyclic β-sheets dimerize in a shifted, antiparallel fashion as observed by 1H-NMR spectroscopy. Additional studies by 1H-NMR and DOSY spectroscopy suggest that the shifted, β-sheet dimers self-associate into a tetramer through face-to-face interaction. Supramolecular interactions of the peptide were explored with different mutations. The results show the structural importance of incorporating Aβ residues and the polymorphism observed in the solution state structure in comparison to the solid-state structure.

Chapter 4 is an extension of the work from Chapter 2 that describes the discovery of a new motif of a macrocyclic β-sheet peptide that forms a fibril-like assembly of oligomers. The results bridge the gap between amyloid oligomers and amyloid fibrils, showing how amyloid oligomers can form fibrillar assemblies in the solid state. In the new macrocycle, the template strand is substituted with an Aβ15-23 hybrid strand. The macrocycle forms a tetramer in aqueous solution, and in X-ray crystallographic studies, the solid-state structure of the macrocycle suggests an alternate mode of assembly for Aβ peptides.