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This dissertation presents studies by magnetization, dc magnetic susceptibility and EPR spectroscopy on several new spin-frustrated polyoxometalate (POM) lattices of increasing spin sizes and complexities. Measurements have been made...
The mammalian olfactory bulb (OB) has a vast population of dopamine (DA) neurons, whose function is to increase odor discrimination through mostly inhibitory synaptic mechanisms. However, it is not well understood whether there is more...
This dissertation attempts to provide insight into the mixing, hydration and annealing of self-assembled, multilayered films based on precise counting of their doping ions and water content. Several practical applications are then...
Integrin signaling is critical for many biological functions including cell survival, cell migration, development, immunity and wound healing. Integrins perform their function through a structural change that is propagated from the...
Tissue engineering is one of the fastest growing biotechnology industries. The overarching research goals of the tissue engineering industry are highly intertwined with the field of medicine. The tissue engineering field seeks to create...
Diphtheria toxin repressor is a regulatory protein from Corynebacterium diphtheriae, the causal agent of Diphtheria. The diphtheria toxin repressor (DtxR) contains an SH3-like domain that forms an intramolecular complex with a proline...
Small nucleolar RNAs (snoRNAs) are localized in the nucleolus as small ribonucleoprotein particle (snoRNP) that are RNA-protein complexes and catalyze site specific modifications on the ribosomal RNA. When compared to many protein...
All functional RNAs contain post-transcriptionally modified nucleotides. 2'-O-ribose methylation and pseudouridylation are the two major types of modifications, which occur by box C/D and box H/ACA ribonucleoprotein (RNP) complexes, ...
Muscle contraction is regulated at the thin filament level by tropomyosin (Tm) and the troponin complex (Tn). Tm is an α-helical coiled coil protein that forms a continuous strand on the actin filament through end-end interactions with...
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) offer an adaptive immune system that protects bacteria and archaea from nucleic acid invaders through an RNA-mediated nucleic acid cleavage mechanism. Our knowledge of...
Two-dimensional gel electrophoresis (2-DE) is used to compare the protein profiles of different crude biological samples. Narrow pH range Immobilized pH Gradient (IPG) strips were designed to increase the resolution of these separations....
Reproduced with permission from Journal of the American Chemical Society, submitted for publication. Unpublished work copyright 2008 American Chemical Society. The development of ternary nanoscale materials with controlled cross...
Orientational restraints resulting from a wide range of anisotropic nuclear spin interactions such as chemical shifts, heteronuclear dipolar interactions, and quadrupolar interactions, have been widely used for determining the structures...
Considerable attention has recently been given to the preparation of the ciguatoxins, the major group of toxins implicated with the onset of ciguatera fish poisoning (CFP) – a seafood-borne illness associated with the consumption of reef...
This thesis analyzes the structure and function of enzymes involved in the biosynthesis of the tetrapyrrole cofactor, siroheme, a critical cofactor used in sulfur and nitrogen metabolism in plants, bacteria, and some archaea. The...
The properties of proteins with reduced sequence complexity--either in the form of primary structure symmetry or restricted amino acid alphabets--are controversial. Studies of protein biophysics and sequence analyses suggest that...
IdeR is an iron-dependent repressor protein, one of the essential proteins found in Mycobacterium tuberculosis. IdeR is a homologue of the diphtheria toxin repressor (DtxR). IdeR controls iron acquisition and storage, moreover it binds...
Molecules containing the phosphate (O—PO32-) moiety are ubiquitous in biochemistry. Phosphoryl transfer reactions that break and form the O—P phosphoryl bond are central to biological processes as diverse as energy metabolism and signal...
M2 is an important drug target, this transmembrane protein forms a tetrameric proton channel essential for the life cycle of the Influenza A virus. The recent S31N mutation rendered this protein resistant to the used antiviral drugs, ...
Oxidoreductase enzyme complexes are one of the known biomolecular machines, which play a crucial role in cellular biochemistry including metabolic, signaling, and electron transport pathways. In these complexes, individual subunits can...
In Chapter I, the photochemistry of enediynes is reviewed. Photo-Bergman cyclization, C1-C5 photocyclization and other photochemical reactions of alkynes in the enediyne moiety are discussed. DNA cleavage by photochemically activated...
Xeroderma Pigmentosum (XP) is an autosomal recessive disorder characterized by extreme sensitivity to sunlight, higher incidence of skin cancers, pigmented alterations in the skin, and in some cases neurological abnormalities. XP is...
Protein residue ionization often plays a vital role in protein function, such as enzyme catalysis and pH-dependent structural changes. Inadequate conformational and protonation state sampling in molecular dynamics (MD) simulations has...
Hydrogen/Deuterium Exchange Monitored by Liquid Chromatorgaphy Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry—Method Optimization and Applications to the Study of Protein Conformation and Protein—Drug Interactions
Proteins are the most versatile macromolecules in the cell. Major biochemical functions of proteins include binding; catalysis; and serving as structural components of cells and organisms. Proteins are made of amino acids that are...
In eukaryotes and archaea 5-25% of transfer RNA (tRNA) precursors contain intervening sequences, or introns, that interrupt the molecules' functional regions. Because functional tRNA molecules are necessary for protein synthesis, ...
As an RNA-guided RNA modification enzyme, the box H/ACA RNP recruits the guide RNA to recognize the substrate RNA, whereas the protein partners carry out the catalysis. Most intriguingly, box H/ACA RNPs share the same four conserved...
The current treatment for hepatitis C virus (HCV) consists of a combination therapy of alpha interferon (IFN-alpha) and ribivirin (RBV). Due to IFN resistance and side effects, new classes of drugs are needed to combat HCV infection....
The cerebral cortex is a thin folded sheet of neural tissue forming the outmost layer of the cerebrum (brain). Several biological hypotheses have suggested dierent mechanisms involved the development of its folding pattern into sulci ...
Ultrathin films consisting of an alternating sequence of positively and negatively charged polyelectrolytes have been prepared by means of the electrostatic layer-by-layer sequential assembly technique. To augment their typical...
Notch signaling plays an important role in tissue differentiation and remodeling and has been extensively studied. Much has been learned about the Notch signaling pathway and consequences of defects within the path, yet little is...
Reversible protein phosphorylation plays an integral role in the regulation of eukaryotic cellular signaling, especially for transcription factors. Yin Yang 1 (YY1) is a ubiquitously expressed and highly conserved multifunctional...
Vortex waves are striking spatial-temporal patterns and observed in diverse systems, such as active galaxies, catalytic reactions, and even biological systems. In the heart, vortex patterns of electrical waves are linked to ventricular...
One of the primary contributors to protein structure and functioning in biological systems is the electrostatic environment experienced by the protein. This environment is caused by charged and polar chemical interactions, with the...
Manual Nuclear Magnetic Resonance (NMR) spectral analysis of proteins is a time intensive effort with methods often specific to each analysis. The method described in this thesis automates the resonance assignment of protein side chains...
Myosin activity and actomyosin interaction play key roles in normal and pathological cardiac muscle contraction. Factors that modulate actomyosin have the potential to exert changes in cardiac contraction that may be necessary for normal...
The Adeno-Associated Virus has moved to the forefront as a vector for human gene therapy. Vectors have been constructed with AAV to repair many genetic deficiencies such as cystic fibrosis and hemophilia and have demonstrated remarkable...
This dissertation describes the synthetic utility of tandem addition / C-C bond cleavage reactions of vinylogous acyl triflates. The first chapter provides background into carbon-carbon bond breaking reactions that have been applied in...
Radical Fragmentations: From Conformational Control of Enediyne Reactivity to 1,2-C,O Transposition and Metal-Free Synthesis of Benzoates and Benzamides from Phenols
The work described in this thesis is a demonstration of how theory and experiment can be used side by side in developing research in organic chemistry, from mechanistic studies to the design of new reactions. In chapter one we describe a...
This dissertation describes the synthesis and characterization of two new compounds that are among the most studied materials in solid state chemistry over the past eight or so years. The compounds investigated are [Mn12O12(CH3COO)16(H2O...
The venom of spider Plectreurys tristis contains a variety of peptide toxins that selectively target neuronal ion channels. O-palmitoylation of a threonine or serine residue, along with a characteristic and highly constrained disulfide...
The scope of this dissertation is two-fold: assembly of histidine-tagged peptides and proteins directly to the surface of a 1.5 nm AuNP and the assembly and delivery of nano-medical materials for MR imaging and gene therapy. Chapter 1 is...
Structural biology has been successful in the characterization of soluble protein, which has given insight in the inner working of several thousands of proteins. However, structural characterization of proteins has been limited in two...
Small helical membrane proteins are functionally very important. They are involved in many cellular transport and signal transduction pathways maintaining the chemical, mechanical and electrical potentials of cells. They constitute...
Hydrogen peroxide (H2O2) regulates an array of physiological functions and acts as a second messenger at low levels. However, the elevation of these levels can lead to oxidative stress, a state that is implicated in the progression of...
A critical consideration in the process of de novo protein architecture design and protein evolution is the folding pathway and behavior a protein undertakes in transitioning to its functional tertiary structure. Of particular interest...
Determining the Solution Conformational Entropy of Oligosaccharides: Isolating the Effects of Anomeric Configuration, Glycosidic Linkage, Degree of Polymerization, Linearity versus Cyclicity and Hydrogen Bonding
Oligosaccharides have various fundamental roles, ranging from providing nutritional and flavoring support to being involved in fertilization and parasite infection processes. Maltooligosaccharides are used heavily in the food and...
Scientists have used computers to model a plethora of systems since the rise of the computer age. The most common use of modeling is to analyze an existing system. With a complete model of an existing system the parameters can be changed...
Proteins, polymer chains comprised of amino acids, are one of the fundamental machines that drive life. They perform a wide variety of functions within the cell such as nutrient transport, cell signaling, energy production, DNA repair, ...
The development and experimental validation of a mathematical model for nanoparticle–based surface energy transfer (SET) between gold nanoparticles and fluorescent dye labels, has enabled biophysical studies of nucleic acid structure and...
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