Chemistry Commons^™

Blood Coagulation Factor Ix: Purification, Activation, Crystallization, Juliet Mcgill

WWU Honors College Senior Projects

This paper presents readers with an optimized procedure for the purification, activation, and crystallization of selected blood coagulation Factor IX double mutant (FIX_2). Through the completion of this work, we aim to enhance future biochemical and structural studies by providing an easier means for the FIX_2 production, in order to increase understanding of the protein’s function within the blood coagulation cascade. The initiation of the blood coagulation cascade is brought on by activation of inactive Factor VIII (FVIII) protein though contact with tissue factor, the FVIII protein then binds to an activated platelet surface where it must wait for its …

Supporting Data For Impact Of The Macrophyte Nymphaea Odorata (Lily Pads) On Dissolved Organic Matter (Dom) In A Lake, Kyle Juetten, Warren J. De Bruyn, Zachary Landram, Aaron Harrison, Angela Strecker, Catherine D. Clark

Chemistry Faculty and Staff Publications

(Files are available for download below.)

This is supporting data for a publication on the role of lily pads in contributing to the dissolved organic matter pool in Lake Louise, a small lake in the Pacific Northwest region of the USA. Specifically, this data includes the absorbance and fluorescence spectra of the Lake Louise water samples (taken weekly over the course of 2018). These files include large spreadsheets with raw and corrected absorbance and fluorescence intensity data as a function of wavelength, as well as the raw and corrected absorbance and fluorescence 3D excitation-emission matrix spectra (EEMs). These files are …

Investigations On The Active Catalyst In Pd Catalyzed Organic Reactions, Riley Mcgraw

WWU Honors College Senior Projects

Cross coupling and C-H functionalization reactions are valuable tools in the synthesis of pharmaceuticals, natural products, fine chemicals, and electronics. Molecular precatalysts are frequently used in both reactions but because the reactions use conditions like those employed in intentional preparation of nanoparticles, the presence of nanoparticles is highly likely for both systems. In the case of the cross-coupling reaction, nanoparticles have been shown to have catalytic relevance, but C-H functionalization reactions are widely thought to occur by means of a homogenous catalyst. To better understand the state of the active catalyst, a method of homogeneity analysis by centrifuge is proposed. …

Synthesis And Characterization Of Hydroxy-Functionalized Copper Indium Disulfide Quantum Dots, Julia Schexnayder

WWU Honors College Senior Projects

Quantum dots offer tunable electronic and optical properties due to the quantum confinement effect, making them desirable for various applications. However, their native hydrophobic form requires surface chemistry modification for certain applications. This research explores the method of ligand exchange using 11-mercapto-1-undecanol for improving the stability of copper indium disulfide (CIS) quantum dot (QD) nanoparticles in polar environments. The effects of this ligand exchange on QD chemical composition, optical properties, hydroxy-reactivity, and hydrodynamic radius are characterized. Analysis of characterization results indicates successful surface modification through hydroxyfunctionalization, as confirmed by 1H-NMR and IR spectroscopy. The desired optical properties of the QDs …

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, …

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 …

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 …

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 …

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 …

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.

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 …

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 …

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 …