Application of Spectroscopy to Protein Characterization

There are two contributions of this thesis. The first contribution, described in chapters one through six, involves studing the relationship between the protein packing structure of bacteriorhodopsin (bR) and its function as a proton pump. In 2002, a novel crystallization method published by Bowie and Farham resulted in an unusual antiparallel monomeric packing structure of bicelle bacteriorhodopsin (bcbR) crystals, the spectroscopic properties of which had not been studied. In this thesis, these bicelle bR crystals are investigated to better understand how the changes in the protein tertiary structure affect the function. Specifically: Does the retinal Schiff base retain its ability to isomerize in this unusual protein packing structure of bR? How is the hydration of its binding pocket affected? Does the protein retain the ability to undergo the photocycle and pump protons? If so, how are the rates of the deprotonation/reprotonation of the Schiff base affected by the antiparallel monomer packing structure of the protein? Is Asp85 still the proton acceptor during the deprotonation process of the photocycle? The second contribution of the thesis, described in chapter seven, describes the surface attachment and growth of the biofilm formed by the pathogenic bacterium Streptococcus pneumoniae using attenuated total reflection/Fourier transform infrared spectroscopy (ATR/FTIR). This organism was chosen for its clinical significance; it is one of the organisms suspected in forming biofilms in individuals who develop otitis media, one of the most common causes of ear infections of childhood. In contrast to previous ATR/FTIR experiments examining the formation of biofilms on surfaces, this method is unique in that it combines two techniques - ATR/FTIR and Epifluorescence microscopy which when used together allow for the simultaneous monitoring of the IR spectrum of the S. pneumoniae biofilm as it develops and as provides a method for quantifying total and viable cell counts at various stages during the development.Ph.D