UC Irvine

Peptides are strings of amino acids that fold and self-assemble. The folding and supramolecular assembly of these peptides are central their function. Amyloid beta (Aβ) aggregates into soluble oligomers responsible for neurodegeneration. However, the structures formed by these soluble toxic oligomers remains poorly understood because of their heterogeneity and metastability. Chemical model systems can be used to investigate the structures formed by these soluble oligomers. The folding and self-assembly of peptides is also involved in the activity of cyclodepsipeptide antibiotics. To better understand peptide folding and self-assembly, my thesis describes the synthesis and study of amyloidogenic and antimicrobial peptides.Chapter 1 outlines a systematic approach for studying peptide model systems using solution-phase NMR spectroscopy. The chapter begins with preparing peptide NMR samples starting from lyophilized peptide. Then the chapter describes selecting, running, and processing NMR experiments. Next the chapter describes how to generate sequence specific peak assignments and identify β-sheet folding. The chapter concludes with the five spectroscopic hallmarks of supramolecular assembly. Although they focus on conformationally constrained β-sheet peptides, these protocols can be generalized to studying peptide folding and supramolecular assembly. Chapter 2 applies the protocols described in Chapter 1 to studying the folding and supramolecular assembly of a peptide that mimics the Aβ16–36 hairpin. This project expands upon a previous Aβ16–36 hairpin mimic that assembles into crystallographic hexamers but does not assemble into well-defined oligomers in solution-phase NMR conditions. A strategic phenylalanine to cyclohexylalanine (Cha) mutation at position 19 stabilizes the solution-phase NMR assembly into an asymmetric hexamer. Diffusion order NMR spectroscopy (DOSY) and molecular dynamic simulations provide a model for the asymmetric hexamer and suggest how two asymmetric hexamers can form a dodecamer. Chapter 2 concludes with remarks on which hydrogen bonding interactions are critical for solution-phase supramolecular assembly and how hydrophobic interactions drive solution-phase oligomerization. Chapter 3 details the first synthesis of hypeptin, a cyclodepsipeptide antibiotic that is active against Gram positive bacteria. The sterochemical configuration of hydroxytyrosine6 was originally reported to be (2S,3S) and later revised to (2S,3R) based on the biosynthesis. I synthesized the suitably protected (2S,3R)-hydroxytyrosine, and (2S,3R)-hydroxyleucine building blocks. These amino acid building blocks were used in the synthesis of hypeptin. LC-MS and NMR comparison of synthetic hypeptin with natural hypeptin confirms the sterochemical configuration of hydroxytyrosine at position 6 to be (2S,3R). Chapter 3 ends with how this synthesis could be applied to other β-hydroxytyrosine peptide natural products and ideas on how to further develop the hypeptin scaffold as a potential drug candidate.