This thesis describes research into second-sphere effects of methionine- and cysteine-ligated metal ions in proteins. Previous research in the Warren lab unearthed a prominent motif present in protein structures that are publicly available in the Protein Databank. Specifically, this motif involves the interaction between a protein-bound metal ion, a metal-ligated sulfur-containing amino acid, and an aromatic amino acid proximal to the sulfur-containing residue. Herein, I explore the influence of this widely conserved microstructure using site-directed variants of Pseudomonas aeruginosa azurin and Pyrococcus furiosus rubredoxin. The physical and electronic properties of proteins modified with natural (azurin) and unnatural (rubredoxin) aromatic amino acid residues were examined. In all cases, subtle but significant changes were found, in particular in the protein's optical and electrochemical properties. The changes in electronic properties can be traced to those properties of the aromatic group and its apparent inductive effect on the metal ion. A systematic evaluation of these changes to a metal site's physical properties provides insights into how aromatic-methionine/cysteine-metal interactions can influence electron transfer and metal binding behaviors, in particular in azurin.
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Thesis advisor: Warren, Jeff
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