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Case Studies Of The Hot Dog-Fold And Acyl-Adenylate-Forming Superfamilies: Characterizing The Importance Of Functional Divergence In Cellular Metabolism, Lucas Zimney
Chemistry and Chemical Biology ETDs
Some of the biggest contributors to cellular respiration (and cellular metabolism in general) are acyl-CoA derivatives, a subclass of biological thioesters. Known to function in a variety of pathways, the regulation of their formation and breakdown are critical, carried about by acyl-CoA synthetases and thioesterases, respectively. The work reported within this dissertation will focus on functional divergence within two enzyme superfamilies -- the hot dog-fold and acyl-adenylate-forming superfamilies — and can be broken down into two main parts. Part one will look at tracking the functional divergence within the hot dog-fold superfamily thioesterases. A highly evolved thioesterase, flK, has been …
Mining Public Databases For Discovery Of Structure And Function Within The Hotdog-Fold Thioesterase And Had Phosphatase Enzyme Families, Sarah Toews Keating
Mining Public Databases For Discovery Of Structure And Function Within The Hotdog-Fold Thioesterase And Had Phosphatase Enzyme Families, Sarah Toews Keating
Chemistry and Chemical Biology ETDs
For my doctoral work, I have developed strategies to mine public databases for data that can be used to infer structural and functional information for the hotdog-fold and HADSF superfamilies. For the hotdog-fold superfamily, I used curated and automatically applied annotations of structure, taxonomic lineage, function, and subfamily membership from the UniProtKB, gene context and taxonomic information from the NCBI, and the results of several in-depth explorations of subfamily/function and structural class membership. Based on the distribution of the aforementioned annotations mapped onto a sequence similarity network (SSN), I applied structural assignments to sequences and/or specific function/subfamily assignments to ~143,000 …
Design, Synthesis And Evaluation Of Bivalent Inhibitors Of Trehalose-6-Phosphate Phosphatase, Chunliang Liu
Design, Synthesis And Evaluation Of Bivalent Inhibitors Of Trehalose-6-Phosphate Phosphatase, Chunliang Liu
Chemistry and Chemical Biology ETDs
The D-glucose disaccharide α, α-D-trehalose is synthesized by a variety of bacteria, fungi, plants and invertebrates to support cell survival by functioning as a fuel, a metabolic regulator or a protectant against environmental stress. Five different trehalose biosynthetic pathways are known to exist, one of which, the OtsA/OtsB pathway is common among pathogenic bacteria and fungi and is also found in parasitic nematodes. Previously reported otsA and otsB gene knockout (or knockdown) experiments have shown that both pathway enzymes are essential for M. tuberculosis cell growth and host colonization. RNAi gene silencing carried out in the nematode model system Caenohabditis …
The Electronic Structure Of The Pyranopterin Dithiolene Cofactor And Radical Reporters Of Excited State Interactions, Benjamin William Stein
The Electronic Structure Of The Pyranopterin Dithiolene Cofactor And Radical Reporters Of Excited State Interactions, Benjamin William Stein
Chemistry and Chemical Biology ETDs
Crystal structures of multiple molybdenum enzymes clearly demonstrate interesting structural distortions involving the pyranopterin dithiolene. These distortions can be correlated with pyranopterin oxidation state through the use of DFT geometry optimized structures of the possible oxidation states, and these are correlated with enzyme family. The potential role of the pyranopterin dithiolene in electron transfer in the varied enzyme familes has been explored through the use of non-equilibrium Green's function (NEGF) electron transport calculations. These calculations demonstrate clear differences in electron transport behavior as a function of pyranopterin oxidation state. The Jahn-Teller effect can strongly impact the geometric and electronic structures …
Electrochemical Investigation Of Homogenous Species At An Electrode Interface, Christopher Larsen Iii
Electrochemical Investigation Of Homogenous Species At An Electrode Interface, Christopher Larsen Iii
Chemistry and Chemical Biology ETDs
CO2 reduction is a pressing problem worldwide, and one obstacle in the electrochemical conversion of CO2 to more useful C1 products such as methanol and formic acid is the kinetic barrier known as overpotential. The overpotential of rearranging the nuclei in CO2 to accommodate electron transfer can be lowered by pre-bending the CO2 molecule in an adduct-mediated complex. The work presented in Part I utilizes a combination of hard and soft donors on pincer-like ligands to effect the bending of CO2 prior to electrochemical reduction. A large majority of the work consists of using Group 4 metallocenes, but Chapter 3 …
Spectroscopic And Computational Studies Of Molybdenum Enzymes And Models, Chao Dong
Spectroscopic And Computational Studies Of Molybdenum Enzymes And Models, Chao Dong
Chemistry and Chemical Biology ETDs
In this dissertation spectroscopic methods such as electronic absorption (EAS), resonance Raman (rRaman), electron paramagnetic resonance (EPR), and MCD spectroscopies have been used in combination with DFT calculations for the interpretation of experimental results. These methods have been used to investigate the molybdenum coordination environment in enzymes and model complexes. Xanthine oxidase (XO), one of the canonical molybdenum enzyme families, hydroxylizes heterocyclic substrates by inserting an oxygen atom from molybdenum-activated water into a substrate C-H bond. This generates reducing equivalents that pass through two iron sulfur clusters and then to FAD, where oxidation of the FAD takes place. In this …
Study Of Novel Synthetic Methodologies For Indolyl Derivatives And Beta-Fluoroenals, Xiaobei Chen
Study Of Novel Synthetic Methodologies For Indolyl Derivatives And Beta-Fluoroenals, Xiaobei Chen
Chemistry and Chemical Biology ETDs
One of the central goals in modern organic synthesis is to develop efficient synthetic strategies for the preparation and study of complex molecules possessing interesting structural, biological, and physical properties. Toward this end, my Ph. D. work focuses on the development of novel synthetic methodologies for the facile construction of synthetically and biologically significant molecular architectures. The tert-prenylated indoles and indolines are widely present in a large collection of natural products and biologically active compounds. Although significant efforts have been made on the development of efficient methods to prepare these intriguing molecular architectures, few methods have been explored to introduce …