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Filtering by: Committee Member Karplus, P. Andrew Remove constraint Committee Member: Karplus, P. Andrew Degree Level Doctoral Remove constraint Degree Level: Doctoral

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  • Crystal structures of DNA four-way junctions

    Creator:
    Eichman, Brandt F.
    Abstract:
    DNA four-way junctions (also known as Holliday junctions) are the primary structural intermediate during recombination, an important process responsible for biological evolution and maintenance of genomes. These junctions arise from the assembly of four nucleic acid strands to produce double-helical regions extending from a central point. Although much progress has...
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    Dissertation
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    would also like to thank Dr. P. Andrew Karplus, as well as the rest of my committee for their helpful

  • Specificity, Allostery, and Multivalency in Binding to the Hub Protein LC8

    Creator:
    Estelle, Aidan B.
    Abstract:
    Interactions between proteins are essential to life, driving and regulating a majority of processes within all living cells. Study of protein-protein interactions reveals that some proteins act as hubs within networks of interactions, binding to many partner proteins. These hubs therefore are of particular importance to understanding protein function, interwoven...
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    Dissertation
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    purified proteins for the work. P. Andrew Karplus conceptualized the project and was closely involved in

  • Protein Disorder in the Evolution of Dynein Regulation

    Creator:
    Jie, Jing
    Abstract:
    Intrinsically disordered proteins (IDP) are a class of proteins that lack a three-dimensional structure and their prevalence and diverse functions in the cell have only been discovered relatively recently. The intermediate chain (IC) subunit of the microtubule motor protein complex dynein contains an N-terminal disordered region, N-IC, which is central...
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    Dissertation
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    committee members, past and present, Dr. Andrew Karplus, Dr. Gary Merrill, Dr. Weihong Qiu, Dr. Barbara

  • Functional, structural and evolutionary analyses of the ferritin-like superfamily of proteins

    Creator:
    Cooley, Richard Bleier
    Abstract:
    The ferritin-like superfamily (FLSF) of proteins is composed of a wide variety of functionally diverse proteins involved in oxygen dependent metal-mediated electron transfer reactions. Their biological importance is exemplified by the fact FLSF proteins are found in almost every organism from all three domains of life. Their functions range from...
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    and chapters. P. Andrew Karplus was involved in the design, analysis and writing of Chapters 4, 5

  • Macromolecular halogen bonds

    Creator:
    Voth, Andrea Regier
    Abstract:
    The halogen bond is a non-covalent, stabilizing interaction analogous to a hydrogen bond in which an anisotropically polarized halogen atom interacts electrostatically with a Lewis base. Until very recently, the ability of halogens to form these stabilizing interactions in biological macromolecules was all but unknown, but examples of halogen bonding...
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    bearable. Elsewhere in the department, thanks to Dr. P. Andrew Karplus for his dedicated teaching and

  • Characterization of the Structure and Dynamics of the Intrinsically Disordered Dynein Intermediate Chain and its Interactions with Regulatory Binding Partners

    Creator:
    Morgan, Jessica L.
    Abstract:
    Cells represent microcosms of spatial and temporal structural organization, with the achievement of internal spatial organization relying upon a collection of macromolecular motor complexes to transport and localize components throughout the cell. Cytoplasmic dynein is one such motor complex, and is the principal ATP-dependent motor for retrograde transport along microtubules...
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    thank all the other members of my graduate committee, including: Dr. Victor L. Hsu and Dr. P. Andrew

  • From ALS to Antibodies: New Techniques in Mass Spectrometry-Based Proteoform Characterization

    Creator:
    Meeuwsen, Joseph C.
    Abstract:
    Altogether, this dissertation highlights the value of mass spectrometry-based analysis of intact proteins for solving problems related to understanding disease mechanisms and developing new therapeutics. Mutations to the antioxidant enzyme Cu, Zn Superoxide Dismutase (SOD1) perturb protein structure in vivo to cause 2-5% of amyotrophic lateral sclerosis (ALS) cases. Metal-deficient...
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    Dissertation
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    , role modeling, and assistance. To my committee members – Drs. Emily Ho, Andy Karplus, Kathy

  • Measuring protein metal binding via mass spectrometry : copper, zinc superoxide dismutase and amyotrophic lateral sclerosis

    Creator:
    Rhoads, Timothy W.
    Abstract:
    Amyotrophic lateral sclerosis (ALS) is a devastating disease characterized by the progressive degeneration of motor neurons. Dominantly-inherited mutations to the antioxidant enzyme Cu,Zn superoxide dismutase (SOD1) cause 3-6% of all ALS cases. The complete mechanism behind the toxicity of mutant SOD1 remains unclear, although significant evidence points to aberrant or...
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    Dissertation
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    committee members Jeff Greenwood, Andy Karplus, Gary Merrill, and Janine Trempy. I would not have

  • Cytoskeletal regulation in cell motility and invasion

    Creator:
    Jang, Hyo Sang
    Abstract:
    Cell motility and invasion are important for development, immunity, wound healing, and tumor cell metastasis. Cells on two dimensional substrates migrate in three steps: protrusion of the front end, translocation of the cell body, and retraction of the rear end. For cells to migrate efficiently, these steps need to be...
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    Ph. D. work. Also, I give my deep appreciation to my committee members Drs. P. Andrew Karplus

  • Genomic-assisted determination of the natural nutrient requirements of the cosmopolitan marine bacterium 'Candidatus Pelagibacter ubique'

    Creator:
    Tripp, H. James
    Abstract:
    To identify factors limiting 'Candidatus Pelagibacter ubique' maximum cell density and growth rate in pure culture on seawater, the genome sequence of 'Cand. P. ubique' was analyzed, culturing experiments with organic and inorganic nutrient additions were made, and radiotracer uptake experiments were performed. The genome was sequenced, custom data mining...
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    ‘Cand. P. ubique’ was analyzed, culturing experiments with organic and inorganic nutrient additions