Graduate Thesis Or Dissertation
 

Exploring Protein Structure: Seeing the Forest and the Trees

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  • Life on Earth intimately depends on the function of countless proteins. For the majority of studied proteins, function absolutely depends on conformation (i.e. 3-dimensional shape in solution). The exact nature of how a protein goes from an unfolded linear polypeptide chain to an organized folded molecule is still not known, and there is still much uncertainty about the details of folded protein structures. Answering both questions fully, especially by being able to accurately predict protein structures from sequence alone, is known as the protein folding problem. In this dissertation, the nature of protein structure research, especially as it pertains to model-building, entropy, and Boltzmann’s principle, is discussed. Original work is presented in three chapters in the form of primary research reports. In chapter 2, high resolution protein crystal structures are used to describe the details of a high-energy transition conformation that occurs during protein folding. These native structures were found to have stabilized individual residues in conformations that represented “snapshots” along the transition pathway, and could be used to model the transition. In chapter 3, the extent and reliability of observed non-planarity of the peptide bond is assessed, using ultra-high resolution protein crystal structures. This work continues a discussion on peptide planarity that exists in the literature, and sets the record straight on the occurrence of this “non-ideal” geometry. In chapter 4, the “Ensemblator” is described and demonstrated. This software package is capable of comparing and analyzing large numbers of related protein models simultaneously, and represents an invaluable tool to protein structure researchers. Lastly, in chapter 5, impacts and highlights of the reported work are discussed, along with directions for future work. The dissertation concludes with a reflection on the nature of problems being researched in protein structure, and a discussion on how the included original work relates to Boltzmann’s principle and model building in general.
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