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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...
    Resource Type:
    Dissertation
    Full Text:
    would also like to thank Dr. P. Andrew Karplus, as well as the rest of my committee for their helpful

  • Characterization and Functionalization of Fabric for use in an Immunoassay

    Creator:
    White, Natalie
    Abstract:
    Paper-based microfluidic assays, like the common pregnancy test, allow for rapid screening at the point- of-care at low cost and with no instrumentation. Fabric has many similar properties to paper, but is more flexible and durable, making it a promising option for use in a variety of diagnostic and screening...
    Resource Type:
    Honors College Thesis
    Full Text:
    _____________________________________________________________________ Andrew Karplus, Committee Member, representing the Department of Biochemistry and Biophysics

  • Catalysis of Biologically Relevant Chlorination Reactions by Nicotine, and Potential Relevance to Tissue Damage

    Creator:
    Dolan, Brigh G.
    Abstract:
    This work is concerned with determining whether nicotine has a role in promoting oxidative damage in human tissue, particularly in lung tissue. This follows from recent reports of a novel lung disease found in some E-cigarette users, characterized by oxidative damage and elevated levels of neutrophils (termed “vaping disease”). It...
    Resource Type:
    Honors College Thesis
    Full Text:
    _____________________________________________________________________ P. Andrew Karplus, Committee Member, representing Biochemistry and Biophysics

  • 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...
    Resource Type:
    Dissertation
    Full Text:
    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...
    Resource Type:
    Dissertation
    Full Text:
    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...
    Resource Type:
    Dissertation
    Full Text:
    and chapters. P. Andrew Karplus was involved in the design, analysis and writing of Chapters 4, 5

  • Synthesis and anticoagulant function of heparin containing block copolymers on polystyrene microspheres

    Creator:
    Fry, Allyson Kaye
    Abstract:
    Contact of blood with the surfaces of synthetic materials is associated with spontaneous protein adsorption, initiating platelet aggregation, the coagulation cascade, and the eventual development of a stable clot. Current therapy to inhibit implant-induced thrombosis is life-long administration of systemic anticoagulants. An alternative to the systemic administration of anticoagulant drugs...
    Resource Type:
    Masters Thesis
    Full Text:
    t < tn-1, 1-α/2 then the null hypothesis is rejected. The p-value is twice the area to the left

  • 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...
    Resource Type:
    Dissertation
    Full Text:
    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...
    Resource Type:
    Dissertation
    Full Text:
    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...
    Resource Type:
    Dissertation
    Full Text:
    , role modeling, and assistance. To my committee members – Drs. Emily Ho, Andy Karplus, Kathy