Date of Award

Spring 5-15-2016

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Plant & Microbial Biosciences)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



Cofactors extend the chemistry of life. Redox reactions in photosynthesis, nitrogen fixation, and other metabolic pathways depend on metal cofactors. Copper is an essential element in biology, participating in redox reactions and biological catalysis. Copper proteins are classified by their copper centers as type-1, type-2, type-3, CuA, CuB, or Cuz. Type-1 proteins, such as azurin or plastocyanin, are primarily involved in electron transport. Type-1 centers are the most studied copper site at the spectroscopic and structural level. In the type-1 center, the copper cofactor is coordinated by a cysteine, two histidines, and generally a weak axial methionine. This coordination geometry gives rise to several ligand-to-metal charge-transfer transitions, producing a characteristic blue or green type-1 spectrum. In blue type-1 copper proteins, the cysteine-copper bond is exceptionally small (2.1 ) and the methionine-copper bond is abnormally long (2.9 ). In green type-1 copper proteins, the cysteine-copper bond elongates and the methionine-copper bond contracts. The redox range varies from +83 mV to over +1000 mV. Protein tuning modulates the large variations observed in the redox range and spectral properties. The mechanism of protein tuning is poorly understood. In chapter 2, I characterize a family of four blue copper proteins called auracyanins. The auracyanins, named A-D, were found to have a redox range from +83 mV to +423 mV, and range in color from blue to green. In chapter 3, I take advantage of the tuning variations within the auracyanin family to map the spectral changes to the protein-protein interaction domain. The protein-protein interaction domain has never previously been implicated in protein tuning. These results likely explain how seemingly energetically uphill electron transfer reactions commonly occur with copper proteins. In chapter 4, I perform mutagenesis on the weak axial ligand in auracyanin D. Auracyanin D is a green copper protein, and has the lowest redox potential ever measured for a copper protein. Significant work has been done on axial ligands in blue type-1 copper proteins, but never in green type-1 copper proteins. I found that substitutions to the axial ligand in green copper sites are much larger than their blue copper protein counterparts. In chapter 5, I conclude with a computational approach showing significant variation in the coordinating ligands of uncharacterized copper proteins. I believe examination of these proteins by a reverse biochemical approach will add more clarity to the role of protein tuning and expand the limits of copper tuning.


English (en)

Chair and Committee

Robert E. Blankenship

Committee Members

Robert G. Kranz, Joseph M. Jez, Liviu M. Mirica, Himadri B. Pakrasi,


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Available for download on Friday, May 15, 2116

Included in

Biochemistry Commons