Protein beta-sheet quaternary interactions: From mimicry to molecular recognition

This dissertation describes development of a new class of chemical models that mimic protein beta-sheet quaternary structure and participate in intermolecular beta-sheet interactions with soluble proteins and peptide aggregates. These chemical models are 54-membered-ring macrocyclic peptides comprising an extended heptapeptide beta-strand, two Hao beta-strand mimics joined by one additional alpha-amino acid, and two delta-linked ornithine beta-turn mimics.;Chapter 1 focuses on the studies of one representative of these Hao-containing 54-membered-ring cyclic peptides. 1H NMR studies of aqueous solutions of this peptide show a partially folded monomer in slow exchange with a folded oligomer. NOE studies clearly show that the peptide self-associates through edge-to-edge beta-sheet dimerization. PFG NMR diffusion coefficient measurements and ultracentrifugation analysis establish that the oligomer is a tetramer. Collectively, these experiments suggest a tetrameric beta-sheet sandwich in which an edge-to-edge beta-sheet dimer is further dimerized through hydrophobic face-to-face interactions involving aromatic groups.;Chapter 2 focuses on sequence variation and structural modification of these cyclic peptides. Studies of homologues with 1-6 variations in the heptapeptide sequence elucidate the importance of aromatic residues across from Hao in the folding, the importance of hydrophobic core in the oligomerization, and the cooperativity between the folding and the oligomerization. Studies of variants with intramolecular or intermolecular cross-linking show that Cys--Cys linkages at non-hydrogen-bonded positions stabilize antiparallel beta-sheet tertiary and quaternary structures.;Chapter 3 focuses on inhibition of Abeta amyloid by a highly cationic class of 54-membered-ring cyclic peptides and the related bivalent structures. These peptides contain a positively charged variant of Hao (HaoK) and heptapeptide sequences complementary to the Abeta recognition sequence. Hydrophobic content of the sequence appears to be important in Abeta inhibition by these peptides. Bivalency only slightly increases the inhibitory efficiencies, likely because of the linker flexibility.;Finally, Chapter 4 focuses on the recognition of a protein by an anionic variant of 54-membered-ring cyclic peptides through beta-sheet interactions. This peptide contains a negatively charged variant of Hao (HaoD) and mimics a beta-strand associated with the protein dimerization interface. Studies with control peptides underline the importance of beta-sheet folding and edge-to-edge interactions in the studied protein-peptide interactions.