Biochemistry, Biophysics, and Structural Biology Commons^™

Visualizing The Spatial Localization Of Active Matrix Metalloproteinases (Mmps) Using Maldi Imaging Ms, Sasirekha Muruganantham

Graduate Theses and Dissertations

Biomaterial implantation induces the foreign body response (FBR). Development of longer-term implants relies on the thorough understanding of the FBR. The progression of the FBR is regulated by a number of biomolecules including cytokines, chemokines, and matrix metalloproteinases (MMPs). The nature of the FBR requires the spatial and temporal regulation of these mediators. MMPs are an extremely large and diverse group of enzymes that play key roles in regulating the FBR. Precise spatiotemporal regulation of MMPs defines their proteolytic activities. The aim of this project is to develop a new bioanalytical method to visualize the localization of active MMPs at …

The Role Of Albino3 And The Lipid Environment In Chloroplast Signal Recognition Particle Targeting, Nathan Lewis

Graduate Theses and Dissertations

Signal recognition particles (SRPs) in pro- and eukaryotes function in cotranslational targeting of nascent poplypeptides to an SRP receptor at the target membrane. A unique chloroplast SRP (cpSRP) functions post-translationally to direct light-harvesting chlorophyll-binding proteins (LHCPs) to the receptor cpFtsY at the thylakoid membrane for LHCP insertion in a process involving the integral membrane protein Albino3 (Alb3) and requiring GTP. Work here focuses on understanding cpSRP targeting events at the thylakoid membrane, specifically those involving Alb3 and the lipid environment.

We show an interaction between the novel cpSRP subunit cpSRP43 and the soluble, stromal-exposed C terminus of Albino3 (Alb3-Cterm). We …

Tryptophan Anchored Peptides In Lipid Bilayer Membranes: Control Of Peptide Orientation And The Phase Behavior Of Cholesterol-Containing Ternary Lipid Mixtures, Johanna Maria Rankenberg

Graduate Theses and Dissertations

Model WALP peptides and "next generation" WALP-derived hydrophobic model peptides were employed to discover principles that govern protein-lipid interactions in biological membranes.

Ternary cholesterol-containing lipid mixtures were examined in the presence of WALP peptides of different lengths (acetyl-GWW(LA)_nLWWA-ethanolamide, with n between 3 and 8). Deuterium NMR spectra from labeled lipids reveal that WALP peptides may stabilize lipid ordered "raft" domains and therefore promote lipid phase separation, albeit to a minor extent. The results depend upon whether dioleolyl- or diphytanoyl-phosphatidylcholine is present as the fluid lipid component.

Several WALP peptides were modified to remove anchoring Trp residues from one …

Stability Of Nucleic Acid Secondary Structures And Their Contribution To Gene Expression, Maged A. Darwish

Seton Hall University Dissertations and Theses (ETDs)

Bacteriorhodopsin (bR) is a highly expressed transmembrane protein that acts as a light-driven proton pump converting light energy into a proton gradient. The extraordinary levels of expression achieved (15-30 mg per liter of culture) are a result of very efficient biogenesis that originates from molecular information encoded in the bacterio-opsin gene {bop) (1). DNA sequence analysis and predictive folding algorithms suggest that the first twenty-five bases of the bop gene mRNA can form a secondary structural element (a "stem-loop"). Using biophysical methods, the goal was to determine if the stem-loop structure exists in solution conditions that mimic the in vivo …

Characterization And Functional Regulation Of Bioactive Peptides In Avian Macrophages And Heterophils, Lakshmi Kannan

Graduate Theses and Dissertations

Oligopeptides and low molecular weight polypeptides play central roles as effectors and signal transducers acting as hormones, neurotransmitters, growth factors, toxins, and antimicrobial factors that are important for the survival of the organism. Owing to the ubiquitous involvement of peptides in many key regulatory processes, we have been interested to identify native peptides in different cells and tissues and understand their functions. To conduct our studies, we used avian macrophages and heterophils as models of specialized cells which constitute central components of innate immunity. These studies involved (a) qualitative identification and characterization of the peptides associated with high intensity mass …

Micro, Nano Encapsulation Methods For Sustained Release Drug Formulations And Biomimetic Applications, Shantanu Balkundi

Doctoral Dissertations

The Layer-by-Layer (LbL) assembly technique was used to obtain a new type of protein/polyphenol microcapsule based on naturally occurring polyphenol (-)-epigallocatechin gallate (EGCG) and gelatin, type A. The dependence of permeability on the molecular weight of permeating substances was studied and compared with commonly used polyallylamine/polystyrene sulfonate capsules. A quartz crystal microbalance was used to monitor the regularities of EGCG adsorption in alternation with type A and B Gelatins and electrophoretic mobility measurements were used that indicated that the nature of assembly was dependent on Gelatin properties. It was shown that EGCG retains its antioxidant activity in the LbL assemblies. …

Gene Synthesis, Cloning, Expression, Purification And Biophysical Characterization Of The C2 Domain Of Human Tensin, Kiran Sukumar Gajula

Doctoral Dissertations

Tensin is a large "docking" protein found in the adhesive junctions of animal cells and recruited early in the development of cell-substrate contacts. There it binds to the cytoplasmic domain of integrin β1 and caps the barbed ends of filamentous actin. This forms a rational basis for its implication in a direct role in the mechanics of membrane-cytoskeleton interactions. Tensin provides a physical link between the actin cytoskeleton, integrins, and other proteins at the cell-substrate contacts. Its overall biochemical properties are a function of its domain composition and architecture, i.e., the domains that are present and their relative positions in …

The Biophysical Analysis Of The Human Telomeric Repeat (Ttaggg)4 And Characterization Of Porphyrin Binding In Potassium Solutions, Cosimo Antonacci

Seton Hall University Dissertations and Theses (ETDs)

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Structural And Thermodynamic Parameters Associated With The Interaction Of Cobalt (Iii) Complexes And Duplex Dna, Jaime M. Ferreira

Seton Hall University Dissertations and Theses (ETDs)

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Characterizing An Rna Aptamer And Binding Studies With Synthetic Porphyrazines, Melanie Bozza

Seton Hall University Dissertations and Theses (ETDs)

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Microcapsule Biosensors Based On Competitive Binding And Fluorescence Resonance Energy Transfer Assays, Swetha Chinnayelka

Doctoral Dissertations

Fluorescent sensing systems offer the potential for minimally invasive monitoring with implantable devices, but they require carrier technologies that provide suitable immobilization, accessibility, and biocompatibility while maintaining adequate response characteristics. Towards the development of this goal, a general design of a biosensor with the capability of detecting different metabolites was investigated. The approach is based on the encapsulation of a competitive binding assay in microcapsules and monitoring the changes in fluorescence resonance energy transfer (FRET) in the presence of analyte. To experimentally demonstrate this type of sensing system, glucose was chosen as the model target analyte. The design, fabrication, and …

Stm And Computational Investigations Of Nanostructured Layered Transition Metal Chalcogenides, Changki Kim

Seton Hall University Dissertations and Theses (ETDs)

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Synthesis Of Novel Porphyrazines And Binding Studies To Dna Quadruplexes, Carlos Ramirez

Seton Hall University Dissertations and Theses (ETDs)

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Layer-By-Layer Self -Assembly For Enzyme And Dna Encapsulation And Delivery, Amish Patel

Doctoral Dissertations

Thin wall microcapsules were formed via Layer-by-Layer Self-Assembly of alternate adsorption of oppositely charged polyelectrolyte on microcores. After the core dissolution, empty polymeric shells with 20–25 nm thick walls were obtained. These microcapsules were loaded with Myoglobin, Hemoglobin and Glucose Oxidase by opening capsule pores at low pH and closing them at higher pH. The native structure of the enzyme was not affected due to different treatments. Biocompatible nanoshells were also prepared for encasing DNA. Using the same Layer-by-Layer Self-Assembly approach nanoparticle were constructed containing DNA as one of the layers. The nanoparticles of different architecture were used to deliver …

A High -Order Finite Difference Method For Solving Bioheat Transfer Equations In Three-Dimensional Triple -Layered Skin Structure, Haofeng Yu

Doctoral Dissertations

Investigations on instantaneous skin burns are useful for an accurate assessment of burn-evaluation and for establishing thermal protections for various purposes. Meanwhile, hyperthermia with radiation is important in the treatment of cancer, and it is essential for developers and users of hyperthermia systems to predict, and interpret correctly the biomass thermal and vascular response to heating. In this dissertation, we employ the well-known Pennes' bioheat transfer equation to predict the degree of skin burn and the temperature distribution in hyperthermia cancer treatment.

A fourth-order compact finite difference scheme is developed to solve Pennes' bioheat transfer equation in a three-dimensional single …

Modeling Of The Inverse Heat -Conduction Problem With Application To Laser Chemical Vapor Deposition And Bioheat Transfer, Peng Zhen

Doctoral Dissertations

This dissertation consists of two parts. Part one deals with three-dimensional laser induced chemical vapor deposition (3D-LCVD), whereas part two deals with a Pennes model of a 3D skin structure. LCVD is an important technique in manufacturing complex micro-structures with high aspect ratio. In part one, a numerical model was developed for simulating kinetically-limited growth of an axisymmetric cylindrical rod by pre-specifying the surface temperature distribution required for growing the rod and then by obtaining optimized laser power that gives rise to the pre-specified temperature distribution. The temperature distribution at the surface of the rod was assumed to be at …

Biochemistry Of Hemolysin Toxin Activation By Fatty Acylation: Characterization Of An Internal Protein Acyltransferase, Michael S. Trent

Electronic Theses and Dissertations

Hemolysin toxin produced and secreted by pathogenic Escherichia coli is one of a family of cytolytic, structurally homologous protein toxins known as RTX (repeats in toxin) toxins. RTX toxins are products of a gene cluster, CABD . The A gene product, nontoxic hemolysin (proHlyA) is made toxic by post-translational fatty acylation of two internal lysine residues. HlyC, C gene product, is essential for acylation, and acyl-acyl carrier protein (ACP) is the acyl donor. HlyB and HlyD are involved in secretion of the toxin. HlyC was thought to serve as an internal protein acyltransferase and remained uncharacterized until now. ProHlyA and …

The Influence Of A Human Repetitive Dna On Genome Stability, Eugenia L. Posey

Electronic Theses and Dissertations

A uniquely human interspersed repetitive DNA sequence family, the L2Hs, are highly polymorphic in human genomes. Several features of interspersed repeated DNA may contribute to the instability observed. Certain motifs (direct repeats, palindromes, and inverted repeats) comprising L2Hs elements may adopt unusual secondary structures such as cruciforms or hairpins. These motifs have been associated with features of genome instability in recombination, insertions and deletions. The L2Hs elements also are AT-rich (76%) compared to the bulk of human DNA (52%). That their dynamic nature (i.e. polymorphisms) may arise from recombination, insertions and deletions has led to the hypothesis that the L2Hs …

Endogenous Alkylglycerol Functions As A Mediator Of Protein Kinase C Activity And Cell Proliferation, Fritz G. Buchanan

Electronic Theses and Dissertations

To explore the possibility that 1-O-alkyl-sn-glycerol (alkylglycerol) may serve a regulatory role in the control of cell proliferation or PKC activity, we examined the ability of alkylglycerol to influence PKC activity and subcellular distribution as well as the ability of alkylglycerol to effect cell proliferation. MDCK cells grown to confluence show a loss of PKC activity associated with the membrane, as reported in fibroblasts. Preconfluent cultures of MDCK cells have a high level of PKC activity associated with the membrane. However, treatment of preconfluent cultures with alkylglycerol causes a reduction of PKC activity. A similar inhibition was observed with alkylglycerol …

Factors Influencing The Oxidation Of Lipoproteins And Plasma Lipids, Yanshan Ma

Electronic Theses and Dissertations

The hypothesis that antioxidant vitamins (ascorbate and tocopherols) along with urate protect blood plasma lipids from oxidation was tested. Dietary fat is also an important factor influencing plasma lipid peroxidation. The purpose of this study was to investigate the role of plasma antioxidants and dietary fat on low density lipoprotein (LDL) and plasma lipid oxidation. In the first part of this study, we compared the ability of urate and ascorbate to protect human LDL from in vitro oxidation. LDL oxidation was initiated by 15 mM of a water soluble azo-initiator in the presence or absence of ascorbate or urate. The …

A Characterization Of Extractable, Hydroxylated Fatty Acid Bearing Components In Legionella Pneumophila, Jonathan R. Lane

Electronic Theses and Dissertations

Extraction of the lipids of Legionella pneumophila yields phases unlike those produced from other Gram-negative bacteria. A viscous interface forms between the aqueous (wash) and organic phases. More than half of the hydroxylated fatty acids were found distributed between the aqueous phase and the interfacial material, fractions in which such constituents have not been reported in other Gram-negative species. It was further observed that after the material from the aqueous/interfacial phase was dissolved in methanol or chloroform/methanol (2:1 (V/V)), the addition of acetone would create a white, flocculent precipitate. Analyses showed that the supernatant contained fatty acids that were nonhydroxylated …

A Molecular Basis For Erythromycin Sensitivity And Resistance In Escherichia Coli, Harold S. Chittum

Electronic Theses and Dissertations

The effect of erythromycin on the 50S ribosomal subunit during cell growth has been extensively investigated. Sucrose density gradient analysis of ribosomes formed in the presence and absence of the drug revealed a 50S specific assembly defect is partially responsible for erythromycin's inhibitory effects on wild type cells. Examination of two erythromycin-resistant mutants of E. coli (N281 and N282) revealed that mutant N281 (L22 mutant) but not N282 (L4 mutant) was assembly defective in the presence of the drug, although only at much higher drug concentrations (300 ug/ml vs. 75 ug/ml for wild type cells). The altered genes from each …

Human Lung Mast Cell Tryptase Isozymes: Separation And Examination Of Structural And Functional Differences, Susan S. Little

Electronic Theses and Dissertations

Tryptases are trypsin-like enzymes found in mast cell granules. Although in vivo substrates have not been positively identified, tryptases cleave a limited number of potential physiological substrates in vitro, including high molecular weight kininogen (HMWK) and vasoactive intestinal peptide (VIP). Purified human lung mast cell tryptase (HLT) apparently exists as a tetramer with an M$\sb{\rm r}$ of 135-144 kDa by gel filtration, whereas SDS-PAGE yielded two bands of M$\sb{\rm r}$ 29 Kda and 33 Kda. Tryptases are resistant to inhibition by most natural trypsin inhibitors and display some affinity for heparin. The existence of tryptase isozymes has been implied from …

Probing Protein-Protein Interactions Among Proteins Of A Nonaggregated Fatty Acid Synthetase From Euglena Gracilis Variety Bacillaris, Sande G. Williams

Electronic Theses and Dissertations

Enoyl-acyl carrier protein (ACP) reductase from chloroplast nonaggregated fatty acid synthetase (FAS) of Euglena gracilis variety bacillaris was purified to a single band on a denaturing polyacrylamide gel. The enzyme was partially characterized with respect to substrate specificity, reduced nucleotide requirement, and the effect of ACP and Ca$\sp{++}$ on enzyme activity. Antibodies against the purified protein were raised in hens and isolated from eggs. ACP was purified from Euglena in yields of about 1mg/100g (wet weight) of cells. Antibodies were raised against the purified protein. ACP antibodies inhibited the Euglena chloroplast FAS using Euglena or E. coli ACP as a …

Nitrogen Dioxide Reaction With Proteins: Evidence For Peptide Bond Cleavage At Lysine Residues, Darryl B. Hood

Electronic Theses and Dissertations

Nitrogen dioxide (NO$\sb2$), an air pollutant produced by burning fossil fuels and a component of cigarette smoke, is thought to contribute to the pathogenesis of pulmonary diseases, such as emphysema. To gain information on the mechanism by which NO$\sb2$ damages the lung, in vitro exposures of $\alpha\sb1$-proteinase inhibitor ($\alpha\sb1$-PI), elastin, bovine serum albumin (BSA), human serum albumin (HSA) and synthetic poly-L-lysine were performed. A genetic deficiency of $\alpha\sb1$-PI predisposes humans to emphysema and NO$\sb2$ has been hypothesized to damage $\alpha\sb1$-PI, which would leave proteases such as human neutrophil elastase, (HNE) free to attack lung structural proteins. The ability of $\alpha\sb1$-PI …

Mouse Mast Cell Proteases: Induction, Molecular Cloning, And Characterization, Wei Chu

Electronic Theses and Dissertations

Tryptase, a mast cell-specific serine protease with trypsin-like specificity, has been identified in a mouse mast cell line (ABFTL-6) based on it's enzymatic activity, inhibition properties, and cross-reactivity to a human mast cell tryptase antibody. The effects of fibroblast-conditioned medium and sodium butyrate on ABFTL-6 mast cell differentiation and tryptase expression have been examined. ABFTL-6 mouse mast cells undergo phenotypic changes upon culturing in media supplemented with fibroblast-conditioned media at 50% or 1 mM sodium butyrate. The induced cells increased in size, had larger and more metachromatic cytoplasmic granules, and increased their total cellular protein about four-fold. Tryptase activity increased …

Metabolism Of Arachidonate-Containing Phospholipid Molecular Species In The Murine Macrophage-Like Cell Line, P388d1, Crystal R. Waites

Electronic Theses and Dissertations

Glycerophospholipids of mammalian cells exist as chemically diverse structures with various fatty acids at the sn-1 and sn-2 positions. Arachidonic acid, a polyunsaturated fatty acid, which may be converted to biologically active eicosanoids such as prostaglandins, thromboxanes, and leukotrienes, is found predominantly in the sn-2 position of glycerophospholipids. The purpose of this study was to examine, at the level of the individual molecular species, the incorporation of arachidonate into phospholipids and its release from phospholipids during stimulation. In this way, the specificity of the enzymes controlling arachidonate metabolism could be examined in order to clarify the processes that control the …

A Temperature-Sensitive Mutant Of Escherichia Coli Affected In The Alpha Subunit Of Rna Polymerase, Majid Mehrpouyan

Electronic Theses and Dissertations

A temperature-sensitive mutant of Escherichia coli affected in the alpha subunit of RNA polymerase has been investigated. Gene mapping and complementation experiments placed the mutation to temperature-sensitivity within the alpha operon at 72 min on the bacterial chromosome. The rate of RNA synthesis in vivo and the accumulation of ribosomal RNA were significantly reduced in the mutant at 44$\sp\circ$C. The thermostability at 44$\sp\circ$C of the purified holoenzyme from mutant cells was about 20% of that of the normal enzyme. Assays with T7 DNA as a template showed that the fraction of active enzyme competent for transcription was reduced as a …

Purification And Characterization Of Enoyl-Acp Reductase From Euglena Gracilis, Margie M. Tucker

Electronic Theses and Dissertations

Enoyl-(acyl-carrier-protein) reductase was purified from the phytoflagellate Euglena gracilis. Its purification employed DEAE-Sephacel chromatography, Matrex Orange chromatography, and affinity chromatography using acyl carrier protein (ACP) covalently bound to Sepharose as the affinity ligand. Matrex Orange chromatography resolved two different enoyl-ACP reductases having different characteristics. Euglena gracilis appears to resemble higher plants in the possession of two isoforms of this enzyme. Antibodies specific for the cofactor binding site of NADP (H)-requiring dehydrogenases were obtained. They were isolated from a polyclonal population of antibodies directed against yeast glucose-6-phosphate dehydrogenase by affinity chromatography using chicken liver malic enzyme as the affinity ligand. The …

Variants And Polymorphisms Of Three Repetitive Dna Families In The Human Genome, Robert M. Roudabush

Electronic Theses and Dissertations

A novel 0.6 kb LINE family in human DNA, designated L2Hs, has been described (Musich and Dykes 1986). Studies employing clone N6.4, containing three 0.6 kb segments of this family, indicate that these sequences are interspersed and moderately repetitive. Two additional variant sequences of the L2Hs family, N6.1 and N6.3, have been identified. Restriction mapping of each cloned segment indicates similarities among N6.4, N6.3 and N6.1. When the cloned DNAs were cleaved with restriction enzymes and subjected to cross-hybridization, each cloned insert produced a pattern indicating that the sequences contained in N6.1 and N6.3 are represented in at least one …