Protein structural investigation using hydroxyl radical protein footprinting
Watson, Caroline McCullough
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The focus of my research is using hydroxyl radical protein footprinting (HRF) coupled with mass spectrometry (MS) to study protein structure, protein – protein, and protein – ligand interactions in solution. Even with high-resolution techniques such as NMR and X-ray crystallography, not all protein structures or protein interactions can be studied using these techniques due to the nature of the protein. Hydroxyl radicals have become a popular labeling technique because they provide a fast, relatively nonspecific, covalent label that probes a variety of solvent accessible amino acid residues with one experiment. The reaction rate of hydroxyl radicals with each amino acid is based on two factors, the chemical nature of the residue and the average accessibility of the residue to the hydroxyl radical. By monitoring the change in the amount of oxidation under different experimental conditions, changes in protein structure can be determined by how the structural changes affect the solvent accessibility of the different regions of the protein. The work presented describes protein pharmaceuticals and a biologically relevant protein complex that were investigated by HRF coupled with mass spectrometry, as well as a new method for producing hydroxyl radicals for protein labeling without the use of hydrogen peroxide.
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