Role of hydrophobicity, aromaticity, and turn nucleation in peptide self-assembly

Abstract

Thesis (Ph. D.)--University of Rochester. Dept. of Chemistry, 2012.Peptide self-assembly into cross-β amyloid is the hallmark of several amyloid pathologies and the inspiration for biomaterials. Peptide self-assembly is governed by noncovalent interactions such as hydrophobic, electrostatic, aromatic, and van der Waals interactions. Aromatic interactions, a specific subset of hydrophobic interactions, have been proposed to play an essential role during amyloid peptide self-assembly. Others contend that the high hydrophobicity and favorable planar geometry of aromatic residues are responsible for the prevalence of these residues in self-assembling peptides. Using a model peptide that self-assembles into fibrils where π−π interactions are not likely to occur, we mutated the single Phe residue with several natural and nonnatural amino acids that varied in hydrophobicity, aromaticity and molecular volume. We performed kinetic and thermodynamic analyses on variant self-assembly and showed that stabilization imparted by aromatic amino acids is a function of their high hydrophobicity and favorable planar geometry, and not the ability to form specific π−π interactions. In the latter part of this thesis, the effect of turn nucleation on peptide selfassembly is examined. Structural models of the amyloid-β peptide (Aβ) in various stages of aggregation consistently indicate the presence of a β-hairpin (pre-oligomeric structures) or β-turn (oligomers and fibrils). We tested the effects of turn nucleation as a potential rate-limiting step in Aβ self-assembly. We incorporated a β-hairpin nucleator, D-ProGly (DPG) into the putative turn region of Aβ40 and found that turn nucleation generally enhanced the kinetics of self-assembly. Cytotoxicity of the variants in different states of assembly indicated that β-hairpin formation likely precedes cytotoxic oligomer formation. Based on these results, we incorporated an azobenzene turn mimetic into the 25–27 region of Aβ to gain temporal control over fibril nucleation and gain mechanistic insight into Aβ self-assembly through turn nucleation. Finally, we used the azobenzene turn mimetic to alter the secondary structure of a peptide hydrogel, (RADA)4. Reversible disruption of the hydrogel fibril network was achieved through trans → cis isomerization resulting in weakened rigidity. The work reported in this thesis has clarified the role of hydrophobicity, aromatic π−π interactions and turn nucleation on amyloid self-assembly processes