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  • Exploring Protein Structure: Seeing the Forest and the Trees

    Creator:
    Brereton, Andrew E.
    Abstract:
    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,...
    Resource Type:
    Dissertation
    Full Text:
    : _____________________________________________________ P. Andrew Karplus Life on Earth intimately depends on the function of countless

  • Modeling protein structure at atomic resolution

    Creator:
    Berkholz, Donald S.
    Abstract:
    This thesis includes three studies involving different aspects of modeling protein structure. The first study illustrates the levels of insight available from atomic-resolution protein structures. The second study derives general trends of protein geometry from atomic-resolution structures and shows their implications for modeling. The third study creates a model of...
    Resource Type:
    Dissertation
    Full Text:
    : P. Andrew Karplus This thesis includes three studies involving different aspects of modeling

  • Structural investigations to understand the mechanisms of two proteins involved in sulfur chemistry : SsuE and cysteine dioxygenase

    Creator:
    Driggers, Camden McCullough
    Abstract:
    Sulfur is one of the six elements required during the early stages of the evolution of life, and enzymes involved in sulfur transfer and oxidation are increasingly being recognized as potential drug targets for antimicrobials as well as for therapies for cancer, neurodegenerative and inflammatory diseases. Bacteria are able to...
    Resource Type:
    Dissertation
    Full Text:
    : . P. Andrew Karplus Sulfur is one of the six elements required during the early stages of the

  • Structural Insights into Novel Sugar Phosphate Cyclases and Flavoenzymes

    Creator:
    Kean, Kelsey M.
    Abstract:
    The function of a protein is defined by its three-dimensional structure, and in understanding the three-dimensional structure of a protein, we gain an understanding of its function and mechanism. Protein structures, especially at high resolution, can provide detailed insights into many elements of enzyme function and catalysis – identifying residues...
    Resource Type:
    Dissertation
    Full Text:
    : _____________________________________________________ P. Andrew Karplus The function of a protein is defined by its three

  • Peptide Non-planarity Regained

    Creator:
    Biel, Justin T.
    Abstract:
    The planar peptide model has guided our understanding and interpretation of protein crystal structures since its origin in the 1950s. It is well understood that deviations from this model occur, but the majority of peptides are planar, as measured by the standard omega torsion angle. Here, we report the first...
    Resource Type:
    Honors College Thesis
    Full Text:
    : ________________________________________ P. Andrew Karplus

  • Biophysical analyses of peroxiredoxins and a partner reductase

    Creator:
    Hall, Andrea Renée
    Abstract:
    Peroxiredoxins (Prxs) are dominant peroxide-reducing enzymes with two important roles: they protect all organisms from oxidative damage induced by peroxides, and in eukaryotes, they participate in hydrogen peroxide signaling pathways. This dissertation presents studies aimed at the biophysical characterization of select Prxs and a Prx reductase to elucidate their structure-function...
    Resource Type:
    Dissertation
    Full Text:
    . Abstract approved: P. Andrew Karplus

  • Crystallographic studies of Pyrenophora tritici-repentis ToxA

    Creator:
    Sarma, Ganapathy N.
    Abstract:
    Tan spot of wheat is an economically significant disease caused by the fungal pathogen, Pyrenophora tritici-repentis. Certain races of the fungus secrete Ptr ToxA (ToxA), a 13.2 kDa proteinaceous host-selective toxin that is responsible and sufficient to cause disease in susceptible wheat varieties. Disease symptoms develop only when the ToxA...
    Resource Type:
    Dissertation
    Full Text:
    : Crystallographic Studies ofPvrenophora Eritéci-repentis ToxA. Abstract approved: P. Andrew Karplus Tan spot of

  • Model systems for structural investigations into peroxiredoxin catalysis, conformation change, and inactivation

    Creator:
    Perkins, Arden
    Abstract:
    Peroxiredoxin (Prx) enzymes catalyze the reduction of hydrogen peroxide, peroxynitrous acid, and organic peroxides, and are extremely efficient peroxidases, with k[subscript cat]/K[subscript M] on the order of 10⁷ - 10⁸ M⁻¹ s⁻¹. Besides their role in oxidative stress defense, evidence has accumulated that some eukaryotes, including humans, use Prxs as...
    Resource Type:
    Dissertation
    Full Text:
    : . P. Andrew Karplus Peroxiredoxin (Prx) enzymes catalyze the reduction of hydrogen peroxide

  • Partial Characterization of the Danio rerio and Xenopus tropicalis MT-­‐Ox Enzyme Involved in Gadusol Biosynthesis

    Creator:
    Roemelt, Taylor
    Abstract:
    Ultraviolet (UV)-protective compounds, such as mycosporine-like amino acids (MAA) are critical for the survival of marine organisms exposed to high-solar radiation. A chemically similar compound, gadusol, was discovered in eggs of the atlantic cod in 1980, and was originally thought to be derived from MAAs that had been ingested. However,...
    Resource Type:
    Honors College Thesis
    Full Text:
    : ______________________________________________________ P.  Andrew  Karplus       Ultraviolet  (UV)-­‐protective  compounds,  such

  • The Crystal Structure of the Potential Drug Target Mycoplasma pneumoniae Glycerol 3-Phosphate Oxidase

    Creator:
    Palioca, Callia K.
    Abstract:
    Mycoplasma pneumoniae is the primary cause of community-acquired pneumonias, including what is commonly known as walking pneumonia. This disease affects people from all demographics, but especially children and older adults. Outbreaks are a significant public health concern and work to develop new pharmacological agents is currently being researched. How M....
    Resource Type:
    Honors College Thesis
    Full Text:
    P. Andrew Karplus Mycoplasma pneumoniae is the primary cause of community-acquired pneumonias