Aromatic donor-acceptor interactions : bridging abiotic and peptide folding

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Bradford, Valerie Jean, 1980-

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Aromatic donor-acceptor interactions have been utilized by the Iverson group in the development of abiotic molecules, called aedamers, that achieve new folding motifs, intermolecular association in heteroduplexes, and new material properties. These molecules exploit the interaction between the electron-rich 1,5-dialkoxynapthalene (DAN) and electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (NDI) units in a face-centered stacking geometry in aqueous solution. This dissertation describes the use of DAN-NDI interactions in the realm of peptides and proteins to expand the scope for applications of this interaction. This work specifically focuses on three areas of aromatic donor-acceptor interactions: achieving protein behavior with abiotic molecules, introducing the interaction into natural peptides, and utilizing the interaction in the intermolecular association of an abiotic molecule and a natural peptide. Chapter 2 refines the model of aggregation of an amphiphilic aedamer, which forms a hydrogel upon heating. The aedamer behaves similarly to proteins called amlyoids, which form fibrils and plaques in vivo which have been implicated in a variety of diseases, including Alzheimer's. Chapter 3 describes the synthesis of [alpha]-amino acids with DAN- and NDI-containing side chains. These amino acids can be used in a peptide model of [beta]-hairpin secondary structure. The model system can determine whether aromatic donor-acceptor interactions are useful in stabilizing peptide and protein structure. Chapter 4 describes the study of the Anchored Periplasmic Expression System (APEx) for use in screening random peptide libraries. A random peptide library is used to determine the sequence of a natural peptide, potentially containing electron-rich aromatic residues, which could bind an NDI oligomer with high affinity for use as a protein expression tag. Chapter 5 describes work toward the use of cyclic NDI bisintercalators for binding both the major and minor grooves of a specific sequence of DNA simultaneously, in addition to the use of cyclic NDI and DAN molecules for the further study of NDI-DAN interactions in abiotic intermolecular assembiles. Overall, this work has advanced the application of aromatic donor-acceptor interactions in peptides and should serve as a foundation for the future study of this interaction in protein folding and behavior in biological systems.