Chemistry Commons^™

Elucidating The Binding Characteristics Of Lrp1 In Factor Viii Blood Coagulation, Nicole Topor-Madry

WWU Graduate School Collection

Abstract

Factor VIII and von Willebrand factor (vWF) are essential for blood coagulation. FVIII, a large glycoprotein with 2332 amino acids, is crucial in the intrinsic pathway of coagulation. After secretion, FVIII circulates in the bloodstream at approximately one nanomolar concentration, bound to vWF, which protects it from rapid clearance. In response to vascular injury, FVIII is proteolytically activated, dissociates from vWF, and binds to activated platelet surfaces and activated Factor IX, dramatically accelerating the rate of blood clot formation. Hemophilia A, affecting 1 in 5000 males, results from functional FVIII deficiency. Standard treatment involves prophylactic FVIII injections but has …

Transition State Kinetics Through Kramers’ Rate For Variationally Enhanced Sampling., David Cummins

WWU Graduate School Collection

Molecular Dynamics (MD) simulations use Newtonian mechanics applied at finite time steps to numerically propagate the time-trajectory of a dynamical system. However, many biochemical processes such as catalysis, ion channel gating, substrate binding, and protein folding evolve over time scales which are orders of magnitudes greater than those afforded by MD and the computational power available today. The development of methods that reduce the computational cost of sampling such rare events help to provide a dynamic insight into these processes. This thesis explores the application of a recently developed enhanced sampling method, Variationally Enhanced Sampling (VES), for calculating kinetic rate …

Revealing Binding And Unbinding Pathways Of Small Molecules And Peptides To Enzymes With Enhanced Sampling Methods, Kayla Ariana Croney

WWU Graduate School Collection

In vitro experiments are critical to understanding the biochemistry of molecular systems but it can be a challenge to obtain atomistic resolution. Computational chemistry gives insight to these results with molecular dynamics (MD) simulations using Newton’s equations of motion to analyze the motion of atoms and molecules. However, due to insufficient sampling and long-lived metastable states separated by high energy intermediates, enhanced sampling methods must be applied. Metadynamics (MetaD) enhances the exploration of MD by adding time-dependent bias. Here, we applied MetaD to two enzymes to study their substrate binding/unbinding pathways with their respective substrates. Yeast cytosine deaminase (yCD) deaminates …

Synthesis And Dft Investigations Of Silver Nanocubes Coated With Gold Layers For Enhanced Stability, Ayomide Daniel Oluwafemi

WWU Graduate School Collection

Silver nanocubes (Ag nanocubes) are one of the most important nanostructures, due to their plasmonic capabilities. However, their susceptibility to oxidation upon exposure leads to rounding of their edges or sharp corners, compromising quality and stability. A feasible option to address this issue is to deposit a second metal, such as gold (Au), which is resistant to oxidation, onto the Ag nanocubes. Regrettably, manipulating the synthetic parameters that shape Au coated Ag nanocubes is difficult. The galvanic replacement reaction between Au and Ag can erode, hollow, and disintegrate the Ag nanocubes. We explore several synthetic pathways to achieve well-controlled shaped …

Post Polymerization Modification And Preparation Of Dynamic Polymer Networks Via Guanylation Of Aryl Carbodiimides, Conner J. Klingler

WWU Graduate School Collection

Styrenic carbodiimide (CDI) polymers have shown an interesting ability to form reversible polymer networks, known as covalent adaptable networks (CANs), through an uncatalyzed reaction with multifunctional amines. CANs have been a topic of interest in polymer chemistry due to their ability to be reprocessed, which is not found in classic thermoset polymer networks. However, not much is known about the capabilities of the nucleophilic addition of amines to aryl CDI repeat unit structures that goes into making these networks due to the understudied reactions involved. This thesis aims to develop a better understanding of the chemistry involved through various post …

Examining The Nexus Between Scientific Literacy And Identity In General Chemistry, Tiffany Chamberlain

WWU Graduate School Collection

Scientific literacy is a crucial goal of science education. All citizens need scientific understanding to make rational and informed decisions, and to feel confident in making such decisions. Many students harbor doubts about belonging in science and their identities as science persons. As such, science educators are tasked with helping students develop these skills as they engage in various courses. College instructors incorporate scientific literacy skills as part of their courses in which students are encouraged to develop a science person identity (i.e. science identity) through science identity work. Therefore, learning can be seen as a process of identity …

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.

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 …

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 …

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 …

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 …

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, …

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 …

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 …

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 …

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 …

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 …

Synthesis, Characterization, And Applications Of Thiolated Silk Fibroin, Jeremy Martinez Talusig

WWU Graduate School Collection

Thiolated polymers, or thiomers, have demonstrated advanced adhesion to biological surfaces such as mucus membranes due to their ability to form disulfide bonds to the cysteine-rich domains in mucin making them an attractive drug delivery system. Silk fibroin, a protein derived from the Bombyx mori silkworm, offers a biocompatible and biodegradable platform absent in other thiomer systems. However, due to the small percentage of native cysteine residues in silk, installation of additional thiols is essential to create an advanced thiomer adhesive. In this research, covalent attachment of non-native thiols to the tyrosine residues of silk fibroin is accomplished with a …

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 …

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 …

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 …

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 …

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 …

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 …

Extension Of Restricted Open-Shell Kohn-Sham Methodology To A Density-Functional Tight-Binding Framework, Reuben Szabo

WWU Graduate School Collection

The restricted open-shell Kohn-Sham (ROKS) approach for singlet excited states provides some advantages over the ∆-self-consistent-field (∆SCF) method, requiring only a single SCF procedure and avoiding the problem of variational collapse. While ROKS is a powerful tool for DFT, its application to density functional tight-binding (DFTB) could offer significant improvements in time complexity when compared to DFT, enabling excited-state simulations of extended molecular systems on longer timescales than ROKS. In this work we discuss the implementation of an RO-DFTB approach in the DFTB+ package, as well as its suitability for the study of organic dyes and photoactive compounds. For benchmarking, …

Chemical Modification Of Silk Protein Via Palladium-Mediated Suzuki-Miyaura Reactions, Racine Santen

WWU Graduate School Collection

Suzuki-Miyaura cross-coupling reactions were used to modify the tyrosine residues on Bombyx mori silkworm silk proteins using a water-soluble palladium catalyst. Utilizing this cross-coupling reaction, molecules with specific functions can be introduced to silk in order to broaden the capabilities of silk proteins in biological systems. Model reactions using tyrosine derivatives were first screened to optimize reaction conditions. For these reactions, a variety of aryl boronic acids, solvents, buffers and temperature ranges were explored. Qualitative information on the reaction progress was collected via high performance liquid chromatography (HPLC), mass spectrometry (MS) and nuclear magnetic resonance (NMR). Reactions were then applied …

Structural And Mutational Characterization Of The Blood Coagulation Factor Viii C Domain Lipid Binding Interface, Shaun C. Peters

WWU Graduate School Collection

Blood coagulation factor VIII (fVIII) functions as a cofactor in the blood coagulation cascade for proteolytic activation of factor X by factor IXa. During coagulation, fVIII is activated and subsequently binds to activated platelet surfaces by coordination of the fVIII C1 and C2 domains to the exposed phosphatidylserine of activated platelet membranes. Structural and mutational studies have suggested that both hydrophobic and electrostatic interactions occur between the two tandem C domains and activated lipid surfaces, but models of C domain phospholipid binding propose conflicting regions that directly interact with the membrane surface. This thesis reports the determination of the molecular …

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 …