Physical Sciences and Mathematics Commons^™

Activity And Selectivity Of Class B Sortase Enzymes, Sophie Jackson

WWU Graduate School Collection

Gram-positive bacteria attach many proteins to their cell walls via sortase enzymes. Sortases are cysteine transpeptidases and are grouped into 6 classes, A-F. Sortase enzymes, particularly sortase A from Staphylococcus aureus, have been used extensively for in vitro protein ligations. Here, we investigate substrate-binding in sortase A from Streptococcus pyogenes. In addition, class B sortases are typically overlooked for research and development due to low in vitro activity and incomplete knowledge of substrate specificity. Here, we investigate the activity of class B sortases from Bacillus anthracis (baSrtB), Clostridioides difficile (cdSrtB), Listeria monocytogenes (lmSrtB), and Staphylococcus aureus (saSrtB). Of these, …

Stereoselective Synthesis Of (+)- And (-)-Cananodine, Haley Holliday

WWU Graduate School Collection

Natural products are an important class of molecules utilized in traditional medicine and inspire drug design in medicinal chemistry. Cananga odorata, a tree commonly known as ylang-ylang, contains natural products known to positively benefit health, and specifically promote liver health. One alkaloid isolated from Cananga odorata, cananodine, possesses cytotoxic properties, specifically against hepatocellular carcinoma (HCC). HCC is the most common type of liver cancer, with one million diagnoses projected by 2025 globally. Cananodine is a member of the guaipyridine alkaloid family, a class of compounds that feature a substituted pyridine bonded to a seven-membered ring. The first enantiomer …

Selectivity And Structure Of Chimeric Loop Swaps In Sh2 Domains, Sarah N. Smith

WWU Graduate School Collection

SH2 (Src Homology 2) domains are protein domains that bind to phosphorylated tyrosine residues within cell signaling cascades. They have been found to play a role in certain cancers and immunological disorders. Despite their importance in cell signaling and medical relevance, the structural basis of the various selectivity classes of SH2 domains is only partially understood. Previous research found that the EF and BG loops of the domains contribute to forming the peptide binding pocket, and thus impact their selectivity. To further understand the role of these loops in selectivity, we engineered chimeric SH2 domains by swapping the EF and …

Tuned Gold Layer Growth Onto Plasmonic Sensing Silver Nanocubes Via Synthetic Control Of Reduction Potentials., Nicolas Hall

WWU Graduate School Collection

Metallic nanoparticles (mNPs) are commonly employed as sensors and detection tools due to their unique plasmonic properties. Silver NPs exhibit these properties in heightened capacity in comparison to other metals. However, Ag NPs are susceptible to oxidation, degradation over time and are biotoxic. These issues are commonly addressed by creating Ag-alloy NPs or by adding additional layers to Ag NPs. This work improves upon these methods by focusing on the growth of an Au layer onto Ag nanocubes (AgNCs), resulting in a layered Au-Ag NC (Au@AgNC). The resulting morphology of these Au@AgNCs are dependent on the synthetic pathway taken and …

Structural And Thermodynamic Studies Of Antibody Binding To Blood Coagulation Factor Viii, Jordan Vaughan

WWU Graduate School Collection

Blood coagulation factor VIII (FVIII) is a 2332 residue glycoprotein expressed in endothelial cells and plays a significant role in the formation of blood clots. Structurally, FVIII’s domains are organized as A1-A2-B-A3-C1-C2. The absence or deficiency of FVIII in the bloodstream gives rise to Hemophilia A; an X-linked bleeding disorder affecting 1 in 5000 males worldwide. To combat this deficiency, patients undergo FVIII replacement therapy which involves frequent injections of FVIII into the bloodstream in the form of blood, plasma, or protein concentrates. Although effective, this treatment commonly results in the development of anti-FVIII inhibitory antibodies in approximately 20-30% of …

Kinetic Analysis Of The Grafting Thermal Ring-Opening Polymerization Reaction Of Benzoxazine With Sulfonyl-Ester Functionalized Polymers, Tawakalt Adetoun Akinjobi

WWU Graduate School Collection

This project will explore the fundamental mechanistic details and kinetics of a grafting polymerization reaction that occurs with blended benzoxazine monomers (or resins) and polymers functionalized with reactive sulfonyl-ester leaving groups [such as tosylate (Ts), nosylate (Ns) or mesylate (Ms) groups]. Isoconversional analysis (ICA) is one of the most important methods for establishing the kinetics of the complex reactions associated with curing thermosets. In the case of ICA, activation energy is measured at fixed values of reaction conversion.²⁶ For thermosets the data are typically based on differential scanning calorimetry (DSC). The combinatorial approach not only provides uncertainty associated with …

Structural, Mutational, And Kinetic Characterization Of Ura4, An Isocytosine Deaminase, Ashlee Hoffman

WWU Graduate School Collection

Cytosine Deaminases (CD) are a class of enzymes found in prokaryotes and fungi that have been studied in the past due to their ability to deaminate the prodrug 5-fluorocytosine (5-FC) producing 5-fluorouracil (5-FU). 5-FU is a common anti-cancer drug that can inhibit DNA synthesis leading to cancer cell death. 5-fluorocytosine can interact with digestive bacteria leading to unwanted side effects for cancer patients. Isocytosine Deaminases (ICD) are enzymes that are of interest in the treatment of cancers using Gene Directed Enzyme Prodrug Therapy (GDEPT). ICDs can deaminate the prodrug 5-fluoroisocytosine (5-FIC) also producing the drug 5-FU.  5-FIC will likely not …

New Synthetic Methods Based On Silicon-Tethered Nucleophilic Addition Reactions, Alexie W. Clover

WWU Graduate School Collection

With the recent discovery of an iodine mediated rearrangement of diallylsilanes, we set out to investigate a similar fluorine mediated rearrangement, aimed at introducing a new method for synthesizing organofluorine compounds. Interest in incorporating fluorine into organic molecules has grown significantly in recent years, primarily for medicinal applications. Since certain fluorination methods require the use of mCPBA, a common epoxidizing reagent, control experiments were performed on the reaction of several diallylsilanes with mCPBA, anticipating that a competing epoxidation of the diallylsilanes might occur. It was found that the formation of the hydroxy ester occurred through a regioselective epoxide opening from …

Regio- And Diastereoselective Samarium-Mediated Allylic Sulfone Reductions, Cody Schwans

WWU Graduate School Collection

A series of allylic sulfones were synthesized containing a stereodirecting group and chelating element and subjected to samarium diiodide reductions in the presence of a proton donor. The resulting products could be obtained with high regioselectivity (no less than 95:5) and high diastereoselectivity (>10:1) that correlated with the size of the stereodirecting group. A mechanism is proposed that includes loss of the sulfone and formation of a chelated organosamarium intermediate followed by intramolecular protonation by a samarium-bound proton source. In this way, both the regioselectivity and absolute stereochemistry of the resulting products are explained.

Class A Sortases: Structures And Alternative Substrate Binding And Cleavage, Brandon Vogel

WWU Graduate School Collection

Sortases, consisting of classes A-F, are cysteine transpeptidases found in the cell wall of Gram-positive bacteria. They play a crucial role in ligating proteins to the cell wall that are responsible for cell adhesion, immune evasion, host cell invasion, and nutrient acquisition through a transpeptidation reaction. Consequently, they are an attractive therapeutic target. Class A sortases are also utilized in protein engineering applications such as sortase-mediated ligations and sortagging. Despite extensive research in the past two decades, gaps persist in understanding how class A sortases recognize their substrates, primarily due to a lack of structural information on sortases non-covalently bound …

Using Qm/Mm Methods To Explore Sortase Enzyme Intermediates, Kinetics, And Stability, Kyle Whitham

WWU Graduate School Collection

Biochemistry has seen advancements in methods and understanding of the inner workings of proteins, yet biochemists struggle to see real time reaction pathways of protein intermediates. This is where computational chemistry comes in and fills in the holes in knowledge through the use of Quantum Mechanical (QM) models. QM chemistry alone does not give results in a reasonable timescale to predict protein chemistry in a reasonable amount of time. Computational chemistry methods such as Quantum mechanical (QM)/ Molecular Mechanical (MM) (QM/MM), allow us to split the in-silico system into two regions that utilize a fast MM force field region and …

The Curious Case Of Concept: A Nation-Wide Survey Of Faculty Beliefs About Quantum Mechanics Concept Inventories Uncovers New Details Regarding Physical Chemistry Experts’ Understanding Of Conceptual Knowledge., Matt Smiley

WWU Graduate School Collection

According to the chemistry education literature, physical chemistry educators strongly believe developing students’ conceptual understanding is important; however, the vast majority of educators (84%) were found to assess students predominantly on mathematical knowledge. To better serve students of physical chemistry, the cause of misalignment between stated learning goals and assessment needs to be elucidated. To this end, the Faculty Perceptions of Published Quantum Mechanics Assessments Survey (FPPQMA) was developed. The FPPQMA is designed to probe physical chemistry educators’ beliefs regarding the dichotomy between conceptual and mathematical knowledge. In addition to free response questions that ask respondents to define conceptual and …

Covalent Modifications As Targets And Means For Research In Intrinsically Disordered Proteins, Derek Mccaffery

WWU Graduate School Collection

A reported 33% of eukaryotic proteins are predicted to contain intrinsically disordered regions (IDRs) over 30 residues in length. IDRs are regions of protein which natively exist in an unfolded conformation. Due to their highly dynamic nature, many common methods of inquiry such as crystallography and NMR can be thwarted. As a result, valuable analysis such as probing function, dynamics and binding interfaces are unable to be performed. To minimize these problems, researchers typically study shorter IDRs. We probed fragments of plant protein villin 4 (VLN4) for covalent modifications to explore its regulation and degradation. Disordered regions of proteins have …

Sortase-Mediated Ligation To Investigate Large Idr-Containing Cytoskeletal Regulators, Melissa Oueld Es Cheikh

WWU Graduate School Collection

About 43% of eukaryotic proteins contain intrinsically disordered regions (IDRs) of 40 residues or longer. These proteins modulate key cellular functions such as transcription, translation, and signal transduction. Despite their vital roles, little is known about the properties of large disordered proteins due to the difficulties encountered studying them. Solution nuclear magnetic resonance (NMR) spectroscopy is a unique tool allowing for their analysis but traditionally requires uniform protein labeling with 15N and 13C isotopesresulting in convoluted spectra which obscure any meaningful information on their structures and interactions. To remedy this issue, we aim at developing a procedure to segmentally label …

Nickel Phosphide Photothermal Catalyst Development For Co2-Derived Solar Fuels, Hannah K. Hennig

WWU Graduate School Collection

Converting CO2 to CO via the photocatalyzed reverse water gas shift (RWGS) reaction satisfies a critical step in the production of C1 solar fuels (e.g., CH4, CH3OH) and longer hydrocarbons via the Fischer-Tropsch process. Oxide-supported nickel phosphides (NixPy) are an emerging class of photocatalysts with a number of accessible crystalline phases. Additionally, the broad-spectrum absorption of NixPy materials affords photo-induced local heating to drive catalytic processes at mild operating temperatures. In the current project, NixPy with different P/Ni molar ratios were investigated as RWGS catalysts on two types of support materials: 1) silica (SiO2) as a relatively inert support, and …

Structural Characterization Of Factor Viii-Inhibitor Complexes And Factor Viii Lipid Binding Mechanics, Corbin Mitchell

WWU Graduate School Collection

Blood coagulation factor VIII (FVIII) is a crucial protein cofactor within the blood coagulation cascade and facilitates the proteolytic activation of factor X by activated factor IX. During coagulation FVIII is activated and binds, via its C1 and C2 domains, to activated platelet membranes coordinated by interactions with exposed phosphatidylserine on the membrane surface. A deficiency of functional FVIII within a patient's bloodstream leads to the blood disorder hemophilia A, which results in prolonged bleeding episodes. Current treatment for hemophilia A relies on FVIII replacement therapy via the injection of exogenous FVIII. The main complication which arises from FVIII replacement …

Synthesis And Characterization Of Plga Capped Gold Nanoparticles For Use In Cancer Therapeutics, Tara Chin

WWU Graduate School Collection

This research project aims to create gold nanoparticles (AuNPs) functionalized with PLGA (poly(lactic co-glycolic acid)) polymers for generating reactive oxygen species (ROS) by way of Xray irradiation for use in cancer therapies. The current methods of cancer treatment rely on drugs and/or chemotherapy depending on the type of cancer present; these methods come with varying success rates which are also dependent on how severe the condition has become (the lower the severity, the higher chance of success). The latest method of cancer treatment is proton beam radiation therapy (PBRT) which can be specific in its targeting but not very cost …

Blood Replacement Therapy By Generation Of Polymeric Recombinant Hemoglobin Using “Click Chemistry” And Circular Tandem Repeat Proteins, Johanna Hamilton Urbach

WWU Graduate School Collection

Our work with hemoglobin-based oxygen carriers (HBOCs) is focused on developing a hemoglobin (Hb) polymer that can be used as a blood replacement in critical care at an affordable cost. For medical use, the Hb must be polymeric since cell-free Hb has multiple adverse side effects when it is not encapsulated in a red blood cell. These include kidney damage and heme-induced toxicity, which is due to cell-free Hb’s ability to extravasate. Challenges in making HBOCs, that have been observed in the past, are low protein expression yields and heterogeneity in polymeric Hb products produced by chemical crosslinking. In conducting …

Signaling And Trafficking In Choanoflagellates And Humans: A Study Of Conserved Peptide-Binding Domains, Haley Wofford

WWU Graduate School Collection

Many crucial cellular processes are regulated by signaling and trafficking pathways, which are largely dependent on protein interactions in the cell. These networks are thought to play a crucial role in the evolution of multicellular organisms from their unicellular ancestors. Choanoflagellates are unicellular organisms that can adopt a multicellular state, called a rosette. Though they evolved independently from and prior to the diversification of metazoans, they are the closest extant nonmetazoan ancestor to animals, making them a compelling model for the study of early multicellularity. Here, we look at two structurally conserved peptide-binding domains that both play important roles in …

Synthesis And Reactions Of Medium-Ring Silyl Ethers, Inna A. Fomina

WWU Graduate School Collection

Olefin metathesis is a reaction that creates new carbon-carbon double bonds by rearranging two alkenes. The reaction has undergone significant development since its discovery in the 1950s, from first reports to new catalysts and industrial uses, culminating in the 2005 Nobel Prize in chemistry. Grubbs ruthenium-based catalysts are widely used for such reactions, including ring closing metathesis (RCM) that involves the rearrangement of two alkenes on a single molecule to form a ring. During the course of investigating RCM reactions to produce eight-membered ring silyl ethers, we observed double bond isomerization when using the second-generation Grubbs catalyst and the Hoveyda-Grubbs …

Synthesis Of Guaipyridine Alkaloids Rupestines C, D And K With Studies Toward The Synthesis Of Rupestines B, J, L And M, Briana J. Mulligan

WWU Graduate School Collection

Hepatocellular carcinoma (HCC) is a type of primary liver cancer that is responsible for roughly 700,000 deaths around the world each year. While invasive treatment methods for HCC have proven to be limited, there are drug treatments available that show promising features. The structural elements of these drugs have given rise to an interest in guaipyridine alkaloids, specifically a family of naturally occurring guaipyridine alkaloids known as the rupestines. The rupestines have previously been isolated from the flowers of the plant Artemisia rupestris. This plant has been known for its reported antitumor, antiviral and antibacterial properties when used in traditional …

Pyridinediimine Complexes With Coordination Sphere Interactions Relevant To Copper And Non-Heme Iron Enzymes, Pui Man Audrey Cheung

WWU Graduate School Collection

Primary and secondary coordination sphere interactions with proximal Brønsted-Lowry acid/base sites were investigated using a family of pyridinediimine (PDI) complexes. The PDI ligands used in this project could be easily prepared by the Schiff base reactions with commercially available diamines as proton relays. Upon activation, the pendant Bronsted site and accessible electrons were arranged in a single scaffold that allowed the transportation of both protons and electrons to occur.

Two new PDI complexes with morpholine and pyrrolidine derivatives were introduced to the pendant PDI family. Their proton dissociation constant in acetonitrile were 17.1 and 18.3, respectively. The PDI complexes were …

Computational Design Of Novel Materials For Solar Energy Conversion And Catalysis, Corey Teply

WWU Graduate School Collection

As synthetic chemists and materials scientists increasingly gain the ability to precisely arrange the atoms in solids, computation can provide guiding insight toward designing materials for a variety of applications. This work focuses on two distinct projects: 1) the use of biaxial strain in all crystallographic directions to tune the structural and electronic properties of perovskites for solar energy conversion, and 2) the extension of the concept of single-atom alloys to design stable motifs of multiple catalyst atoms on metal surfaces.

Perovskite solar cells have been shown to have band gap tunability when compressive or tensile-biaxial strain is enacted on …

Exploring Biochemical Mechanisms With Hybrid Quantum Mechanics/Molecular Mechanics And Enhanced Sampling Methods, Edwin Enciso

WWU Graduate School Collection

In the field of molecular dynamics (MD), a long-standing issue is the time frame required in order to fully observe a chemical reaction. Enhanced sampling methods have been the primary way of overcoming this issue for the past 40 years. In this experiment our goal was to combine new and existing sampling methods in order to create an efficient and accurate way of retrieving kinetics data from simulations. In order to do this, we examined two test cases: the enzymes chorismate mutase and cytosine deaminase. We did this using hybrid quantum mechanics/molecular mechanics simulations coupled with enhanced sampling methods. The …

Organic Crystal Nucleation In Ultrathin Liquid Films: Applications Of Computational And Experimental Methods For The Exploration Of Dynamic Spatial Relationships And Controlled Growth, Haley Doran

WWU Graduate School Collection

The advancement of semiconducting materials is paramount to the future of electronics. Organic semiconducting materials are of particular interest due to their significantly lower processing cost compared to traditional inorganic semiconducting materials, such as silicon. However, the present toolkit for solution-based controlled growth of polycrystalline thin films is lacking. Therefore, the purpose of this research is to build such a toolkit, wherein tunable parameter relationships of organic thin-film growth are evaluated and compared both experimentally and computationally. A multi-scale model has been developed, which combines mean field rate equations with a self-consistent treatment of the critical stable monomer cluster size, …

Demystifying Denitrification: Coordination Complexes Give Valuable Insight Into The Reduction Of Nitrogen Oxides, Walker R. Marks

WWU Graduate School Collection

Increasing human population is driving the need to produce increasing amounts of food without the ability to dramatically increase farmland area. This has been accomplished by the application of increasing amounts of nitrogen containing fertilizers onto croplands. Nitrogen fertilizer overuse is causing imbalance in the natural nitrogen cycle via excessive amounts of high oxidation-state nitrogen entering both the atmosphere and aquatic ecosystems, which are major contributors to global warming and environmental damage. There is a need to explore synthetic systems which are capable of the reduction of these pollutants through pathways such as denitrification. This thesis will explore the functionalization …

Implementation Of A Constraint And Configuration Interaction Methodology Into Density Functional Tight Binding, Gunnar J. Carlson

WWU Graduate School Collection

This research aims to implement a charge constraint in conjunction with a small configuration interaction scheme into a density-functional tight-binding (DFTB) method within the DFTB+ quantum mechanical software package. This method aims to model the electron transfer rate of chemical systems by calculating the electronic couplings between two constrained states more efficiently. Electronic couplings are directly proportional to electron transfer, making them important parameters to efficiently compute the optimal minimum or maximum of an electron transfer rate, for example, when screening chemical systems based on their ability as a conductor. Other methods such as constrained density-functional theory followed by a …

Enhancing Plasmonic Nanomaterials: Colorimetric Sensing And Sers, John Crockett

WWU Graduate School Collection

Nanomaterials, materials with at least one dimension on the nanoscale have become an area of extreme scientific interest due to their many unique properties with applications in catalysis, optics, and sensing, just to name a few. Metal nanoparticles are particularly interesting because of the interactions between light and surface electrons in the metal’s conduction band, called localized surface plasmons. In anisotropic metal nanoparticles these plasmons are especially exciting due to the highly responsive quality of the plasmonic resonance associated with their varied nano dimensions. Gold nanorods and nano dendrites in particular exhibit electromagnetic effects which are specifically associated to the …

Structural Studies Of The Von Willebrand Factor D’ Domain And Its Binding Mechanism To Factor Viii, Ap Wang

WWU Graduate School Collection

Hemophilia A is an X-linked disorder that results in uncontrolled bleeding, which is caused by a lack of activity for blood coagulation factor VIII, an essential protein cofactor in the clotting cascade. Factor VIII consists of multiple domains, and binding disruptions between factor VIII and its circulatory partner, von Willebrand Factor, may cause von Willebrand disease. Von Willebrand Disease type 2N is an autosomal recessive disease, and it is caused by binding disruptions between the D’ domain (also known as TIL’E’) of von Willebrand Factor and a3 domain of factor VIII. A 2.9Å Cryoelectron microscopy structure of the FVIII:vWF complex …

Engineering Segmentally Labeled Intrinsically Disordered Proteins, Erin Rosenkranz

WWU Graduate School Collection

It has long been accepted that a protein’s fold informs its function, but for the vital proteins that don’t adopt one specified fold, this is uninformative. Intrinsically disordered proteins have non-folded regions (IDRs) in their native functional state, which make up 30% of eukaryotic proteins, perform vital cellular processes and contribute to a multitude of disease states. Yet, IDR’s function, interactions and dynamics remain unknown due to their unstable, dynamic, lengthy and solvent-exposed nature. This, along with their tendency for insolubility and aggregation provide formidable challenges to not only their analysis, but their purification, requiring lengthy optimizations. NMR is valuable …