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Articles 1 - 23 of 23
Full-Text Articles in Biochemistry, Biophysics, and Structural Biology
Functional Genomic Investigation Of Aromatic Aminotransferases Involved In Ephedrine Alkaloid Biosynthesis In Ephedra Sinica (Stapf), Korey G. Kilpatrick
Functional Genomic Investigation Of Aromatic Aminotransferases Involved In Ephedrine Alkaloid Biosynthesis In Ephedra Sinica (Stapf), Korey G. Kilpatrick
Electronic Thesis and Dissertation Repository
Ephedra sinica (Ephedraceae) is a broom-like shrub cultivated in arid regions of China, Korea and Japan. This medicinal plant accumulates large amounts of the ephedrine alkaloids, including (S)-cathinone, (1R,2S)-norephedrine, (1R,2S)-ephedrine and (1S,2S)-pseudoephedrine in its aerial tissues. These analogues of amphetamine mimic adrenaline and stimulate the sympathetic nervous system. While much is known about their pharmacological properties, the biological mechanisms by which they are synthesized remains largely unknown. A functional genomics platform was established in order to investigate alkaloid biosynthesis. RNA was extracted from Ephedra sinica stems …
Involvement Of Interleukin-33/St2 In Myocardial Dysfunction In Murine Model Of Sepsis, Yoonmi Choe
Involvement Of Interleukin-33/St2 In Myocardial Dysfunction In Murine Model Of Sepsis, Yoonmi Choe
Electronic Thesis and Dissertation Repository
The disruption of myocardial extracellular matrix (ECM) has been implicated in myocardial dysfunction during sepsis. However, the underlying mechanism(s) are not clear. Interleukin-33 (IL-33) is a cytokine which regulates collagen synthesis in various cardiac pathologies. The purpose of the present study is to test whether IL-33 contributes to sepsis-induced myocardial dysfunction through regulation of matrix metalloproteinase-9 (MMP-9). The in vivo, feces-induced peritonitis (FIP) in mice and in vitro lipopolysaccharide (LPS) treatments to isolated cardiomyocytes were used. In FIP mice, myocardial IL-33 and MMP-9 expression were increased and myocardial contractility was decreased. Myocardial function in FIP mice was improved when treated …
Characterization Of A Tumour Suppressor Function Of Ranbpm, Elnaz Atabakhsh
Characterization Of A Tumour Suppressor Function Of Ranbpm, Elnaz Atabakhsh
Electronic Thesis and Dissertation Repository
Ran-binding protein M (RanBPM) is an evolutionarily conserved nucleocytosolic protein that has been proposed to regulate various cellular processes, including protein stability, gene expression, receptor-mediated signalling pathways, cell adhesion, development, and apoptosis. Despite the multitude of functions attributed to RanBPM however, little is known regarding the precise mechanisms by which RanBPM executes these cellular roles. In this work, we seek to address this matter by describing functions for RanBPM in the regulation of apoptotic and pro-survival signalling pathways, and in cellular transformation.
We first identify RanBPM as a pro-apoptotic protein that regulates the activation of the intrinsic apoptotic signalling pathway …
Characterization Of Cardiomyopathy In A Mouse Model Of Duchenne Muscular Dystrophy (Dmd) Using Echocardiography, Dce-Ct, And Pet-Fdg, Seyed Hamed Moazami
Characterization Of Cardiomyopathy In A Mouse Model Of Duchenne Muscular Dystrophy (Dmd) Using Echocardiography, Dce-Ct, And Pet-Fdg, Seyed Hamed Moazami
Electronic Thesis and Dissertation Repository
Duchenne muscular dystrophy (DMD) is an X-linked recessive neuromuscular disease that is the result of a loss of functional dystrophin, which causes cardiomyocyte fibrosis and death, leading to cardiomyopathy. In this thesis, I have utilized dynamic contrast-enhanced computed tomography (DCE-CT), positron emission tomography-fluorodeoxyglucose (PET-FDG), echocardiography, and traditional histology to longitudinally assess disease progression and degree of cardiomyopathy in a murine model of DMD (mdx:utrn-/-). No significant changes were observed in the blood flow, blood volume, or cardiac volume measured via DCE-CT, nor in standard uptake value (SUV) of glucose as measured by PET-FDG in the left myocardium between and within …
The Regulation Of Prokaryotic Transposable Elements By The Rna Binding Protein Hfq, Brian J. Munshaw
The Regulation Of Prokaryotic Transposable Elements By The Rna Binding Protein Hfq, Brian J. Munshaw
Electronic Thesis and Dissertation Repository
This thesis investigates the role that the RNA binding protein Hfq has in regulating the mobility of IS Elements and the expression of their transposase genes. Hfq is a known regulator of the IS Element IS10 and is a major component of sRNA pathways in E.coli. In this work, I demonstrate that through the use of a bioinformatics approach to identify a list of additional IS Elements from the IS Finder database, one can successfully identify IS Elements containing Hfq binding sites which may implicate Hfq regulation. One of the identified elements, IS1413, was characterized by …
(1)H, (15)N And (13)C Backbone Resonance Assignments Of The Tpr1 And Tpr2a Domains Of Mouse Sti1., Andrzej Maciejewski, Marco A Prado, Wing-Yiu Choy
(1)H, (15)N And (13)C Backbone Resonance Assignments Of The Tpr1 And Tpr2a Domains Of Mouse Sti1., Andrzej Maciejewski, Marco A Prado, Wing-Yiu Choy
Biochemistry Publications
Hop/STI1 (Hsp-organizing protein/stress-induced-phosphoprotein 1) is a molecular co-chaperone, which coordinates Hsp70 and Hsp90 activity during client protein folding through interactions with its TPR1 and TPR2A domains. Hsp90 substrates include a diverse set of proteins, many of which have been implicated in tumorigenesis. Over-expression of Hsp90 in cancer cells stabilizes mutant oncoproteins promoting cancer cell survival. Disruption of Hsp90 and its co-chaperone machinery has become a promising strategy for the treatment of cancer. STI1 has also been described as a neurotrophic signaling molecule through its interactions with the prion protein (PrP(C)). Here, we report the (1)H, (13)C and (15)N backbone assignments …
Elastic Deformations Of The Rotary Double Motor Of Single F(O)F(1)-Atp Synthases Detected In Real Time By Förster Resonance Energy Transfer., Stefan Ernst, Monika G Düser, Nawid Zarrabi, Stanley D Dunn, Michael Börsch
Elastic Deformations Of The Rotary Double Motor Of Single F(O)F(1)-Atp Synthases Detected In Real Time By Förster Resonance Energy Transfer., Stefan Ernst, Monika G Düser, Nawid Zarrabi, Stanley D Dunn, Michael Börsch
Biochemistry Publications
Elastic conformational changes of the protein backbone are essential for catalytic activities of enzymes. To follow relative movements within the protein, Förster-type resonance energy transfer (FRET) between two specifically attached fluorophores can be applied. FRET provides a precise ruler between 3 and 8nm with subnanometer resolution. Corresponding submillisecond time resolution is sufficient to identify conformational changes in FRET time trajectories. Analyzing single enzymes circumvents the need for synchronization of various conformations. F(O)F(1)-ATP synthase is a rotary double motor which catalyzes the synthesis of adenosine triphosphate (ATP). A proton-driven 10-stepped rotary F(O) motor in the Escherichia coli enzyme is connected to …
Elastic Deformations Of The Rotary Double Motor Of Single F(O)F(1)-Atp Synthases Detected In Real Time By Förster Resonance Energy Transfer., Stefan Ernst, Monika G Düser, Nawid Zarrabi, Stanley D Dunn, Michael Börsch
Elastic Deformations Of The Rotary Double Motor Of Single F(O)F(1)-Atp Synthases Detected In Real Time By Förster Resonance Energy Transfer., Stefan Ernst, Monika G Düser, Nawid Zarrabi, Stanley D Dunn, Michael Börsch
Biochemistry Publications
Elastic conformational changes of the protein backbone are essential for catalytic activities of enzymes. To follow relative movements within the protein, Förster-type resonance energy transfer (FRET) between two specifically attached fluorophores can be applied. FRET provides a precise ruler between 3 and 8nm with subnanometer resolution. Corresponding submillisecond time resolution is sufficient to identify conformational changes in FRET time trajectories. Analyzing single enzymes circumvents the need for synchronization of various conformations. F(O)F(1)-ATP synthase is a rotary double motor which catalyzes the synthesis of adenosine triphosphate (ATP). A proton-driven 10-stepped rotary F(O) motor in the Escherichia coli enzyme is connected to …
Involvement Of Hexokinase1 In Plant Growth Promotion As Mediated By Burkholderia Phytofimans, Jae Min Park
Involvement Of Hexokinase1 In Plant Growth Promotion As Mediated By Burkholderia Phytofimans, Jae Min Park
Electronic Thesis and Dissertation Repository
Burkholderia phytofirmans strain PsJN consistently enhanced the growth of potato plants in vitro. The role of hexokinase1 in glucose phosphorylation was investigated in plants with PsJN. Increased hexokinase1 activity only in roots of PsJN-treated plants cultivar Kennebec suggests that hexokinase1 is associated with plant root and stem growth.
Plant growth with PsJN was determined when plants were grown with different sugars at various concentrations. PsJN-treated plants expressed diverse forms of growth promotion. When growth promotion did occur, hexokinase1 activity also increased. Growth promotion and hexokinase1 activity appear to be correlated to the enzyme to recognize the substrate for catalytic activity. …
Cadmium Accumulation And Distribution In Lettuce And Barley, Fardausi Akhter
Cadmium Accumulation And Distribution In Lettuce And Barley, Fardausi Akhter
Electronic Thesis and Dissertation Repository
Cadmium (Cd) is a non-essential trace element and its environmental concentrations are increasing due to human activities. Edible plants can accumulate high concentrations of Cd, which could be toxic to humans. Understanding how and where Cd is stored in plants is important for ensuring lower concentration of Cd in the food. In this thesis, the accumulation and distribution of Cd in three agricultural plants, namely lettuce (Lactuca sativa L.), barley (Hordeum vulgare L.) and radish (Raphanus sativus L.), were investigated with a focus on the potential mechanisms involved in the localization of Cd in the root. The …
Protein Body Formation In Stable Transgenic Plants Of Nicotiana Tabacum Expressing Elastin-Like Polypeptide And Hydrophobin Fusion Proteins, Sonia P. Gutierrez
Protein Body Formation In Stable Transgenic Plants Of Nicotiana Tabacum Expressing Elastin-Like Polypeptide And Hydrophobin Fusion Proteins, Sonia P. Gutierrez
Electronic Thesis and Dissertation Repository
Plants are recognized as an efficient and inexpensive system to produce valuable recombinant proteins. However, the use of plants still faces two main limitations: the low accumulation levels of some recombinant proteins and the lack of efficient protein purification methods. Two fusion partners, elastin-like polypeptides (ELP) and hydrophobin I (HFBI) were found to increase the accumulation of recombinant proteins and induce the formation of protein bodies (PBs) when targeted to the ER in transient expression assays. In this study I examined the effect of these tags in stable transgenic plants of two Nicotiana tabacum cultivars when fused to green fluorescent …
Human Equilibrative Nucleoside Transporter Subtype 1: Structure-Function Analysis Using Cysteine Mutagenesis And Thiol Modifying Techniques, Jamie Park
Electronic Thesis and Dissertation Repository
Human equilibrative nucleoside transporter 1 is the main mediator of bi-directional nucleoside flux and is found ubiquitously. Inhibitor and substrate interactions with ENT1 are known to be affected by cysteine-modifying reagents. Our aim was to investigate the importance of cysteine residues in hENT1 function and identify which residues were sensitive to thiol modification for further application of cysteine scanning mutagenesis on extracellular loop 5. Transporter function was assessed by the binding of [3H]NBMPR and the cellular uptake of [3H]2-chloroadenosine. Treatment of hENT1 with the neutral sulfhydryl-modifier methyl methanethiosulfonate (MMTS) enhanced [3H]NBMPR binding but decreased …
Characterization Of The Interaction Between The Parkin Ubiquitin-Like Domain And Ataxin-3 Ubiquitin Interacting Domains, Jane J. Bai
Electronic Thesis and Dissertation Repository
The ubiquitin signaling pathway (USP) consists of hundreds of enzymes which are tightly regulated for proper maintenance of intracellular protein level homeostasis. The main goals of this thesis were to characterize the interaction of two proteins involved in the USP, the E3 ubiquitin ligase called parkin, and the Deubiquitinating (DUB) enzyme, ataxin-3. The effect of disease-state substitutions in the parkin ubiquitin-like domain (UbLD) on the interaction with ataxin-3 was investigated through NMR 1H-15N HSQC titration experiments and affinity binding assays. The three UIM regions in ataxin-3bind the hydrophobic patch of parkin UbLD (KD = 680 μM) …
Telomere Length Dynamics In Aging Mice, Paul J. Comartin
Telomere Length Dynamics In Aging Mice, Paul J. Comartin
Electronic Thesis and Dissertation Repository
Leukocyte telomere length (TL) shortens with age and is associated with age-related pathologies. However, inherited and acquired variation in telomere length in individuals complicates clinical interpretations of TL as a biomarker of aging and age-related pathologies. Therefore, it is critical to identify a post-mitotic tissue as a surrogate marker of TL at birth. In my thesis project, I used quantitative PCR to trace TL dynamics of a variety of tissue types of inbred mice during 1st year of life. I found that TL of smooth muscle of aortic media did not shorten with age and represents birth TL. Notably, birth …
Structural And Bioinformatic Analysis Of The B Subunit Of F-Atp Synthase, Ardeshir Goliaei
Structural And Bioinformatic Analysis Of The B Subunit Of F-Atp Synthase, Ardeshir Goliaei
Electronic Thesis and Dissertation Repository
F1Fo ATP synthases are rotary enzymes that produce most ATP in living organisms. The enzymes’ b2δ subunits form a stator stalk that holds the F1 sector against the torque of the rotor. In Escherichia coli, b2 is an asymmetric homodimer. However, ATPases from some species have a heterodimer of subunits b and b’. Here, a modified E. coli ATP synthase containing a heterodimeric stator stalk was engineered by replacing residues 34-110 of E. coli b with sequences of Rhodobacter capsulatus b and b’, and expressing both chimeras. This produced a …
(1)H, (15)N And (13)C Backbone Resonance Assignments Of The Kelch Domain Of Mouse Keap1., Elio Cino, Jingsong Fan, Daiwen Yang, Wing-Yiu Choy
(1)H, (15)N And (13)C Backbone Resonance Assignments Of The Kelch Domain Of Mouse Keap1., Elio Cino, Jingsong Fan, Daiwen Yang, Wing-Yiu Choy
Biochemistry Publications
Kelch-like ECH-associated Protein 1 (Keap1) is a multi-domain protein that functions as an inhibitor of the transcription factor nuclear factor E2-related factor 2 (Nrf2) in the cellular response to oxidative stress. Under normal conditions, Keap1 binds to Nrf2 via its C-terminal Kelch domain and the interaction ultimately leads to the ubiquitin-dependent degradation of Nrf2. It has been proposed that designing molecules to selectively disrupt the Keap1-Nrf2 interaction can be a potential therapeutic approach for enhancing the expression of cytoprotective genes. Here, we reported the (1)H, (13)C, and (15)N backbone chemical shift assignments of the Kelch domain of mouse Keap1. Further, …
Identification And Characterization Of The Arabidopsis Homolog Of The Yeast Trex-2 Complex, Gang Tian
Identification And Characterization Of The Arabidopsis Homolog Of The Yeast Trex-2 Complex, Gang Tian
Electronic Thesis and Dissertation Repository
Nuclear pore complexes (NPCs) are vital to nuclear-cytoplasmic communication in eukaryotes. The yeast Thp1-Sac3-Cdc31-Sus1 complex, also known as the TREX-2 complex, is anchored to the NPC via the nucleoporin Nup1, and is essential for mRNA export. In this study, the Arabidopsis homolog of the yeast TREX-2 complex was discovered. Physical and functional evidence support the identification of the Arabidopsis orthologs of the yeast Thp1 and Nup1. Of three Sac3 Arabidopsis homologs, two are putative TREX-2 components. Surprisingly, none are required for mRNA export as is the yeast Sac3. Physical association with TREX-2 was observed for the two Cdc31 homologs, but …
Structural Motifs Of Novel Metallothionein Proteins, Duncan E K Sutherland
Structural Motifs Of Novel Metallothionein Proteins, Duncan E K Sutherland
Electronic Thesis and Dissertation Repository
Metallothioneins (MT) are a family of small cysteine rich proteins, which have been implicated in toxic metal detoxification, protection against oxidative stress, and as a metallochaperone. The most well studied member of the family is the mammalian MT, which consists of two domains: a β-domain with 9 cysteine residues, which sequesters 3 Cd2+/Zn2+, and an α-domain with 11 cysteine residues, which sequesters 4 Cd2+/Zn2+. The exact functions of MT are unknown but must relate to its metalation status. Several areas that could lead to the assignment of function include 1) the determination …
Mass Spectrometry-Based Proteomics Analysis Of The Matrix Microenvironment In Pluripotent Stem Cell Culture, Christopher Hughes
Mass Spectrometry-Based Proteomics Analysis Of The Matrix Microenvironment In Pluripotent Stem Cell Culture, Christopher Hughes
Electronic Thesis and Dissertation Repository
The stem cell microenvironment contains soluble factors, support cells, and components of the extracellular matrix (ECM) that combine to effect cellular behavior. Mass spectrometry based proteomics offers the opportunity to directly assay components of extracellular microenvironments, thereby providing a sensitive means for obtaining insight into the stem cell niche. In this study we present the generation and analysis of human embryonic stem cell (hESC) and human induced pluripotent stem cell (hiPSC) matrix microenvironments using an MS-based proteomics approach.
One of the primary limitations in the proteomics analysis of hESCs and hiPSCs is the reproducible generation of sufficient cell numbers amenable …
Applications Of Rapid Cardiac Micro-Ct, Sarah A. Detombe
Applications Of Rapid Cardiac Micro-Ct, Sarah A. Detombe
Electronic Thesis and Dissertation Repository
Mouse models are an important tool in cardiovascular disease research and a non-invasive imaging method is an advantageous way of monitoring disease progression. Cardiac micro-CT is rapid imaging technique capable of quantifying changes in cardiac structure and function in mice. The goal of this thesis was to demonstrate the utility of this technique in monitoring disease progression in a longitudinal study, as well as its capability for evaluating other methods of measuring cardiac function in mice.
In a longitudinal study, a mouse model of myocardial infarction was scanned weekly for four weeks; left ventricular volume and ejection fraction were measured …
Structural Characterization Of Protein Folding Intermediates By Oxidative Labeling And Mass Spectrometry, Bradley B. Stocks
Structural Characterization Of Protein Folding Intermediates By Oxidative Labeling And Mass Spectrometry, Bradley B. Stocks
Electronic Thesis and Dissertation Repository
A key challenge associated with protein folding studies is the characterization of short-lived intermediates that become populated en route to the native state. In this work, a covalent labeling method was developed that provides insights into the structures of these transient species. Hydroxyl radical (·OH) reacts with solvent-exposed side chains, whereas buried residues are protected. Mass spectrometry is used for monitoring the locations and the extent of labeling. Pulsed ·OH labeling of proteins at selected time points during folding results in high temporal and spatial resolution when compared to existing other labeling methods.
This novel technique was validated by studying …
Molecular Dynamics Simulations Of Peptide-Mineral Interactions, Susanna Hug
Molecular Dynamics Simulations Of Peptide-Mineral Interactions, Susanna Hug
Electronic Thesis and Dissertation Repository
We present molecular dynamics (MD) simulations providing information about the mechanisms of biomineralization. We focus on osteopontin-related peptides, which inhibit the growth of calcium oxalate monohydrate (COM) the primary constituent of kidney stones.
First, we performed two ab initio MD simulations: aspartic acid (Asp) and the dimer of aspartic acid and phosphoserine (Asp-pSer) interacting with a fully hydrated COM crystal slab exposing the {100} face. For Asp we found that one of the carboxyl and the amine group both interact with the crystal surface but neither forms a stable contact during the simulation. Asp-pSer interacts preferably with its carboxyl groups …
Regulation Of The Bacterial Transposon Tn5, Crystal R. Mclellan
Regulation Of The Bacterial Transposon Tn5, Crystal R. Mclellan
Electronic Thesis and Dissertation Repository
Transposons play an integral role in bacterial adaptation, therefore it is important to understand the chemical steps and regulatory factors that govern their mobility. The properties that drive insertion of transposons into subsequent DNA sites have been studied for few elements. The transposon Tn5 in particular has few defined insertion sites and little is known about how its targets are selected. An objective of this thesis was to determine the molecular details of target insertion in Tn5 transposition in vitro. To this end, I assessed whether Tn5 could preferentially insert into short oligonucleotide substrates. I detected a Tn5 transpososome …