Theses and Dissertations
This collection includes both ASU Theses and Dissertations, submitted by graduate students, and the Barrett, Honors College theses submitted by undergraduate students.
Hybrid metalloproteins incorporating synthetic organometallic active sites within a protein scaffold are being researched as viable catalysts for the production of hydrogen fuel. Our group and others have shown that the incorporation of cobalt protoporphyrin IX in cytochrome b₅₆₂ yields artificial enzymes that reduce protons to molecular hydrogen in the presence of photoinductive light and photosensitizers. Using random mutagenesis via error-prone PCR we have created a library of mutants to use in directed evolution to optimize hydrogen catalysis, though a challenge in this project is that testing individual variants by gas chromatography is not feasible on a large scale. For this reason, we are developing a gasochromic, hydrogen assay that is based on the interaction of molecular hydrogen with tungsten trioxide with a palladium catalyst. Initially, results show this assay to be qualitatively accurate between trials; however, its application in screening remains a challenge.
The incidence of childhood obesity has become increasingly prevalent in the United States in recent years. The development of obesity at any age, but especially in adolescence, can have lasting negative effects in the form of cardiometabolic disease, increased incurred healthcare costs, and potential negative effects on quality of life. In recent years, a rising trend of obesity, in both adults and adolescents, has been observed in lower income and ethnic groups. Increased adiposity can be influenced by modifiable factors -(physical activity, caloric intake, or sleep) or by non-modifiable factors (ethnicity, genetic predispositions, and socioeconomic status). The influence of these factors can be observed in individuals of all ages, including infants. A common indicator of the development of childhood obesity is rapid weight gain (RWG) within an infant’s first year of life. The composition of the gut microbiome can act as a predictor for RWG and the development of childhood obesity. Infants are exposed to an immense microbial load when they are born and their gut microbiome is continually diversified through their method of feeding and the subsequent introduction to solid foods. While currently understudied, it is understood that cultural and socioeconomic factors influence the development of the gut microbiome, which is further explored in this analysis. The DNA from 51 fecal samples from infants ranging from 3 weeks to 12 months in age was extracted and sequenced using next-generation sequencing, and the resulting sequences were analyzed using QIIME 2. Results from alpha-diversity and beta-diversity metrics showed significant differences in the gut microbiome of infants when comparing groups based on baby race/ethnicity, household income, and mom’s education. These findings suggest the importance of sociodemographic characteristics in shaping the gut microbiome and suggest the importance of future studies including diverse populations in gut microbiome work.
Oceanic life is facing the deleterious aftermath of coral bleaching. To reverse the damages introduced by anthropological means, it is imperative to study fundamental properties of corals. One way to do so is to understand the metabolic pathways and protein functions of corals that contribute to the resilience of coral reefs. Although genomic sequencing and structural modeling has yielded significant insights for well-studied organisms, more investigation must be conducted for corals. Better yet, quantifiable experiments are far more crucial to the understanding of corals. The objective is to clone, purify, and assess coral proteins from the cauliflower coral species known as Pocillopora damicornis. Presented here is the pipeline for how 3-D structural modeling can help support the experimental data from studying soluble proteins in corals. Using a multi-step selection approach, 25 coral genes were selected and retrieved from the genomic database. Using Escherischia coli and Homo sapiens homologues for sequence alignment, functional properties of each protein were predicted to aid in the production of structural models. Using D-SCRIPT, potential pairwise protein-protein interactions (PPI) were predicted amongst these 25 proteins, and further studied for identifying putative interfaces using the ClusPro server. 10 binding pockets were inferred for each pair of proteins. Standard cloning strategies were applied to express 4 coral proteins for purification and functional assays. 2 of the 4 proteins had visible bands on the Coomassie stained gel and were able to advance to the purification step. Both proteins exhibited a faint band at the expected migration distance for at least one of the elutions. Finally, PPI was carried out by mixing protein samples and running in a native gel, resulting in one potential pair of PPI.
sustainable, carbon neutral energy source to curb the reliance on fossil fuel combustion as the primary source of energy. To overcome this challenge, research efforts have turned to biology for inspiration, as nature is adept at inter-converting low molecular weight precursors into complex molecules. A number of inorganic catalysts have been reported that mimic the active sites of energy-relevant enzymes such as hydrogenases and carbon monoxide dehydrogenase. However, these inorganic models fail to achieve the high activity of the enzymes, which function in aqueous systems, as they lack the critical secondary-shell interactions that enable the active site of enzymes to outperform their organometallic counterparts.
To address these challenges, my work utilizes bio-hybrid systems in which artificial proteins are used to modulate the properties of organometallic catalysts. This approach couples the diversity of organometallic function with the robust nature of protein biochemistry, aiming to utilize the protein scaffold to not only enhance rates of reaction, but also to control catalytic cycles and reaction outcomes. To this end, I have used chemical biology techniques to modify natural protein structures and augment the H2 producing ability of a cobalt-catalyst by a factor of five through simple mutagenesis. Concurrently I have designed and characterized a de novo peptide that incorporates various iron sulfur clusters at discrete distances from one another, facilitating electron transfer between the two. Finally, using computational methodologies I have engineered proteins to alter the specificity of a CO2 reduction reaction. The proteins systems developed herein allow for study of protein secondary-shell interactions during catalysis, and enable structure-function relationships to be built. The complete system will be interfaced with a solar fuel cell, accepting electrons from a photosensitized dye and storing energy in chemical bonds, such as H2 or methanol.
The estimates of metal-ligand equilibrium constants at 25°C and 1 bar were made using multiple linear free energy relationships in accordance with the metal-coordinating properties of ligands such as denticity, identity of electron donor group, inductive effects and steric hindrance. Analogous relationships were made to estimated metal-ligand complexation entropy that facilitated calculation of equilibrium constants up to 125°C using the van’t Hoff equation. These estimates were made for over 250 ligands that include carboxylic acids, phenols, inorganic acids, amino acids, peptides and proteins.
The stability constants mentioned above were used to obtain metal speciation in several microbial growth media including past bioavailability studies and compositions listed on the DSMZ website. Speciation calculations were also carried out for several metals in blood plasma and cerebrospinal fluid that include metals present at over micromolar abundance (sodium, potassium, calcium, magnesium, iron, copper and zinc) and metals of therapeutic or toxic potential (like gallium, rhodium and bismuth). Metal speciation was found to be considerably dependent on pH and chelator concentration that can help in the selection of appropriate ligands for gallium & rhodium based anticancer drugs and zinc-based antidiabetics. It was found that methanobactin can considerably alter copper speciation and is therefore a suitable agent for the treatment of Wilson Disease. Additionally, bismuth neurotoxicity was attributed to the low transferrin concentration in cerebrospinal fluid and the predominance of aqueous bismuth trihydroxide. These results demonstrate that metal speciation calculations using thermodynamic modeling can be extremely useful for understanding metal bioavailability in microbes and human bodily fluids.
