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Comparison of protein structures to infer enzyme function and identify structurally significant amino acids
AuthorCaswell, Benjamin Todd
AdvisorCantu, David C
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Biomolecules, particularly proteins, are increasingly taking center stage as an area of research in myriad industries and disciplines. Deepening our understanding of how protein structure affects function will impact our approaches to modern medicine, environmental treatment, and chemical production. In the first part of this work, primary sequence similarity was used to classify all available thioesterases into families whose similarities were confirmed by sequence alignment and structure superimposition. Thirty- five thioesterase families were identified, analyzed, and made available in the updated thioester-active enzyme (ThYme) database. In the second part of this work, a method was developed to determine spatially correlated residues between two protein structures without formal structural superimposition. This method was used to determine the mutation space of four sets of protein structures by correlating residues that occupy the same spatial position within their structures. A target structure was selected from each set to serve as a comparison point, and a scoring system was developed to quantify, for each residue in the target protein, the mutations in that spatial position. Results demonstrate that residues located on the exterior of a protein tend to have a greater diversity of composition than those located on interior surfaces, and that this contrast seems uniform across different secondary structures.