Biochemistry Commons^™

Assessing The Biocatalytic Promiscuity Of Pep- Transformations For Geminal-Difluorination, Eloy Jose Torres Garcia

Theses and Dissertations (Comprehensive)

Fluorine is the most electronegative chemical element and can drastically change molecular properties, such as drug pharmacokinetics and agrochemical half-life. Although a great deal of progress is occurring in synthetic methods to access various organofluorines, these methods struggle with harsh conditions and limited substrate scope. Biocatalytic approaches offer the potential to access organofluorines that are difficult or impossible with the current methodology. Phosphoenolpyruvate (PEP) is a central metabolite and biosynthetic precursor for diverse molecules. Phosphoenol pyruvate mutase (Ppm) catalyses the interconversion of Phosphonopyruvate (PnPy) to Phosphoenolpyruvate (PEP). This research successfully expressed and …

Engineering And Characterizing Proteins: A Dual Study On Canine P53 Protein And Cyan Thermal Protein, Dhruv B. Sitapara

Graduate Theses/Dissertations

This research aims to explore protein development and characterization, focusing on a dual study of canine p53 protein and cyan thermal protein. For the canine p53 protein, the goal is to comprehend its structure to better understand a key component of canine cancers. This multi-step process involved expressing the canine p53 DNA-binding domain in E. coli and purifying it through affinity and ion-exchange chromatography. The purified protein was studied to test the binding of canine p53 protein to human DNA sequences using Surface Plasmon Resonance (SPR) experiments and an Electrophoretic Mobility Shift Assay (EMSA), visualized with a SYBR-safe stain. The …

Development Of Multivalent Dna-Peptide Nucleosome Mimetics And Multi-Domain Protein Inhibitors That Directly Or Indirectly Target The E3 Ligase Uhrf1, Li Gu

University of the Pacific Theses and Dissertations

UHRF1 is an E3 ubiquitin ligase and a key epigenetic regulator establishing a crosstalk between DNA methylation and histone modification. Despite the important biochemical role of UHRF1 in cells, its overexpression has been found in almost all primary cancer types including breast cancer, lung cancer and so on. Numerous evidence indicates a strong link between tumorigenesis and UHRF1 overexpression, supporting its potential as a universal biomarker for cancer. However, UHRF1 is “yet-to-be drugged” and no highly potent chemical probes have been developed to target UHRF1 to date. In this study, we proposed two drug design approaches for UHRF1. The first …

Concentrated Wastewater Treatment Using A Ferric Iron-Dosed Anaerobic Upflow Sludge Blanket Reactor For Recovery Of Phosphorus And Ammonium, Carley E. Shingleton

Graduate Theses, Dissertations, and Problem Reports (ETD)

This study evaluated the performance of a novel, ferric iron-dosed anaerobic bioreactor to recover two separate nutrient products from concentrated wastewaters -- phosphorus as vivianite (Fe₃(PO₄)₂×8H₂O) and an ammonium-containing effluent with low organics. A bench-scale upflow anaerobic sludge blanket (UASB) reactor fed with a synthetic wastewater (458.0 mg/L total organic carbon, 282.7 mg/L ammonium, and 84.4 mg/L phosphate) was dosed with a ferric chloride solution at an org. C/Fe³⁺ molar ratio ~17.5 to facilitate organic carbon oxidation coupled to iron reduction. The reactor design allowed natural settling of vivianite to its …

Investigating The Role Of Nudt7-Mediated Peroxisomal Coa Degradation In The Regulation Of Hepatic Coa Levels And Lipid Metabolism, Schuyler Dan Adams Vickers

Graduate Theses, Dissertations, and Problem Reports (ETD)

Coenzyme A (CoA) is a crucial cofactor required to support many essential metabolic processes, including fatty acid oxidation and synthesis, the TCA cycle, and bile acid synthesis. In order to support the proper functioning of these pathways, CoA levels within the cell must be properly regulated. The regulation of CoA levels is achieved through a balance between CoA synthesis and CoA degradation. While the regulation of CoA synthesis has been extensively characterized, the degradation of CoA has received less attention. As such, the contribution of CoA degradation to the regulation of metabolism is poorly understood. NUDT7 is a CoA-specific Nudix …

Heat Shock Protein 90 (Hsp90) System In Health And Disease., Daniella Munezero

Graduate Theses, Dissertations, and Problem Reports (ETD)

Cells rely on heat shock proteins (HSP) to facilitate and regulate the folding of the substrate proteins into their native state, and degradation if misfolding cannot be prevented. HSP90, a member of the HSP family, is a potential target for treatment of cancer and neurodegenerative diseases. Unfortunately, several clinical trials for cancer treatment have been discontinued due to cell toxicity accompanying HSP90 inhibition. HSP90 has four distinct but structurally similar paralogs. HSP90 inhibitors target all the paralogs despite increasing proof of functional differences among the paralogs. Understanding the in vivo function of HSP90 and the role played by each paralog …

Gestational Vulnerability To Ozone Air Pollution - A Placental Story, Vishnupriya Alavala, Sarah Brent, Russell Hunter, Matthew J. Campen, Andrew Ottens

Undergraduate Research Posters

About 99% of the global population resides in areas with air pollution surpassing World Health Organization standards. Air pollution is associated with adverse neonatal health outcomes such as low fetal birth weight and an increased risk for maternal pre-eclampsia. A particularly reactive air pollutant is ozone, which forms reactive oxygen species that induce cellular damage. Research exists on the dispersion of reactive oxygen species through the bloodstream leading to fetal vulnerability during pregnancy, specifically via the placenta. Yet, placental and fetal development is a temporal process with varied susceptibility to negative gestational outcomes.

To addressing this gap, our laboratory utilized …

Engineering Ph-Dependent Antibody Interactions Through Introduction Of Linked Protonation Equibria Within The Antigen Binding Interface Or Linked Oligomeric Interfaces, Tosha Laughlin

Graduate Research Theses & Dissertations

Antibodies are widely applied as affinity reagents across a variety of fields, due to their high affinity and specificity. While high affinity across a range of conditions is useful for many applications, the ability to modulate affinity with environmental conditions (e.g., pH) opens new opportunities for antibody applications. This dissertation focuses on exploring the impact of an antibody’s interface size on engineered pH dependence, as well as exploring engineered pH-dependence through perturbing oligomerization equilibria that are linked to target binding. An anti-maltose binding protein (MBP) Fab 7O antibody fragment was used as a large protein-protein interface model to explore a …

Development Of A Chemical Biology Approach To Uncover The Influence Of Sequence Variations On Ces1 Activity In Live Cells, Samuel James Knebel

Masters Theses

Drug metabolism is the biochemical process of modifying drugs to detoxify and remove them through enzymatic transformations. These biotransformation’s occur primarily in the liver and are critical to understanding how pharmaceutical compounds are chemically altered inside the human body. Human carboxylesterases (CESs) catalyze the hydrolysis of esters, amides, thioesters, and carbamates. CES-mediated hydrolysis plays an important role in the metabolism of many drugs including the first FDA approved antiviral treatment for COVID-19, remdesivir (Veklury), the seizure control medication rufinamide (Banzel), and the flu antiviral drug oseltamivir (Tamiflu). CES activity is known to be influenced by a variety of factors including …

Evaluating The Contribution Of Adjacent Charges On The Observed Ph-Dependent Binding Profile For A Vhh/Antigen Interaction With A Linked Histidine Protonation Equilibria, Kiruthika Arulmoly

Graduate Research Theses & Dissertations

pH dependent protein-protein interactions are of great importance for various biological processes. In addition, the generation of engineered pH-dependent therapeutic antibodies opens opportunities for the extension of therapeutic half-life, thereby reducing drug dosage or frequency of administration, as well as providing pH-dependent targeting, such as the tumor microenvironment. Engineering pH-dependent antibody-antigen interaction is mostly achieved through the incorporation of ionizable residues within the antigen binding interface. These ionizable residues must undergo a change in environment upon forming a protein-protein complex, which causes a change in the ionizable group’s pKa value. This coupled protonation equilibria is responsible for the observed pH-dependent …

Bioanalytical Studies Of Disease Protein Profiles: Maldi-Tof Ms, Prajkta Satish Chivte

Graduate Research Theses & Dissertations

Coronavirus disease-2019 (COVID-19), which is caused by a novel coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has ravaged the world for the past 3 years. Even today, there still exists a need for rapid, accurate, economical and non-invasive diagnostic testing platforms that yield high specificity and sensitivity towards the constantly mutating SARS-CoV-2. Research has consistently indicated saliva to be a more amenable specimen type for early detection of SARS-CoV-2, compared to the oral and nasopharyngeal swabs. Considering the limitations and high demand of the existing COVID-19 testing platforms, this dissertation work studies used MALDI-ToF MS (matrix-assisted laser desorption/ionization-time of …

The Role Of Cadherins And Ryk On Metastasis And Invasion In Triple Negative Breast Cancer Cell Model: Hs578t/Hs578ts(I)8, Ibis Iser

Electronic Theses and Dissertations

Breast cancer is a major cause of death among women in European and North American countries, even with improved methods for diagnosis and therapy. The mortality of breast cancer is mainly due to the migration of the primary tumor to distinct sites in the body and is very common in triple negative breast cancer (TNBC). This type of breast cancer affects younger woman and has a high recurrence rate. Unfortunately, TNBC is extremely difficult to control because of the absence of specific targets for treatment. Therefore, our research aim is to discover new therapeutic targets and identify novel approaches for …

Food Waste Storage Gaseous Emissions Detection And Quantification Using Infrared Spectroscopy, Ryley A. Burton-Tauzer

Cal Poly Humboldt theses and projects

A growing interest in sustainable waste management and the implementation of new policies have prompted a shift towards alternative resource recovery methods for organic waste, including food waste. To effectively assess alternative food waste treatment scenarios, it is important to evaluate the life cycle impacts associated with each scenario. The storage phase of food waste, encompassing its accumulation in kitchens, and storage in bins for collection and transportation, has been overlooked as a source of greenhouse gases in previous studies. This investigation aimed to identify the greenhouse gases emitted during the initial five-day period of low-oxygen storage. An open dynamic …

Elucidating Mechanisms Of Proteasome Modulation By Small Molecules To Treat Neurodegenerative Diseases And Cancer, Janelle Joo Yee Chuah

Graduate Theses, Dissertations, and Problem Reports (ETD)

Maintaining protein homeostasis, or proteostasis, is crucial for cellular function, and protein degradation through the proteasome plays a pivotal role in this process. Dysregulation of the proteasome can lead to proteostasis collapse and has been linked to the development of neurodegenerative diseases and cancers. Neurodegenerative diseases often exhibit proteasome impairment, whereas proteasome upregulation is frequently observed in cancer. Although the use of proteasome inhibitors as a pharmaceutical approach has shown success in certain cancers, it has yet to demonstrate efficacy in neurodegenerative diseases due to the absence of drug-like small molecules capable of effectively reversing proteasome impairment and/or activating the …

Characterizing The Dynamic Localization Of Cmi In Early Drosophila Development, Asra Habibullah

Master's Theses

The COMPASS-like family of lysine methyltransferases, MLR/MLX complexes, are epigenetic regulators that are essential for normal development through the methylation of the fourth lysine residue on histone 3 (H3K4), a universal epigenetic mark associated with active transcription. This family of complexes is highly conserved from yeast to mammals and the genes encoding the human MLR complexes have been associated with various developmental diseases and cancers (Dingwall and Fagan, 2019). In D. melanogaster, the enzymatic methyltransferase core of this complex is composed of two proteins: Cara Mitad (Cmi, also known as Lpt) and Trithorax-related (Trr). Although these proteins have been shown …

Functional Characterization Of Pacific White Shrimp Litopenaeus Vannamei Heat Shock Protein 90 In Response To White Spot Syndrome Virus Infection, Warumporn Yingsunthonwattana

Chulalongkorn University Theses and Dissertations (Chula ETD)

Heat shock proteins (HSPs) are host chaperones that can be used by viruses to facilitate various steps of viral infections. In this study, we found that Litopenaeus vannamei heat shock protein 90 (LvHSP90) is a viral-responsive protein, due to a significant transcriptional and translational upregulation following white spot syndrome virus (WSSV) infection. Suppression of LvHSP90 significantly reduced WSSV infection which was corresponded with significantly decreased expressions of viral genes, including the immediate-early genes and viral DNA polymerase. Conversely, injecting shrimp with WSSV that had been co-incubated with a recombinant LvHSP90 (rLvHSP90) promoted WSSV infection as evidenced by an increased cumulative …

Solubility And Anti-Cancer Efficiency Enhancement Of Phytochemicals By Complexation With Β-Cyclodextrin And Derivatives, Saba Ali

Chulalongkorn University Theses and Dissertations (Chula ETD)

Phytochemicals, abundant in plants, showcase diverse pharmacological effects, with an increasing focus on their potential as anticancer agents. Three bioactive natural compounds with pharmaceutical potential are piperine (PP), oxyresveratrol (OXY), and tanshinone IIA (Tan IIA). However, these three phytochemicals have low water solubility and susceptibility to UV light degradation. To address this problem, we explored the potential of β -cyclodextrins (βCDs), renowned for their ability to enhance the solubility and stability of lipophilic drugs by encapsulating them within their molecular structure. Our focus centered on β-cyclodextrin (βCD) and its derivatives, including hydroxypropyl-β-cyclodextrin (HPβCD), dimethyl-β-cyclodextrin (DMβCD), and sulfobutylether-β-cyclodextrin (SBEβCD). In this …

Regulation Of Cell Cycle And Apoptosis By Mirna Via Jak-Stat/Akt Pathway In White Spot Syndrom Virus-Infected Shrimp, Waqar Ahmad

Chulalongkorn University Theses and Dissertations (Chula ETD)

WSSV infection is one of the most serious threats to the aquaculture industry. To fight against WSSV, shrimp rely on several immune effectors and pathways, i.e. the JAK/STAT pathway, which is considered an essential communication gateway for cell function. It has been reported previously that the JAK/STAT pathway interconnects with other pathways and regulates the cell cycle and apoptosis in vertebrates, but the mechanism of this pathway in the regulation of cell cycle and apoptosis in shrimps is still unclear. Thus, the purpose of this study is to investigate how the JAK/PI3K/AKT pathway controls cell cycle and cell death, as …

Identification And Functional Characterization Of Myb Transcription Factors Regulating Flavonoid Biosynthesis In Durian Durio Zibethinus L. Pulps, Kamonwan Weerawanich

Chulalongkorn University Theses and Dissertations (Chula ETD)

Durian fruit possesses high nutritional value due to its enriched bioactive compounds such as phenolics, carotenoids, and vitamins. While various transcription factors (TFs) regulate the phenylpropanoid biosynthetic pathway, MYB TFs play a pivotal role in controlling key genes in this pathway. In this study, we identified candidate v-Myb myeloblastosis viral oncogene homolog, MYB TFs from our transcriptome database of the Monthong cultivar including five developmental/postharvest ripening stages. MYBs that were upregulated during the ripening stage were considered as candidate transcriptional activators, based on the positive correlation observed between flavonoid biosynthetic genes and flavonoid contents in ripe durian pulps. Conversely, MYBs …

Analyzing The Impact Of Zip Subfamily Ii Mutations On The Zinc And Iron Transport Of Zupt From Escherichia Coli, Bradley Vandecar

Wayne State University Theses

The disfunction or misregulation of the ZIP family of metal ion transporters has been linked to a plethora of diseases and cancers in humans. Zn2+ is the primary substrate for ZIPs and is transported through the M1 metal binding site, though this activity is stimulated through the binding of Fe2+ in the M2 metal binding site. The members of ZIP Subfamily II are predicted to have an inactive M2 site due to the lack of Fe2+ transport and from a previously generated homology model. This work utilizes homology modelling, whole cell metal ion uptake assays, and growth studies in minimal …

In Silico Drug Discovery For Sars-Cov-2 Papain-Like Protease, Olivia Haskin

Wayne State University Theses

SARS-CoV-2 Papain-like protease is an essential viral protein for viral replication. In our lab, we hypothesize that successful inhibition of this protease will stop viral replication and allow for clearance of the infection by the host. The work described here aimed to design and execute an in silico drug discovery workflow for successfully selecting PLpro inhibitors from the Mcule purchasable compound database. This work reports such a workflow and nine potential compounds for in vitro testing. This work also describes structural activity relationship analysis of a proprietary set of PLpro inhibitors synthesized by medicinal chemistry collaborators and makes recommendations for …

Cup Is Essential For Oskar Mrna Translational Repression During Early Drosophila Oogenesis, Livia V. Bayer, Samantha Milano, Stephen K. Formel, Harpreet Kaur, Rishi Ravichandran, Juan A. Cambeiro, Lizaveta Slinko, Irina E. Catrina, Diana P. Bratu

Publications and Research

Study of the timing and location for mRNA translation across model systems has begun to shed light on molecular events fundamental to such processes as intercellular communication, morphogenesis, and body pattern formation. In D. melanogaster, the posterior mRNA determinant, oskar, is transcribed maternally but translated only when properly localized at the oocyte’s posterior cortex. Two effector proteins, Bruno1 and Cup, mediate steps of oskar mRNA regulation. The current model in the field identifies Bruno1 as necessary for Cup’s recruitment to oskar mRNA and indispensable for oskar’s translational repression. We now report that this Bruno1-Cup interaction leads …

C-Glycopyranosyl Aldehydes: Emerging Chiral Synthons In Organic Synthesis, Sandeep Kumar, Vinod Khatri, Priyanka Mangla, Rajni Johar Chhatwal, Virinder S. Parmar, Ashok K. Prasad

Publications and Research

Herein, we have summarized the vast array of synthetic processes that have been developed for the synthesis of C-glycopyranosyl aldehydes and diverse C-glycoconjugates derived from them by covering the literature reported from 1979 to 2023. Notwithstanding its challenging chemistry, C-glycosides are considered stable pharmacophores and are used as important bioactive molecules. The discussed synthetic methodologies to access C-glycopyranosyl aldehydes take advantage of seven key intermediates, viz. allene, thiazole, dithiane, cyanide, alkene, and nitromethane. Furthermore, the integration of complex C-glycoconjugates derived from varied C-glycopyranosyl aldehydes involves nucleophilic addition/substitution, reduction, condensation, oxidation, cyclo condensation, coupling, and …

Molecular Mechanism Behind The Safe Immunostimulatory Effect Of Withania Somnifera, Kriti Kalpana, Shen Yap, Moriya Tsuji, Akira Kawamura

Publications and Research

Withania somnifera (L.) Dunal (family Solanaceae) is a medicinal plant known for, among many pharmacological properties, an immune boosting effect. Our recent study revealed that its key immunostimulatory factor is lipopolysaccharide of plant-associated bacteria. This is peculiar, because, although LPS can elicit protective immunity, it is an extremely potent pro-inflammatory toxin (endotoxin). However, W. somnifera is not associated with such toxicity. In fact, despite the presence of LPS, it does not trigger massive inflammatory responses in macrophages. To gain insights into the safe immunostimulatory effect of W. somnifera, we conducted a mechanistic study on its major phytochemical constituent, …

Tcga Expression Analyses Of 10 Carcinoma Types Reveal Clinically Significant Racial Differences, Brian Lei, Xinyin Jiang, Anjana Saxena

Publications and Research

Epidemiological studies reveal disparities in cancer incidence and outcome rates between racial groups in the United States. In our study, we investigated molecular differences between racial groups in 10 carcinoma types. We used publicly available data from The Cancer Genome Atlas to identify patterns of differential gene expression in tumor samples obtained from 4112 White, Black/African American, and Asian patients. We identified race-dependent expression of numerous genes whose mRNA transcript levels were significantly correlated with patients’ survival. Only a small subset of these genes was differentially expressed in multiple carcinomas, including genes involved in cell cycle progression such as CCNB1 …

Treponema Denticola Synthesizes C-Di-Amp And Encodes The Cdaa-Type Diadenylate Cyclase Cdaa, Claire R. O'Brien

Theses and Dissertations

Periodontitis is a form of oral disease characterized by dysbiosis of the oral microbiome, leading to inflammation, bone resorption, and in severe cases, entire tooth loss, affecting 42% of adults in the US. One of the bacteria most associated with periodontal disease progression is Treponema denticola (Td), an oral spirochete which inhabits the mouth in small quantities during health but which can dominate the biofilms that form during periodontal disease. The ability of Td to survive in a disease environment and contribute to the progression of disease requires the use of robust signaling networks. Analysis of Td cultures …

Characterization Of The Clostridioides Difficile Glycosyl Hydrolase Ccsz, Brian Lowrance

Theses and Dissertations (Comprehensive)

Bacteria inhabit many of the harshest environments on Earth; persisting and thriving in conditions thought to be unsuitable for life. One common strategy to withstand these environments is the formation of a biofilm. Biofilm composition varies greatly, depending on the underlying community that produces it. Cellulose, a polymer consistently prevalent in biofilms, has been identified as a virulence factor in many pathogens and is suspected to be involved in pathogenesis by Clostridioides difficile. C. difficile is the #1 cause of hospital acquired diarrhea, which can range from mild to life-threatening infections. Biofilm formation is hypothesized to be involved in …

Functional Residues Of Cjpata, Robert Lamont

Theses and Dissertations (Comprehensive)

Antibiotic resistance in pathogenic bacteria continues to challenge clinicians and threaten the lives of infected individuals. For this reason, new classes of antibiotics or new targets for antibiotic therapy are needed to circumvent this global health crisis. In Gram-negative bacteria, the enzymes peptidoglycan O-acetyltransferase A and B (PatA and PatB), are responsible for adding acetyl groups to the C-6 hydroxyl group of N-acetyl muramic acid (MurNAc) in peptidoglycan (PG). These acetyl groups are responsible for inhibiting the activity of lysozyme from host organisms that hydrolyze the β1-4 glycosidic linkage between MurNAc and N-acetylglucosamine (GlcNAc). The acetyl groups …

Exploring The Membrane Protein And Peptide Interactions Of Mitochondrial And Bacterial Lipid Systems, George Saudan

Theses and Dissertations (Comprehensive)

This study aims to expand the understanding of interactions between membrane lipids and proteins, and relate it to their biological functions in two experimental systems. The first system focuses on the interaction and conformation of a membrane protein Uncoupling Protein 4 (UCP4) in mitochondrial inner membrane lipids, in the absence and presence of cardiolipin; a lipid specific to mitochondrial inner membranes. The second system considers the interaction and conformation of a cell penetrating peptide, Penetratin, which can interact with both mammalian and bacterial cells. A N- and C-termini protected form of this 16-meric peptide (Pen2) was used to explore its …

Interactions Of Amyloid Peptides With Lipid Membranes, Yanxing Yang

Dissertations

The aggregation of amyloid proteins into fibrils is a hallmark of several diseases including Alzheimer’s (AD), Parkinson’s, and Type II diabetes. This aggregation process involves the formation of small size oligomers preceding the formation of insoluble fibrils. Recent studies have shown that these oligomers are more likely to be responsible for cell toxicity than fibrils. A possible mechanism of toxicity involves the interaction of oligomers with the cell membrane compromising its integrity. In particular, oligomers may form pore-like structures in the cell membrane affecting its permeability or they may induce lipid loss via a detergent-like effect. This dissertation aims to …