Author's School

Graduate School of Arts & Sciences

Author's Department/Program



English (en)

Date of Award

January 2011

Degree Type


Degree Name

Doctor of Philosophy (PhD)

Chair and Committee

Michael Gross


Converting gene-sequence information into functional information about a protein is a major challenge of post-genomic biology. Proteins have a variety of functions from serving as catalysts to acting as structural components; all these functions are closely related to protein structure. The first step to understand protein function is often a structural study of that protein. Two major approaches, NMR spectroscopy and X-ray crystallography, can provide an atomic-level, 3D structural model of a protein. The applications of these high resolution approaches, however, are limited by protein size, conformational flexibility, and aggregation propensity. To obtain complementary structural information about proteins, a variety of approaches from traditional structural biology: e.g., circular dichroism, fluorescence spectroscopy) to new advances: e.g., computational prediction, protein footprinting) are required. Mass spectrometry: MS) has become an important tool for studying protein structure, dynamics, interactions, and function. In particular, detailed characterization of protein-ligand interactions is now possible, a critical step toward understanding biological function.Mass spectrometric analysis of protein structure can take two approaches. First, protein-ligand interactions can be probed by chemical labeling followed by MS analysis to determine the resulting mass shift: extent of labeling) and the location of the labeling. This approach in a titration format gives protein-ligand affinities. The labeling takes place in solution, where biochemistry occurs, and can be under physiological conditions, whereas the mass spectrometer is used for analysis typically by bottom-up proteomic strategies. In the other approach, protein assemblies can also be transferred directly into the gas phase and interrogated by MS to afford structural insights. One can view this is a top-down approach. The measurements refer to a gas-phase species, and that raises the question of whether the outcomes of the measurements have relevance to the structure and properties of proteins in solution or in a living system. Although there are differences in experimental format, results, and sensitivity between the two approaches of MS-based protein structural analysis, the similarity of those approaches must not be overlooked. All MS-based structural analyses rely heavily on the identification of peptides, purified protein species, or protein complexes. This analysis has been accelerated by the developments of MS instrumentation and methodology in protein analysis; the structural information provided by MS-based analysis is greatly facilitated by having a structural model of the protein. The integrated results from MS approaches, traditional structural biology approaches: e.g., NMR and X-ray), and computational modeling give more complete structural information of proteins than that from any one of the approaches alone. In the first part of thesis, we focus on the development and application of chemical-labeling methods: protein footprinting) in studies of protein conformation. In the second part, a combined top-down approach of native ESI and electron-capture dissociation: ECD) in FTICR MSis presented for structural studies of protein assemblies in the gas phase.


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