Physical Sciences and Mathematics Commons^™

A Control Switch For Prothrombinase: Characterization Of A Hirudin-Like Pentapeptide From The Cooh Terminus Of Factor Va Heavy Chain That Regulates The Rate And Pathway For Prothrombin Activation, Michael A. Bukys, Paul Y. Kim, Michael E. Nesheim, Michael Kalafatis

Chemistry Faculty Publications

Membrane-bound factor Xa alone catalyzes prothrombin activation following initial cleavage at Arg(271) and prethrombin 2 formation (pre2 pathway). Factor Va directs prothrombin activation by factor Xa through the meizothrombin pathway, characterized by initial cleavage at Arg(320) (meizo pathway). We have shown previously that a pentapeptide encompassing amino acid sequence 695-699 from the COOH terminus of the heavy chain of factor Va (Asp-Tyr-Asp-Tyr-Gln, DYDYQ) inhibits prothrombin activation by prothrombinase in a competitive manner with respect to substrate. To understand the mechanism of inhibition of thrombin formation by DYDYQ, we have studied prothrombin activation by gel electrophoresis. Titration of plasma-derived prothrombin activation …

Phosphorus-31 Nmr Of The Intact Crystalline Lens: I. The Living Lens Spectrum. Ii. The Spectroscopic Effects Of Deuterium Oxide Incubation, Thomas Glonek, Stephen J. Kopp, Jack V. Greiner

President's Research

Spectra of intact bovine and canine crystalline lenses in vitro at 37°C were generated using phosphorus-31 nuclear magnetic resonance (NMR). Lens incubation in a pure D2O buffer results in a progressive narrowing of the tissue P-31 NMR signals.

Attachment Of Motile Bacterial Cells To Prealigned Holed Microarrays, Sergey Rozhok, Zhifang Fan, Dorjderem Nyamjav, Chang Liu, Chad A. Mirkin, Richard C. Holz

Chemistry Faculty Research and Publications

Construction of biomotors is an exciting area of scientific research that holds great promise for the development of new technologies with broad potential applications in areas such as the energy industry and medicine. Herein, we demonstrate the fabrication of prealigned microarrays of motile Escherichia coli bacterial cells on SiOx substrates. To prepare these arrays, holed surfaces with a gold layer on the bottom of the holes were utilized. The attachment of bacteria to the holes was achieved via nonspecific interactions using poly-l-lysine hydrobromide (PLL). Our data suggest that a single motile bacterial cell can be selectively attached to an individual …

Incorporation Of Capillary-Channeled Polymer (C-Cp) Fibers Into Micropipette Tips For Solid Phase Extraction With Applications In Bioanalysis, Donald Fornea

All Theses

Solid phase extraction (SPE), is a widely used sample preparation method that is currently experiencing a surge in research interest, clever architecture/format development, and stationary phase characterization.1-3 SPE devices commonly exist in syringe, cartridge, disk, and micropipette tip formats.4 Micropipette tip SPE has enhanced the determination of proteins by electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI) mass spectrometry (MS) by handling micro-liter volumes of sample and buffer removal/solvent exchange.5-7 Buffers have deleterious effects on ionization taking place in MS sources due to preferential ionization, ion suppression effects, and the formation of adduct species competing for ionization in …

Biomass Burning And Anthropogenic Sources Of Co Over New England In The Summer 2004, Carsten Warneke, J. A. De Gouw, A. Stohl, O. R. Cooper, P. D. Goldan, W. C. Kuster, J. S. Holloway, E. J. Williams, B. M. Lerner, S. A. Mckeen, M. Trainer, F. C. Fehsenfeld, E. L. Atlas, Stephen G. Donnelly Ph.D., Verity Stroud, Amy Lueb, S. Kato

Chemistry Faculty Publications

During the summer of 2004 large wildfires were burning in Alaska and Canada, and part of the emissions were transported toward the northeast United States, where they were measured during the NEAQS-ITCT 2k4 (New England Air Quality Study-Intercontinental Transport and Chemical Transformation) study on board the NOAA WP-3 aircraft and the NOAA research vessel Ronald H. Brown. Using acetonitrile and chloroform as tracers the biomass burning and the anthropogenic fraction of the carbon monoxide (CO) enhancement are determined. As much as 30% of the measured enhancement is attributed to the forest fires in Alaska and Canada transported into the region, …

Perfluoroalkyl (Aryl) Sulfonimide Zwitterions, Hua Mei

All Dissertations

This research focuses on superacid perfluoroalkyl(aryl) sulfonimides and their derivatives as a source of stable zwitterionic salts. The strong resonance stabilization of sulfonimides imparts unexpected stability to the zwitterions.
Two types of zwitterions were investigated. The first are symmetrical diaryliodonium zwitterions (DZs) as potential photo acid generators (PAGs) for microlithography. Driven by the demand for smaller feature sizes in the microelectronics industry, microlithography using shorter wavelength light has evolved and new PAGs are of interest. New DZs are potentially useful because they have good thermal stability and may be structurally modified to alter their spectral absorption characteristics. As an extension …

Characterization Of Capillary-Channeled Polymer Fibers As Stationary Phases For High-Performance Liquid Chromatography Of Macromolecules, Dwella Nelson

All Dissertations

Capillary-channeled polymer (C-CP) fibers are being developed and characterized as high-performance liquid chromatography (HPLC) stationary phases for reversed-phase separations of proteins. Conventional porous phases are not well suited for separating large macromolecules due to the slow diffusivity of the molecules, large diffusional distances, and stagnant mobile phase zones within the column. Stationary phases are continually being developed to address the challenges associated with HPLC of proteins and other macromolecules in general. C-CP fiber stationary phases are an alternative to conventional bead technology and offer a variety of chemical and physical advantages. The fibers can be selected for their chemical functionality …

Path Integral Formulation Of Langeinv Dynamics With Applications To Rare-Event Systems, Bradley Dickson

All Dissertations

In the last decade great efforts have been made to efficiently study the behaviors of rare-event systems. The methods and theories developed in pursuit of this goal are far from unified and are instead applied on a case-by-case basis where one makes a best educated guess as to which approach may afford the greatest chance of studying the rare-event system in question. The work contained here is directed at further development of one of these sets of methods and theories. Specifically, a new theory of dynamics in the Langevin path space is developed with emphasis on generating and sampling Langevin …

Selective Recognition Of Quadruplex Dna By Small Molecules, Elizabeth W. White

Chemistry Dissertations

Structure-specific recognition of nucleic acids is a promising method to reduce the size of the recognition unit required to achieve the necessary selectivity and binding affinity for small molecules. It has been demonstrated recently that G-quadruplex DNA structures can be targeted by organic cations in a structure-specific manner. Structural targets of quadruplexes include the planar end surfaces of the G-tetrad stacked columns as well as four grooves. The significant structural differences between quadruplex DNA and duplex DNA make quadruplex DNA a very attractive target for highly selective, structure-specific drug design. We have used a variety of biophysical techniques including circular …

Insights Into Sulfonated Phthalocyanines; Insights Into Anionic Tetraaryl Porphyrins; Irradiation Of Cationic Metalloporphyrins Bound To Dna, Anila Fiaz Gill

Chemistry Dissertations

Sulfonated porphyrins and phthalocyanines have been under consideration as microbicides, compounds which, when used in a topical formulation, can prevent transmission of the human immunodeficiency virus. Our studies have been directed toward the characterization of members of these classes. For the sulfonated phthalocyanines, matrix-assisted laser desorption/ionization (MALDI) mass spectrometry was helpful in determining the extent of sulfonation. We present the first report of spectroscopic characterization of a pentasulfonated phthalocyanine. Capillary electrophoresis data were sensitive to the concentration of the compounds (Chapter 1). Mass spectrometry was also very useful for establishing the extent of sulfonation in series of sulfonated porphyrins. Capillary …

Synthesis Of Boronic Acid Based Sensors For Glucose And Sialic Acid And Synthesis Of Novel And Selective Pde4 Enzyme Inhibitors, Gurpreet Kaur

Chemistry Dissertations

The boronic acid functional group is known to bind compounds with the diol group tightly and reversibly in aqueous environment and has been used as a recognition moiety for the design of carbohydrate sensors. The first chapter of the dissertation studies the synthesis and substitution effect on the affinity and selectivity of a known boronic acid-based glucose sensor. In such a sensor design effort, the availability of a signaling event, whether it is fluorescence or UV, is crucial. The second chapter studies the detailed mechanism on how a well-known fluorescent boronic acid compound changes fluorescent properties upon binding. A new …

Syntheses And Dna Interactions Of Acridine And Phenothiazine Based Photosensitizers, Beth Wilson

Chemistry Dissertations

Photosensitizing molecules and/or metal complexes that interact with DNA via intercalation and groove binding have potential applications as molecular structural probes, as footprinting reagents and in photodynamic therapeutics. To this regard, small molecules that bind to DNA and the energetics involved in these interactions, acridine-based therapeutics, photosensitization, photodynamic therapy, phenothiazine-mediated photosensitization, DNA photocleavage reaction mechanisms and photosensitizing metal complexes are introduced in Chapter I. Next, in Chapter II, the synthesis of a photonuclease consisting of a 3,6-acridinediamine chromophore attached to four metal-coordinating imidazole rings is described. The DNA photocleavage yields, emission quantum yields, and thermal denaturation studies by this acridine-imadazole …

Development Of Polymer Monoliths For The Analysis Of Peptides And Proteins, Binghe Gu

Theses and Dissertations

Several novel polymer monoliths for the analysis of peptides and proteins were synthesized using polyethylene glycol diacrylate (PEGDA) as crosslinker. Photo-initiated copolymerization of polyethylene glycol methyl ether acrylate and PEGDA yielded an inert monolith that could be used for size exclusion liquid chromatography of peptides and proteins. This macroscopically uniform monolith did not shrink or swell in either water or tetrahydrofuran. More importantly, it was found to resist adsorption of both acidic and basic proteins in aqueous buffer without any organic solvent additives. A strong cation-exchange polymer monolith was synthesized by copolymerization of 2-acrylamido-2-methyl-1-propanesulfonic acid (AMPS) and PEGDA. A ternary …

Synthesis And Optical Properties Of Four Oligothiophene-Ruthenium Complexes And Synthesis Of A Bidentate Ligand For C-F Bond Activation, Joseph S. Bair

Theses and Dissertations

Photovoltaic cells and fluorescence sensing are two important areas of research in chemistry. The combination of photon-activated electron donors with electron acceptors provides a strong platform for the study of optical devices. A series of four oligothiophene-ruthenium complexes has been synthesized. Variation in oligothiophene length and bipyridine substitution allowed comparison of these variables on electronic properties. The longer oligothiophenes display lower energy absorption and emission compared to the shorter ones. Aromatic conjugation appears more complete with para-, rather than meta-, substitution. Oligothiophenes and Ru(bpy)32+ are highly fluorescent individually, but fluorescence is quenched when connected. Bonds of carbon to fluorine are …

The Effect Of Mobile Phase Composition And Temperature On The Adsorption Behavior Of Tryptophan, Tarab Jamil Ahmad

Doctoral Dissertations

Single-component adsorption isotherm data were acquired by frontal analysis for tryptophan on a C₁₈-Kromasil packed column, using acetonitrile-water solutions of various compositions (2.5, 5, and 7.5% ACN + 1% ACOH). These isotherms have a complex behavior, exhibiting at least one clear inflection point at an intermediate concentration and, possibly, another such point, close to the origin. The isotherm for 2.5 % ACN has the strongest curvature. At high concentrations, all these isotherms tend toward a limit, showing that the adsorbent has a finite saturation capacity. At low concentrations, these isotherms seem to exhibit langmuirian behavior. The isotherm model …

Thermodynamic And Neutron Structural Studies Of Hydrocarbon Adsorption On Mgo Nanocubes, Richard E. Cook

Doctoral Dissertations

Presented is a series of thermodynamic and neutron scattering experiments used to probe the nature of the hydrocarbon - MgO (100) interaction. High-resolution volumetric isotherms are used to probe the wetting, layer transitions, heats of adsorption, two-dimensional compressibilities, and identify possible phase transitions of thin films of benzene, ethane, and n - pentane on MgO powders. Neutron diffraction experiments were used to probe the structure and identify any phase transitions within monolayer films of ethane, butane and n -pentane.

Benzene adsorption, while showing no visible layering steps, shows a shift in the shape of the isotherm for p/p_o > 0.7. …

Characterization Of Aβ Aggregates Using Hydrogen/Deuterium Exchange Mass Spectrometry, Maolian Chen

Doctoral Dissertations

The work presented in this dissertation aimed to localize the hydrogen-bonding interaction sites within Aβ aggregates associated with Alzheimer’s disease using hydrogen/deuterium exchange mass spectrometry (HDX-MS) coupled with proteolysis. Toward this end, an on-line digestion system utilizing a triaxial electrospray probe as the front end to MS was developed. Using this approach, regions of Aβ(1-40) fibrils and protofibrils that are protected from HDX have been identified. The HDX data show that the C-terminal segment 35-40 and the N-terminal segment 1-19 are highly exposed to exchange in both fibrils and protofibrils, while the internal fragment 20-34 is highly protected from exchange …

Direct Integration Of Surface Enhanced Raman Spectroscopy As A Detection Mode For Microfluidic Separations And Fluid Handling: Μfluidic-Sers, Raynella Magdalene Connatser

Doctoral Dissertations

The arena of microfluidics (µfluidics) has grown over the past decade to encompass myriad separation techniques and exploit copious detection modes. The direct integration of a vibrational spectroscopic detection technique, rich with structural information, onto a platform that is portable and potentially highly controllable such as µfluidics, could offer redress for some of the problems inherent in many of the electrophoretically driven separations carried out on said devices. Herein, this direct integration is explored, and methods of device fabrication, spectroscopic data collection conditions, analytical figures of merit of the detection technique, and separations method development results are discussed. The creation …

The Reaction Of Telechelic Polymers At Multicomponent Interfaces: A Molecular Loop Study, James Kevin Rice

Doctoral Dissertations

The work presented in this dissertation attempts to form an understanding of the reaction parameters that govern the reaction of telechelic polymers to form multiply bound polymer chains, resulting in polymer loop formation, at both soft and hard polymeric interfaces. Both theoretical and experimental studies offer evidence that blocky copolymers, as opposed to random or alternating morphologies, are the best compatibilizers of a given polymer blend system. This has been attributed to the fact that blocky copolymers spread across the interface, with each block lying in or near the homopolymer region in which it is miscible, effectively “stitching” the interface …

Multiple Approaches To The Separation Of Amino Acids And Biologically-Relevant Compounds, Lance Andrew Riddle

Doctoral Dissertations

The branch of analytical chemistry known as separations has continued to grow and expand ever since its beginnings a century ago. With all the technological advances occurring to make separations a more powerful technique, the main goal continues to be the desired separation of the compounds of interest in a mixture. Although a desired separation may be achieved, there can always be room for improvement with regards to the time necessary for the separation as well as better resolution of closely-related species as well as enantiomers of the same analyte.

In this work, a variety of separation methods and variations …

Synthesis And Radiolabeling Of Potassium Trifluoroborate Benzylidene Anabaseine Derivatives, Aaron Landon Smith

Doctoral Dissertations

Anabaseine has demonstrated a high, non-selective, affinity for the α7- bungarotoxin sensitive neuronal nicotinic acetylcholine receptor binding site found in small cell lung carcinoma. The benzylidene anabaseine derivatives of anabaseine have shown a selective affinity for these binding sites. These studies suggest that radiolabeled benzylidene anabaseine derivatives could act as potential imaging agents to aid in the early detection of lung cancer.

This dissertation outlines the strategy and methods employed in the synthesis of a family of potassium trifluoroborate derivatives of benzylidene anabaseine and their subsequent halogenation. Two of the trifluoroborate salts were converted to their radiolabeled analogues for potential …

Tb195: Element Concentrations In Maine Forest Vegetation And Soils, Chandra J. Mcgee, Ivan J. Fernandez, Stephen A. Norton, Constance S. Stubbs

Technical Bulletins

Bioaccumulation of trace metals in plant tissues can present a health risk to wildlife, and potentially to humans. The Passamaquoddy Tribe in Maine was concerned about health risks of cadmium (Cd) because of a health advisory for moose liver and kidney consumption due to high Cd levels. In addition to Cd, this study evaluated concentrations of aluminum (Al), calcium (Ca), copper (Cu), iron (Fe), potassium (K), magnesium (Mg), manganese (Mn), nickel (Ni), phosphorus (P), lead (Pb), and zinc (Zn) in four common terrestrial moose-browse species, associated forest soils, and two species of aquatic vegetation on Passamaquoddy tribal land in eastern …

Adsorption Of Small Molecules On Mgo And Graphite, Peter Nikolaivich Yaron

Doctoral Dissertations

The physical adsorption of molecules on metal oxide surfaces has direct implications in a number of industrial applications such as; catalysis, electronics, and fuel cells to name a few. Despite the large number of adsorption studies to date, only a small number of systems can be explained with the most advanced ab initio calculations currently available.

One of the simplest metal oxide systems to study is magnesium oxide due to its simple cubic rock-salt structure. Using a patented method, nearly defect-free MgO cubes can be synthesized with a narrow size distribution exposing exclusively the (100) equilibrium crystal face. The use …

Expression And Characterization Of Hyperthermophilic Aqujfex Pyrophilus Flagellin Protein In Mesophilic Bacterial Systems, Srivani V. Mukkamala

Masters Theses

The structural protein flagellin, FlaA derived from hyperthermophilic Aquifex pyrophilus, a rod shaped eubacterial species that grows near hydrothermal vents at an optimum growth temperature of 85 °C forms elongated thermostable flagella nanotubes. FlaA was successfully over-expressed for the first time using pET28c plasmid in E. coli BL21 cells at 37 °C. The protein was isolated from inclusion bodies that were solubilized by alkaline pH, refolded by dialysis and purified by chromatographic techniques. The FlaA was characterized by fluorescence, light scattering and circular dichroism. The FlaA was not in the correct folded form to form flagella as efforts to …

Generating New Specific Rna Interaction Interfaces Using C-Loops, Kirill A. Afonin, Neocles B. Leontis

Chemistry Faculty Publications

New RNA interaction interfaces are reported for designing RNA modules for directional supramolecular self-assembly. The new interfaces are generated from existing ones by inserting C-loops between the interaction motifs that mediate supramolecular assembly. C-Loops are new modular motifs recently identified in crystal structures that increase the helical twist of RNA helices in which they are inserted and thus reduce the distance between pairs of loop or loop-receptor motifs from 11 to 9 base-stacking layers while maintaining correct orientation for binding to cognate interaction interfaces. Binding specificities of C-loop-containing molecules for cognate molecules that also have inserted C-loops were found to …

Incorporating Electron-Transfer Functionality Into Synthetic Metalloproteins From The Bottom-Up, Jing Hong, Olesya A. Kharenko, Michael Y. Ogawa

Chemistry Faculty Publications

The alpha-helical coiled-coil motif serves as a robust scaffold for incorporating electron-transfer (ET) functionality into synthetic metalloproteins. These structures consist of a supercoiling of two or more R helices that are formed by the self-assembly of individual polypeptide chains whose sequences contain a repeating pattern of hydrophobic and hydrophilic residues. Early work from our group attached abiotic Ru-based redox sites to the most surface-exposed positions of two stranded coiled-coils and used electron-pulse radiolysis to study both intra- and intermolecular ET reactions in these systems. Later work used smaller metallopeptides to investigate the effects of conformational gating within electrostatic peptide-protein complexes. …

Synthesis And Characterization Of Complex Polymer Architectures, Brandon Scott Farmer

Doctoral Dissertations

Anionic polymerization based upon high vacuum technique has been used to synthesize different star polymers using varying linking techniques. In particular chlorosilanes, divinylbenzene, and polyhedral oligomeric silsesquioxane (POSS) chlorosilane derivatives were used in the synthesis of star polymers. These polymers, along with polymers synthesized by others, have been characterized by a range of methods in this work.

A series of polyisoprene (PI) stars were synthesized from dimethylaminopropyllithium (DMAPLi) and subsequently hydrogenated to form poly (ethylene-co-propylene) (PEP) these were characterized by size exclusion chromatography (SEC) coupled with online two angle laser light scattering (TALLS). These polymers were synthesized in an attempt …

Regulation Of A Dna-Compacting Plastid Nucleoid Protein, Steven William Adamson

Dissertations

DCP68, a DNA-compacting nucleoid protein, was further characterized in order to understand how plastid nucleoid proteins affect the structure and function of chloroplast DNA. Previously, DCP68 was identified as ferredoxin: sulfite reductase, an enzyme that participates in reductive sulfur assimilation and inhibits chloroplast DNA replication and transcription in vitro [1, 2]. In this study, the portion of SiR that was found to be present in soluble and plastid nucleoid-enriched fractions indicated that most SiR was stromal in Arabidopsis and soybean plants. Although SiR was detected in Arabidopsis chloroplast nucleoid-enriched fractions, the study of nucleoid dynamics proved to be difficult due …

The Proteomics Of N-Terminal Methionine Cleavage, Frédéric Frottin, Aude Martinez, Philippe Peynot, Sanghamitra Mitra, Richard C. Holz, Carmela Giglione, Thierry Meinnel

Chemistry Faculty Research and Publications

Methionine aminopeptidase (MAP) is a ubiquitous, essential enzyme involved in protein N-terminal methionine excision. According to the generally accepted cleavage rules for MAP, this enzyme cleaves all proteins with small side chains on the residue in the second position (P1′), but many exceptions are known. The substrate specificity of Escherichia coli MAP1 was studied in vitro with a large (>120) coherent array of peptides mimicking the natural substrates and kinetically analyzed in detail. Peptides with Val or Thr at P1′ were much less efficiently cleaved than those with Ala, Cys, Gly, Pro, or Ser in this position. Certain residues …

Statistical Thermodynamics And Kinetics Of Dna Multiplex Hybridization Reactions, Albert S. Benight, M. T. Horne, D. J. Fish

Chemistry Faculty Publications and Presentations

A general analytical description of the equilibrium and reaction kinetics of DNA multiplex hybridization has been developed. In this approach, multiplex hybridization is considered to be a competitive multichannel reaction process: a system wherein many species can react both specifically and nonspecifically with one another. General equations are presented that can consider equilibrium and kinetic models of multiplex hybridization systems comprised, in principle, of any number of targets and probes. Numerical solutions to these systems for both equilibrium and kinetic behaviors are provided. Practical examples demonstrate clear differences between results obtained from more common simplex methods, in which individual hybridization …