Protein folding studies have provided important insights about the key role of non-covalent interactions in protein structure and conformational stability. Some of these interactions include salt bridges, cation-π, and anion-Ï€ interactions. Understanding these interactions is crucial to developing methods for predicting protein secondary, tertiary, quaternary structure from primary sequence and understanding protein-protein interactions and protein-ligand interactions. Several studies have described how the interaction between two amino acid side chains have a substantial effect on protein structure and conformational stability. This is under the assumption that the interaction between the two amino acids is independent of surrounding interactions. We are interested in understanding how salt bridges, cation-π, and anion-π interactions affect each other when they are in close proximity. Chapter 1 is a brief introduction on noncovalent interactions and noncovalent interaction cooperativity. Chapter 2 describes the progress we have made measuring the cooperativity between noncovalent interactions involving cations, anions and aromatic amino acids in a coiled-coil alpha helix model protein. Chapter 3 describes cooperativity between cation, anion, and nonaromatic hydrophobic amino acids in the context of a coiled-coil alpha helix. In chapter 4 we describe a strong anion-π interaction in a reverse turn that stabilizes a beta sheet model protein. In chapter 5 we measure the interaction between a cysteine linked maleimide and two lysines in a helix and show that it is a general strategy to stabilize helical structure.



College and Department

Physical and Mathematical Sciences; Chemistry and Biochemistry



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cation, anion, noncovalent interaction, coiled coil, protein structure, Conformational stability.