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Mechanism and inhibition of the phenylethylamine oxidase from Arthrobacter globiformis: Author: Juda, Gregory Alexander; Date: 2005-05-15; Program: Biochemistry; Abstract: Copper amine oxidases (CuAOs) catalyze the oxidative deamination of primary amines to the corresponding aldehydes, utilizing O₂ as the oxidant with concomitant production of H₂O₂ and NH3. The discovery that the human vascular adhesion protein (HVAP-1) is a copper amine oxidase has sparked considerable interest in the mechanism and inhibition of these enzymes. With the potential for therapeutic applications, substantial efforts have been made to determine the molecular factors which govern inhibitor sensitivity and selectivity for copper amine oxidases. In order to contr...; Download File | View full details

Nucleotide Dependent Conformational Changes in the Nitrogenase Fe Protein: Author: Sen, Sanchayita; Date: 2005-08-15; Program: Biochemistry; Abstract: Nitrogenase is a complex metal-containing enzyme that catalyzes the conversion of nitrogen gas to ammonia. During nitrogenase catalysis the Fe protein and the molybdenum-iron protein associate and dissociate in a manner resulting in the hydrolysis of two molecules of MgATP and the transfer of at least one electron to the MoFe protein. The role of nucleotide binding and hydrolysis in nitrogenase catalysis is one of the most fascinating aspects of nitrogenase function. The Fe protein upon binding to MgATP undergoes a huge conformational change which is important for subsequent steps of nitrogena...; Download File | View full details

Oxidation of human nitrosylhemoglobin monitored by UV-Vis and EPR Spectroscopies: detection of products and intermediates: Author: Williams, Elizabeth Mary; Date: 2005-08-15; Program: Biochemistry; Abstract: Once viewed only as a toxic free radical, nitric oxide (NO) has been established as an essential and ubiquitous signaling and regulatory molecule in biological systems. Notably, NO was identified as the endothelium-derived relaxing factor (EDRF) in the blood. NO is capable of complex redox chemistry and interaction with a host of protein families. Among these proteins is hemoglobin (Hb) which can interact with NO at the level of the heme and can bind NO at Cys93 on its β subunit to form S-nitrosylated Hb (SNO-Hb). NO bound as SNO-Hb is chemically labile and thus preserves bioavaila...; Download File | View full details

Structural investigations of the cancer-associated laminin binding protein and Nos L: a novel copper binding protein: Author: Taubner, Lara Marie; Date: 2005-12-15; Program: Biochemistry; Abstract: This thesis consists of two distinct projects, one on the metastasis-associated laminin binding protein and the other on the putative copper chaperone NosL, both related by the common aim of investigation of the relationship between protein structure and function using nuclear magnetic resonance techniques. In the first part of this dissertation, the role that the metastasis-associated laminin binding protein or LBP plays in the spread and development of cancer was investigated. Functional domains of LBP were delineated by limited proteolysis, overexpressed, and then assayed for their ability ...; Download File | View full details

Understanding the molecular factors governing inhibitor potency and oxygen activation in copper amine oxidases: Author: Shepard, Eric Michael; Date: 2006-05-15; Program: Biochemistry; Abstract: Copper amine oxidases (CuAOs) catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with the concomitant reduction of O₂ to H₂O₂. CuAOs are known to have a multitude of physiological roles, and activity levels are upregulated in several pathological states. With the potential for therapeutic applications, substantial efforts were made to determine the molecular factors governing inhibitor selectivity. As such, several mechanism-based inhibitors were screened against CuAOs from bacterial, yeast, plant, and mammalian sources. The results pro...; Download File | View full details

X-ray crystallographic studies of Sulfolobus Turetted Icosahedral Virus (STIV): a hyperthermophilic virus from Yellowstone National Park: Author: Larson, Eric Thomas; Date: 2006-12-15; Program: Biochemistry; Abstract: Sulfolobus turreted icosahedral virus (STIV) was isolated from acidic hot springs of Yellowstone National Park and was the first hyperthermophilic virus described with icosahedral capsid architecture. Structural analysis of the STIV particle and its major capsid protein suggests that it belongs to a lineage of viruses that predates the division of the three domains of life. Functional predictions of the viral proteins are hindered because they lack similarity to sequences of known function. Protein structure, however, may suggest functional relationships that are not apparent from the sequence...; Download File | View full details

Structural studies of enzymes involved in propylene and acetone metabolism in Xanthobacter autotrophicus: Author: Krishnakumar, Arathi Mandyam; Date: 2007-05-15; Program: Biochemistry; Abstract: X-ray crystallography has been an indispensable tool in understanding the mechanism of the enzymes of the epoxide carboxylation pathway in Xanthobacter autotrophicus. The main focus of this dissertation involves providing the structural basis for the stereoslectivity of the two stereospecific dehydrogenases of the pathway namely R- and S-HPCDH. The crystal structure of R- HPCDH cocrystallized with the substrate has been determined. The key elements of interactions between the enzyme and substrate are electrostatic interactions between the sulfonate oxygen atoms and two arginine residues (Arg15...; Download File | View full details

Structure based mechanistic studies on 2-ketopropyl coenzyme M oxidoreductase / carboxylase from Xanthobacter autotrophicus and [FeFe] hydrogenase from Clostridium pasteurianum: Author: Pandey, Arti Sharma; Date: 2007-08-15; Program: Biochemistry; Abstract: X-ray crystallography was employed to probe the mechanism of the enzyme 2- ketopropyl coenzymeM oxidoreductase / carboxylase (2-KPCC). We were able to determine the enzyme structure in various catalytically relevant states, providing insights into substrate binding, intermediate stabilization, product formation and release. Structures of 2-KPCC were obtained with the substrate 2-ketopropyl coenzyme M (KCoM), product acetoacetate, 6-oxoheptanoic acid (OHA), 2-oxopropyl phosphonate (OPP), NADP+ and coenzymeM (CoM), the oxidized and reduced states. The binding sites for these ligands in relation ...; Download File | View full details

Investigating host response to viral infection through proteomics: a study of murine norovirus: Author: Furman, Linnzi M.; Date: 2008-05-15; Program: Biochemistry; Abstract: Norovirus causes roughly 23 million cases of foodborne illnesses in the United States each year. While this virus was characterized over 30 years ago, it remains non-cultivatable in human cells, resulting in an incomplete understanding of the host cell's response to infection. However, in 2004 murine norovirus (MNV) was found to be cultivatable in mice and has since been successfully cultured in RAW 264.7 cells. MNV has become an important model system for studying norovirus, as it is structurally and genetically similar to human norovirus. A global proteomics approach using fluorescently tagg...; Download File | View full details

Investigations of nucleotide-dependent electron transfer and substrate binding in nitrogen fixation and chlorophyll biosynthesis: Author: Sarma, Ranjana; Date: 2009-12-15; Program: Biochemistry; Abstract: The studies presented in this thesis include studies of nucleotide-dependent conformations of the electron donor protein in nitrogenase and dark-operative protochlorophyllide reductase (DPOR) characterized using small-angle x-ray scattering and x-ray diffraction methods. Nitrogen fixation and chlorophyll synthesis are involved in the reduction of high energy bonds under physiological conditions. Both make use of elegant reaction mechanisms made possible by complex enzyme systems which are evolutionarily related. Nitrogenase reduces nitrogen to ammonia and is a two-component metalloenzyme compo...; Download File | View full details

Chemical approaches to probe environmental stress in Archaea: Author: Tarlykov, Pavel Victorovich; Date: 2009-05-15; Program: Biochemistry; Abstract: Little is known about strategies and mechanisms employed by thermophilic organisms to adapt to environmental stress. Sulfolobus solfataricus is a thermophile that belongs to Archaea, the third domain of life, and can be found in unusual habitats, such as the hot springs of Yellowstone National Park. This archaeon can tolerate high temperature, extreme acidity and high concentrations of heavy metals and other toxic substances. Thus, S. solfataricus has been chosen by many researchers as a model system for biochemical, structural, and genetic studies. In this work S. solfataricus has been expose...; Download File | View full details

Insights into the role of HydF-catalyzed GTP activity in hydrogenase maturation: Author: Bueling, Alexandra Lee; Date: 2009-08-15; Program: Biochemistry; Abstract: The [FeFe]-hydrogenase contains an unusual active-site cluster, the H-cluster, composed of a [4Fe-4S] cluster bridged to a 2Fe subunit coordinated by CO, CN-, and a nonprotein bridging dithiolate. Three accessory proteins, HydE, HydF, and HydG are required for maturation of the H-cluster. It has been proposed that the GTP-hydrolyzing protein HydF acts as a scaffold for assembly of the [2Fe] subcluster, which is then transferred to hydrogenase to produce the active enzyme[McGlynn, S.M.; Shepard, E.M.; Winslow, M.A.; Naumov, A.V.; Duschene, K.S.; Posewitz, M.C.; Broderick, W.E.; Broderick, J.B.;...; Download File | View full details

X-ray crystallographic studies of the proteins from sulfolobus spindle-shaped viruses (SSVs): Author: Menon, Smita Kesavankutty; Date: 2009-08-15; Program: Biochemistry; Abstract: Viruses populate virtually every ecosystem on the planet. Fuselloviridae are ubiquitous crenarchaeal viruses found in high-temperature acidic hot springs around the world. However, compared to eukaryotic and bacterial viruses, our knowledge of viruses infecting the archaea is limited. Fuselloviral genomes show little similarity to other organisms, generally precluding functional predictions. However, structural studies can reveal distant evolutionary relationships and provide functional insights that are not apparent from the primary amino acid sequence alone. Several such structural studies h...; Download File | View full details

Solution-phase dynamics of the hepatitis B virus capsid: kinetics-based assays for study of supramolecular complexes: Author: Hilmer, Jonathan Kyle; Date: 2009-12-15; Program: Biochemistry; Abstract: Viruses are the most abundant form of life on the planet. Many forms are pathogenic and represent a major threat to human health, but viruses can also be useful nanoscale tools: as adjuvants, gene therapy agents, antimicrobials, or functionalized nanoscale building blocks. Viruses have historically been viewed as static and rigid delivery vehicles, but over the last few decades they have been recognized as flexible structures. Their structural dynamics are a crucial element of their functionality, and they represent a substantial target for antiviral strategies. To overcome the inherent proble...; Download File | View full details

Structure of the membrane proximal oxidoreductase domain of human Steap3, the dominant ferrireductase of the erythroid transferrin cycle: Author: Sendamarai, Anoop Kumar Balakrishnan; Date: 2009-12-15; Program: Biochemistry; Abstract: The daily production of 200 billion erythrocytes requires 20 mg of iron, accounting for nearly 80% of the iron demand in humans. Thus, erythroid precursor cells possess an efficient mechanism for iron uptake in which iron loaded transferrin (Tf) binds to the transferrin receptor (TfR) at the cell surface. The Tf:TfR complex then enters the endosome via receptor-mediated endocytosis. Upon endosomal acidification, iron is released from Tf, reduced to Fe²⁺ by Steap3, and transported across the endosomal membrane by divalent metal ion transporter 1. Steap3 is comprised of ...; Download File | View full details

Biochemical, spectroscopic, and structural investigations on [FeFe]-hydrogenase maturation and complex metallocluster assembly: Author: Mulder, David Wayne; Date: 2010-05-15; Program: Biochemistry; Abstract: Metals are present in nearly half of all enzymes, often at the active site, where they modulate catalytic function. Some of these metalloenzymes exist with a single bound metal ion while many others contain complex metal clusters. Complex FeS assemblies are associated with the interconversion of the small molecules H₂, CO, CO₂, N₂, and NH₃. One such complex metalloenzyme, [FeFe]-hydrogenase, catalyzes the reversible oxidation of molecular H₂. The active site of [FeFe]-hydrogenases, the Hcluster, exists as a [4Fe-4S]-subcluster bridged by a prot...; Download File | View full details

Investigations on [FeFe]-hydrogenase active site biosynthesis: Author: McGlynn, Shawn Erin; Date: 2010-08-15; Program: Biochemistry; Abstract: Hydrogenase enzymes, which catalyze the reversible oxidation of molecular hydrogen, occupy important roles as catalysts in microbial energy transfer and conservation. This seemingly simple reaction between protons and electrons necessitates the utilization of some of nature's most complicated organo-metallic cofactors. Remarkably, two evolutionarily independent types of enzymes capable of catalyzing this reaction exist - termed the [NiFe] and [FeFe]-hydrogenases. The biosynthesis of the cofactors harbored by these enzymes poses questions as to the assembly pathways involved in constructing hyd...; Download File | View full details

Proteomics and systems biology analysis of the response of monocytes to infection by Coxiella burnetii and exposure to innate immune adjuvants: Author: Shipman, Matthew Richard; Date: 2010-08-15; Program: Biochemistry; Abstract: Coxiella burnetii is an obligate intracellular pathogen that infects human monocytes, specifically inhabiting the phagolysosome. C. burnetii is a potential bioterror agent and is classified by the National Institute for Allergies and Infectious Diseases (NIAID) as a category B pathogen. This bacterium is remarkably infectious, requiring as little as one bacterium to cause infection. We used phase II C. burnetii, an avirulent laboratory strain that acts as a model for wild type phase I strains. Our research was directed towards a deeper understanding of the monocyte proteome in response to a) i...; Download File | View full details

Binding and repair of DNA by spore photoproduct lyase: Author: Zilinskas, Egidijus; Date: 2010-08-15; Program: Biochemistry; Abstract: Bacterial spores are extremely resistant to chemical and physical stresses, including UV irradiation, which in spores results in the formation of 5-thyminyl-5,6-dihydrothymine (spore photoproduct, SP). While SP accumulates in UV-irradiated bacterial spores, it is rapidly repaired during germination. Spore photoproduct lyase (SPL) is the enzyme that catalyzes the specific repair of spore photoproduct to two thymines. It utilizes S-adenosylmethionine (SAM) and a [4Fe-4S] cluster to catalyze this reaction, and is a member of the radical SAM superfamily. Presented here is an investigation of SPL r...; Download File | View full details

Type-2 diabetes and innate immunity: new connections revealed by multi-dimensional fractionation of blood plasma prior to proteomic analysis: Author: Laffoon, Scott Bradley; Date: 2010-12-15; Program: Biochemistry; Abstract: We compared levels of protein isoforms in human blood plasma from patients with newly diagnosed and untreated type-2 diabetes (T2DM) with non-diabetic controls in samples obtained from US NIH. We immunodepleted fourteen of the most abundant proteins from pooled plasma samples and separated the depleted samples into six fractions by reverse-phase liquid chromatography at 80°C. Proteins from these fractions were labeled with new high quantum yield, hydrophilic and spectrally resolved fluorescent detection dyes developed at MSU and resolved on large-format (24cm x 20cm) two-dimensional...; Download File | View full details

Evaluating protein-carbohydrate interactions induced by multivalent carbohydrate-functionalized dendrimers: Author: Schlick, Kristian Henri; Date: 2010-12-15; Program: Biochemistry; Abstract: Understanding protein-carbohydrate interactions is essential for elucidating biological pathways and cellular mechanisms but is often difficult due to the prevalence of multivalent interactions. A better understanding of the basic behavior of protein-carbohydrate interactions is critical for controlling cellular proliferation and recognition processes for novel therapeutic methods to be successful. Many procedures that exist for evaluating protein-carbohydrate interactions are often limited to monovalent interactions or small polymers. Given that many cellular processes, such as those attribut...; Download File | View full details

Kinetic, mechanistic and spectroscopic studies of spore photoproduct lyase: Author: Silver, Sunshine Christine; Date: 2010-12-15; Program: Biochemistry; Abstract: Spore forming organisms are a health threat to humans and other animals in part due to a remarkable resistance to UV irradiation. This resistance results from two events: first, the formation of a unique thymine dimer, 5-thyminyl-5,6-dihydrothymine (spore photoproduct, or SP) upon UV irradiation; and more importantly, the rapid and specific repair of this DNA photoproduct to two thymines by spore photoproduct lyase (SP lyase). Understanding the molecular basis of this radical-mediated DNA repair will ultimately allow for a better understanding of how to address the health risks caused by spore...; Download File | View full details

Glycodendrimer mediation of Galectin-3 induced cancer cell aggregation: Author: Sprenger, Julie Jeannine; Date: 2010-12-15; Program: Biochemistry; Abstract: Galectin-3 is a cell surface protein that plays an important role in tumor aggregation, tumor progression and metastasis via its interaction with carbohydrates in the biological system. A synthetic, carbohydrate-functionalized, multivalent framework is ideal to study biological protein/carbohydrate interactions. In this research, dendrimers are used as a platform for the display of carbohydrates to study multivalent galectin-3/carbohydrate interactions as they pertain to tumor aggregation. The hypothesis is that the addition of carbohydrate functionalized dendrimers will mimic natural galectin...; Download File | View full details

Using chromatographic and mass spectrometry tools to probe albumin and its cargos: in search of understanding type II diabetes: Author: Bowden, Jared Newell; Date: 2011-05-15; Program: Biochemistry; Abstract: We measured molecules carried as cargos on the abundant blood protein human serum albumin (1) in patients with newly diagnosed, untreated type II diabetes (T2D) compared to healthy controls (HC). The HSA cargos measured included lipids, minerals, peptides, and metabolites. Differences in these cargos associated with T2D were measured, using chromatography and mass spectrometry, seeking to identify biological markers that may enhance early diagnosis of T2D. An extrinsic fluorescent probe of binding sites on HSA, ANS, revealed that there were distinct differences in loading of hydrophobic cargo ...; Download File | View full details

Monitoring protein cage nanoparticle morphology for applications in medicines and materials: Author: Johnson, Benjamin Lawrence; Date: 2011-05-15; Program: Biochemistry; Abstract: Protein cage nanoparticles are naturally occurring proteins found in all domains of life. The breadth of structural knowledge and the ability to modify protein cage nanoparticles both chemically and genetically set them apart for use as platforms for biomedical templates and materials synthesis. The work described herein focuses on the use of protein cage nanoparticles as a protective agent from a suite of viral pathogens. Protein cage nanoparticles exist in many different morphological forms both within a specific particle and between particles. It is essential to characterize these different...; Download File | View full details

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