Biochemistry, Biophysics, and Structural Biology Commons^™

Reaction Of Zinc Proteome With Biologically Important Metal Binding Ligands, Kaniz Fatema

Theses and Dissertations

Fluorescent sensors have been widely used as microscopic tools to image Zn2+ on a cellular level. Recently, it has been established that the sensors TSQ and Zinquin form adducts with Zn-proteins and image fractions of the Zn-proteome.1 Since TSQ and Zinquin bind specifically to many Zn-proteins, it is hypothesized that other metal binding ligands, both synthetic and natural, may also bind to the Zn-proteome. Biologically active 1,10-phenanthroline (Phen) and related molecules were investigated for their ability to bind to Zn-proteome. Similarly, the cellular tripeptide, glutathione was investigated. It was observed that Phen and some other metal binding, bidentate ligands, were …

Arylboronates As H2o2 Or Photo-Inducible Dna Cross-Linking Agents: Design, Synthesis, Mechanism, And Anticancer Activity, Yibin Wang

Theses and Dissertations

Interest in the development of cancer therapies with improved selectivity and reduced host toxicity has been growing. In this thesis, we designed and synthesized a series of novel non-toxic arylboronic ester and biarylboronic ester derivatives that can be activated by hydrogen peroxide (H2O2) to induce DNA interstrand cross-link formation. The mechanism of DNA cross-linking induced by these arylboronates involves generation of phenol intermediates 1 followed by departure of leaving group (L) leading to quinone methides (QMs) 2, which directly cross-link DNA via alkylation. The QM formation is the rate-determining step for DNA cross-linking. The activity and selectivity of these compounds …

Transport Mechanisms For Human Fecal Indicator Bacteria In An Urban Stormwater Basin In Southeastern Wisconsin, Chelsea M. Corson

Theses and Dissertations

Discharge of stormwater runoff to receiving waters is a known source of human pathogens; however the primary mechanisms by which these pathogens enter the stormwater system have yet to be quantified. This study builds upon and utilizes prior research findings in an attempt to explain the influence of the age of the pipes within stormwater and sanitary conveyance systems, rainfall and hydrogeological characteristics, and select infrastructure variables that contribute to the observed contamination of an urban stormwater basin in Southeastern Wisconsin.

Over the course of approximately two years from 2012 to 2014, a total of 260 samples from 22 stormwater …

Time-Resolved, Near Atomic Resolution Structural Studies At The Free Electron Laser, Jason James Tenboer

Theses and Dissertations

Time-resolved serial femtosecond crystallography (TR-SFX) employs X-ray free electron lasers (XFELs) to provide X-ray pulses of femtosecond (fs) duration with 1012 photons per pulse. These XFELs are more than a billion times more brilliant than 3rd generation synchrotron X-ray sources. For structure determination, protein crystals on the micrometer length scale (microcrystals) are injected into the X-ray beam and the resulting diffraction patterns are recorded on fast-readout pixel detectors. Although these intense pulses deposit enough energy to ultimately destroy the protein, the processes that lead to diffraction occur before the crystal is destroyed. This so-called diffraction-before-destruction principle overcomes radiation damage, which …

Porphyrin As A Spectroscopic Probe Of Net Electric Fields In Heme Proteins, Hannah Elizabeth Wagie

Theses and Dissertations

Heme proteins have diverse functions as well as varied structures but share the same organic, conjugated cofactor. Similarly varied approaches have been taken to deduce how heme can take on different roles based on its protein environment. A unique approach is to view the protein matrix as a constellation of point charges that generates a defined, reproducible, net internal electric field that has influence over the electronic properties of the heme cofactor. This work considers how porphyrins, the basic chromophore building block of heme, can be used as a native spectroscopic sensor of internal electric field at the active site …

Theoretical Investigation Of Interactions And Relaxation In Biological Macromolecules, Koki Yokoi

Theses and Dissertations

One of the major challenges posed to our quantitative understanding of structure, dynamics, and function of biological macromolecules has been the high level of complexity of biological structures. In the present work, we studied interactions between G protein-coupled receptors (GPCRs), and also introduced a theoretical model of relaxation in complex systems, in order to help understand interactions and relaxation in biological macromolecules.

GPCRs are the largest and most diverse family of membrane receptors that play key roles in mediating signal transduction between outside and inside of a cell. Oligomerization of GPCRs and its possible role in function and signaling currently …

Mechanistic Study Of Heme Protein-Mediated Nitric Oxide Dioxygenation Using Photolytically Produced Nitric Oxide, Karl Joseph Koebke

Theses and Dissertations

The previously reported NO precursor [Mn(PaPy2Q)(NO)]ClO4 (1), where (PaPy2QH) is N,N-bis(2-pyridylmethyl)-amine-N-ethyl-2-quinoline-2-carboxamide, was synthesized and proven capable of producing as much as 180 µM NO when irradiated by a single 3 mJ 500nm laser pulse, in a 0.15 cm path cell, without the need for additional sacrificial reductants or oxidants. Species 1 was first used to study the reaction of nitric oxide with oxy-myoglobin (oxyMb) to form ferric myoglobin (metMb) and nitrate. This reaction had long been assumed to proceed via the same iron-bound peroxynitrite intermediate (metMb(OONO)) as the metMb-catalyzed isomerization of peroxynitrite to nitrate. Recent research showed that the metMb-catalyzed …

Molecular Identification Of Mycobacterium Tuberculosis In The Milwaukee County Institution Grounds Cemetery, Helen Marie Werner

Theses and Dissertations

The possibility of identifying Mycobacterium tuberculosis in skeletal remains has been a debated topic for many years. This study utilizes the remains from the 1991 and 1992 excavations of the Milwaukee County Institution Grounds Cemetery, a collection of human skeletons ranging from 1882 to 1925, of various ages and sexes, to address that possibility. To test the utility of previously used methods of osteological identification of tuberculosis, the collection has been analyzed for the IS6110 repetitive element marker using molecular biological techniques, such as Polymerase Chain Reaction (PCR). Eighty-six skeletons from the collection have been analyzed, with nine of them …

Application Of Coumarin Derivatives In Dna-Associated Study: Mutation Detection, Site-Specific Labeling, Photoinduced Interstrand Cross-Links And Ligation Reactions, Huabing Sun

Theses and Dissertations

Coumarin derivatives have been widely utilized as cross-linking agents in polymer science, being fluoroprobes in biochemistry and as medicines in pharmacy. But the coumarin's fluorogenic properties and reactivities in DNA were rarely reported and unclear, which limits its bioapplications due to possible side reactions towards biomolecules. In this thesis, we investigated the activity of coumarin moiety towards natural DNA and expanded its application in DNA-associated study. We have found that coumarin derivatives can serve as perfect DNA cross-linking agents, as alkylation agents for site-specific labeling, and fluoroprobes for single nucleotide polymorphism (SNP) analysis, which provided a novel insight of biotoxicity …

Role Of Non-Muscle Myosin Ii And Calcium In Zebrafish Midbrain-Hindbrain Boundary Morphogenesis, Srishti Upasana Sahu

Theses and Dissertations

Elucidating the molecular mechanisms that play a role in cellular morphogenesis is critical to our understanding of brain development and function. The midbrain-hindbrain boundary (MHB) is one of the first folds in the vertebrate embryonic brain and is highly conserved across species. We used the zebrafish MHB as a model for determining the molecular mechanisms that regulate these cell shape changes. Cellular morphogenesis is tightly regulated by signaling pathways that rearrange the cytoskeleton and produce mechanical forces that enable changes in cell and tissue morphology. The generation of force within a cell often depends on motor proteins, particularly non-muscle myosins …