Date of Award

5-2010

Degree Type

Dissertation

Degree Name

Doctor of Philosophy

Major

Life Sciences

Major Professor

Robert L. Hettich

Committee Members

Cynthia Peterson, Jeffrey Becker, Hong Guo, Dean Myles

Abstract

Oxidative protein surface mapping has gained popularity over recent years within the mass spectrometry (MS) community for gleaning information about the solvent accessibility of folded protein structures. The hydroxyl radical targets a wide breadth of reactive amino acids with a stable mass tag that withstands subsequent MS analysis. A variety of techniques exist for generating hydroxyl radicals, with most requiring sources of radiation or caustic oxidizing reagents. The purpose of this research was to evaluate the novel use of electrochemistry for accomplishing a comparable probe of protein structure with a more accessible tool. Two different working electrode types were tested across a range of experimental parameters, including voltage, flow rate, and solution electrolyte composition, to affect the extent of oxidation on intact proteins. Results indicated that the boron-doped diamond electrode was most valuable for protein research due to its capacity to produce hydroxyl radicals and its relatively low adsorption profile. Oxidized proteins were collected from the electrochemical cell for intact protein and peptide level MS analysis. Peptide mass spectral data were searched by two different “hybrid” software packages that incorporate de novo elements into a database search to accommodate the challenge of searching for more than forty possible oxidative mass shifts. Preliminary data showed reasonable agreement between amino acid solvent accessibility and the resulting oxidation status of these residues in aqueous solution, while more buried residues were found to be oxidized in “non-native” solution. Later experiments utilized higher flow rates to reduce protein residence time inside the electrochemical flow chamber, along with a different cell activation approach to improve controllability of the intact protein oxidation yield. A multidimensional chromatographic strategy was employed to improve dynamic range for detecting oxidation of lower reactivity residues. Along with increased levels of oxidation around “reactive hotspot” sites, the enhanced sensitivity of these measurements uncovered a significant level of background oxidation in control proteins. While further work is needed to determine the full utility that BDD electrochemistry can lend protein structural studies, the experimental refinements reported here pave the way for improvements that could lead to a high-throughput structural pipeline complementary to predictive modeling efforts.

Appendix-Tables.xls (334 kB)
File 1: Peptide Spectral Counts Mined from Mass Spectral Data (Tables A-1 through A-8)

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