Biochemistry Commons^™

Do The Inter-Nucleotide Domain Loops Act As An Entropic Sink In The Catalytic Activity Of 3-Phosphoglycerate Dehydrogenase (3pgdh)?, Cristina Adelia Meeham

Honors Theses

In protein science the relationship between protein dynamics and catalytic activity are the subject of considerable contemporary interest. Although protein motions are frequently observed during ligand binding and release steps, the contribution of protein motions to the catalysis of bond making/breaking processes is more difficult to probe and verify. Currently, the field of protein science is trying to uncover the deeper role that dynamics plays in the catalytic activity and allosteric regulation of proteins and to better understand how to more effectively and efficiently target proteins in cancer therapeutics and other metabolic pathways.

Comparative Analyses Of Three Chlorella Species In Response To Light And Sugar Reveal Distinctive Lipid Accumulation Patterns In The Microalga C. Sorokiniana, Julian N. Rosenberg, Naoko Kobayashi, Austin Barnes, Eric A. Noel, Michael J. Betenbaugh, George A. Oyler

Department of Biochemistry: Faculty Publications

While photosynthetic microalgae, such as Chlorella, serve as feedstocks for nutritional oils and biofuels, heterotrophic cultivation can augment growth rates, support high cell densities, and increase triacylglycerol (TAG) lipid content. However, these species differ significantly in their photoautotrophic and heterotrophic characteristics. In this study, the phylogeny of thirty Chlorella strains was determined in order to inform bioprospecting efforts and detailed physiological assessment of three species. The growth kinetics and lipid biochemistry of C. protothecoides UTEX 411, C. vulgaris UTEX 265, and C. sorokiniana UTEX 1230 were quantified during photoautotrophy in Bold’s basal medium (BBM) and heterotrophy in BBM supplemented …

Virus Purification, Detection And Removal, Khrupa Saagar Vijayaragavan

Dissertations, Master's Theses and Master's Reports - Open

The biopharmaceutical industry has a growing demand and an increasing need to improve the current virus purification technologies, especially as more and more vaccines are produced from cell-culture derived virus particles. Downstream purification strategies can be expensive and account for 70% of the overall manufacturing costs. The economic pressure and purification processes can be particularly challenging when the virus to be purified is small, as in our model virus, porcine parvovirus (PPV). Our efforts are focused on designing an easy, economical, scalable and efficient system for virus purification, and we focused on aqueous two-phase systems. Industry acceptable standards for virus …

Evaluation Of Effects Of Epigenetic Modifications, Macromolecular Crowding, Degree Of Hydration, And Transcription Factor Binding On The Thermodynamic Stability Of Dna I-Motif Structures, Yogini Bhavsar

Electronic Theses and Dissertations

No abstract provided.

A Comparative Approach To Assessing The Functional And Structural Characteristics Of Human Fkbp52 In The Regulation Of Steroid Hormone Receptor Signaling Pathway, Diondra Crystal Harris

Open Access Theses & Dissertations

The 52 kDa FK506 binding protein (h52) is a key positive regulator of Androgen Receptor (AR) in cellular and animal models and is an attractive target for the treatment of prostate cancer. Human FKBP52 is a known regulatory protein and co-chaperone that has been shown to play an important role in the regulation of the AR signaling pathway, and in the development of the male sexual phenotype. Cellular studies in mammalian and yeast cells reveal that FKBP52 is a positive regulator of AR, glucocorticoid receptor (GR), and progesterone receptor (PR), potentiating receptor-mediated gene expression up to 60-fold in some systems. …

Mechanisms To Mitigate Neurodegeneration By Maintaining Mitochondrial Health, Parijat Kabiraj

Open Access Theses & Dissertations

Cerebral accumulation of amyloidogenic protein aggregates is most frequently observed in the pathogenesis of neurodegenerative diseases. Recent studies showed prion like spreading of beta amyloid (A beta) in Alzheimer's disease (AD) and alpha synuclein protein in Parkinson's disease (PD) brain. Failure or compromise to the chaperone activity of protein disulfide isomerase (PDI) is also been reported as a major factor of aggregate formation. Nitrosative stress mediated S-nitrosylation (SNO) of protein disulfide isomerase (PDI), a housekeeping oxidoreductase, has been implicated in the pathogenesis of sporadic PD and AD. Mitochondrial dysfunction, leading to elevated levels of reactive oxygen species (ROS), is associated …

The Role Of Surface Chemistry In The Toxicity Of Manufactured Cerium Dioxide Nanomaterials To Caenorhabditis Elegans, Emily Kay Oostveen

Theses and Dissertations--Plant and Soil Sciences

Manufactured CeO₂ nanomaterials (CeO₂-MNMs) are used for a wide variety of applications including diesel fuel additives and chemical/mechanical planarization media. To test the effects of CeO₂-MNM surface coating charge on to model organism Caenorhabditis elegans, we synthesized 4 nm CeO₂ with cationic (DEAE-), anionic (CM-), and neutral (DEX) coatings. In L3 nematodes exposed for 24 hours, DEAE-CeO₂ induced lethality at lower concentrations than CM- or DEX-CeO₂. Feeding slightly decreased CeO₂ toxicity, regardless of coating. In L2 nematodes exposed for 48 hours with feeding, DEAE-CeO₂ caused lethality at the …

Understanding The Chemical Gymnastics Of Enzyme-Catalyzed 1’-1 And 1’-3 Triterpene Linkages, Stephen A. Bell

Theses and Dissertations--Plant and Soil Sciences

Squalene synthase (SS) is an essential enzyme in eukaryotic systems responsible for an important branch point in isoprenoid metabolism that leads to sterol formation. The mechanistic complexity of SS has made it a difficult enzyme to study. The green alga Botryococcus braunii race B possesses several squalene synthase-like (SSL) enzymes that afford a unique opportunity to study the complex mechanism of triterpene biosynthesis. SSL-1 catalyzes presqualene diphosphate (PSPP) formation, which can either be converted to squalene by SSL-2 or botryococcene by SSL-3. A rationally designed mutant study of B. braunii squalene synthase (BbSS) and SSL-3 was conducted to understand structure-function …

Structural Basis Of Epigenetic Regulation And Protein Scaffolding In Development And Diseases, Yuanyuan Jiang

Wayne State University Dissertations

Protein X-ray crystallography is a powerful approach for elucidating protein structure and function. The high-resolution data generated by X-ray allow us to visualize protein structures in a three-dimensional (3D) space, which is vital for our understanding of the protein intra- and intermolecular interactions that explain the mechanisms of various biological events. More importantly, such information can provide a structural basis for developing new methods and strategies of targeted drug discovery. In this dissertation, by using X-ray crystallography as the primary approach, we have performed the structural and functional studies of SMYD2 and NHERF1 and have determined their mechanisms of action …

General Transcription Factors Play Dual Roles In Initiation And Termination, Scott Alan Medler

Wayne State University Dissertations

Gene looping, defined as the interaction of the promoter and the terminator regions of a gene during transcription, is emerging as an important gene regulatory mechanism in eukaryotes. The role of promoter bound general transcription factors during initiation is well established. However, recent studies have revealed that some initiation factors also interact with the 3' end of a gene. The biological role of initiation factors at the 3' end of a gene is unknown. The general transcription factors TFIIB and TFIIH have been found to interact genetically with Ssu72, a component of CPF 3' end processing complex. Accordingly, we found …

Characterization Of Initial Iron Binding Location And The Structure/Iron Binding Site On S.Cerevisiae Isu And On D.Melanogaster Frataxin, Andria V. Rodrigues

Wayne State University Dissertations

Iron-induced free radical damage has been implicated in the pathology of diseases of iron overload such as Friedreich's Ataxia, a genetic disorder characterized by an accumulation of iron in actively metabolizing tissues ultimately leading to cardio- and neuro- degeneration and cell death. It is caused by an inability to synthesize the mitochondrial protein, frataxin. Frataxin has been shown by numerous groups to be a part of the iron-sulfur cluster (ISC) multicomplex, where it functions in the capacity of a potential iron provider and an allosteric modulator of both the cysteine desulfurase and scaffold protein ISU. My research has been focused …

Structure And Dynamics Of The Hiv-1 Frameshift Element Rna, Kathryn Mouzakis

Chemistry and Biochemistry Faculty Works

The HIV-1 ribosomal frameshift element is highly structured, regulates translation of all virally encoded enzymes, and is a promising therapeutic target. The prior model for this motif contains two helices separated by a three-nucleotide bulge. Modifications to this model were suggested by SHAPE chemical probing of an entire HIV-1 RNA genome. Novel features of the SHAPE-directed model include alternate helical conformations and a larger, more complex structure. These structural elements also support the presence of a secondary frameshift site within the frameshift domain. Here, we use oligonucleotide-directed structure perturbation, probing in the presence of formamide, and in-virion experiments to examine …

Neuropilin In The Vascular System: Mechanistic Basis Of Angiogenesis, Hou-Fu Guo

Theses and Dissertations--Molecular and Cellular Biochemistry

The vascular system is critical for maintaining homeostasis in all vertebrates. Structural studies of Neuropilin (Nrp), an essential angiogenic receptor, have defined its role in regulating angiogenesis, the formation of new vessels from the existing vasculature. Utilizing biochemical and biophysical tools we describe the ability of Nrp to function as a co-receptor for the VEGFR receptor tyrosine kinase. Two families of Nrp-1 ligands, Vascular Endothelial Growth Factor A (VEGF-A) and Semaphorin3F (Sema3F), physically compete for binding to the Nrp-1 b1 domain, and have opposite roles. VEGF-A is a potent pro-angiogenic cytokine while Sema3F is an angiogenesis inhibitor. Using coupled structural …

Characterization Of Jabba, A Ricin-Resistant Mutant Of Leishmania Donovani, Megan Rhea Phillips

Theses and Dissertations--Molecular and Cellular Biochemistry

The abundant cell-surface lipophosphoglycan (LPG) of Leishmania parasites plays a central role throughout the eukaryote’s life cycle. A number of LPG-defective mutants and their complementing genes have been isolated and have proven invaluable in assessing the importance of LPG and related glycoconjugates in parasite virulence. While ricin agglutination selection protocols frequently result in lpg- mutants, one L. donovani variant we isolated, named JABBA, was found to be lpg+. Procyclic (logarithmic) JABBA expresses significant amounts of a large-sized LPG, larger than observed from procyclic wild-type but similar in size to LPG from wild-type from metacyclic (stationary) phase.

Structural analysis of …

Molecular Mechanisms Of Neuropilin-Ligand Binding, Matthew W. Parker

Theses and Dissertations--Molecular and Cellular Biochemistry

Neuropilin (Nrp) is an essential cell surface receptor with dual functionality in the cardiovascular and nervous systems. The first identified Nrp-ligand family was the Semaphorin-3 (Sema3) family of axon repulsion molecules. Subsequently, Nrp was found to serve as a receptor for the vascular endothelial growth factor (VEGF) family of pro-angiogenic cytokines. In addition to its physiological role, VEGF signaling via Nrp directly contributes to cancer stemness, growth, and metastasis. Thus, the Nrp/VEGF signaling axis is a promising anti-cancer therapeutic target. Interestingly, it has recently been shown that Sema3 and VEGF are functionally opposed to one another, with Sema3 possessing potent …

Leptin Resistance Induced Obesity And Diabetes Promote Neuropathological Changes In The Aging Brain, Thomas Platt

Theses and Dissertations--Molecular and Cellular Biochemistry

The aging brain is prone to the development of pathology and dementia. With a rapidly growing elderly population diagnoses of neurodegenerative diseases, such as Alzheimer’s disease (AD), frontotemporal dementia (FTD), and Parkinson’s disease are on the rise. Additionally, diabetes and obesity are linked to an increased risk of dementia. The convergence of this increasingly aged population with the obesity and diabetes epidemic give rise to new concerns regarding the future of prevention and treatment of neurodegenerative diseases. Our lab has previously shown that leptin, an adipokine involved in signaling satiety to the hypothalamus, can modulate the generation of the amyloid …

Group Via Calcium-Independent Phospholipase A2 Regulates Bcl-Xl Protein Levels In Mice Lung, Sang-Jin Nam

Theses and Dissertations

With previous indication of the Group VIA phospholipase A2 (iPLA2β) enzyme regulating ER-stress induced apoptosis in β-cells by regulating the anti-apoptotic protein Bcl-xL via alternative splicing, our lab postulated iPLA2β to be utilizing a similar mechanism to regulate apoptosis in mice lung. Our previous lab work has shown implications of lung function compromise in iPLA2β-/- mice, and we speculated the cause to be due altered lung architecture stemming from the attenuation of apoptosis. The western blot analysis in this study suggested that iPLA2β is involved in the regulation of Bcl-xL, but the mRNA ratios of the splice variants suggested that …

Structural Mechanisms Of Glucan Phosphatase Activity In Starch Metabolism, David A. Meekins

Theses and Dissertations--Molecular and Cellular Biochemistry

Starch is a water-insoluble glucose biopolymer used as an energy cache in plants and is synthesized and degraded in a diurnal cycle. Reversible phosphorylation of starch granules regulates the solubility and, consequentially, the bioavailability of starch glucans to degradative enzymes. Glucan phosphatases release phosphate from starch glucans and their activity is essential to the proper diurnal metabolism of starch. Previously, the structural basis of glucan phosphatase activity was entirely unknown. The work in this dissertation outlines the structural mechanism of activity of two plant glucan phosphatases called Starch EXcess4 (SEX4) and Like Sex Four2 (LSF2). The crystal structures of SEX4 …

Book Review Of Dane Kennedy, The Last Blank Spaces: Exploring Africa And Australia, Adrian S. Wisnicki

Department of Biochemistry: Faculty Publications

Mid-nineteenth-century British exploration, particularly the stories of the “heroic” individuals who carried out this exploration, remains a topic of worldwide interest, as most recently evidenced by the many events in Britain and Africa celebrating the 2013 bicentenary of David Livingstone’s birth. Dane Kennedy’s intriguing study takes issue with such readings of the historical record by foregrounding an epistemological tension that lies at the heart of nineteenthcentury British exploration discourse and practice. The book examines the collision—as it played out in the exploration of African and Australia—between metropolitan scientific protocols and non-Western quotidian realities. Nineteenth-century explorers, argues Kennedy, left home with …

Protein/Protein Interactions In The Mammalian Heme Degradation Pathway: Heme Oxygenase-2, Cytochrome P450 Reductase, And Biliverdin Reductase, Andrea L. M. Spencer, Ireena Bagai, Donald F. Becker, Erik R. P. Zuiderweg, Stephen W. Ragsdale

Department of Biochemistry: Faculty Publications

Heme oxygenase (HO) catalyzes the rate-limiting step in the O₂- dependent degradation of heme to biliverdin, CO, and iron with electrons delivered from NADPH via cytochrome P450 reductase (CPR). Biliverdin reductase (BVR) then catalyzes conversion of bili­verdin to bilirubin. We describe mutagenesis combined with kinetic, spectroscopic (fluorescence and NMR), surface plasmon resonance, cross-linking, gel filtration, and analytical ultracentrifugation studies aimed at evaluating interactions of HO-2 with CPR and BVR. Based on these results, we propose a model in which HO-2 and CPR form a dynamic ensemble of complex(es) that precede formation of the productive electron transfer complex. The …