Chemistry Commons^™

Computational Approaches To Anti-Toxin Therapies And Biomarker Identification, Rebecca Jane Swett

Wayne State University Dissertations

This work describes the fundamental study of two bacterial toxins with computational methods, the rational design of a potent inhibitor using molecular dynamics, as well as the development of two bioinformatic methods for mining genomic data.

Clostridium difficile is an opportunistic bacillus which produces two large glucosylating toxins. These toxins, TcdA and TcdB cause severe intestinal damage. As Clostridium difficile harbors considerable antibiotic resistance, one treatment strategy is to prevent the tissue damage that the toxins cause. The catalytic glucosyltransferase domain of TcdA and TcdB was studied using molecular dynamics in the presence of both a protein-protein binding partner and …

Development Of Peptide Inhibitors Targeting Clostridium Difficile Toxins A/B And Characterizing The Regulatory Role Of A Putative Negative Regulator Tcdc In Clostridium Difficile Toxin Gene Expression, Sanofar Jainul Abdeen

Wayne State University Dissertations

Clostridium difficile infections cause one of the most common and vital hospitalacquired

diseases often associated with broad-spectrum antibiotic usage. TcdA and TcdB

are the key virulence factors involved in major patho-physiology. While standard

antibiotics provide some respite, due to the high relapse rates and the emergence of more

severe disease presentations, antibiotics alone have often proven to be suboptimal.

Therefore there is a desperate need to develop an effective non-antimicrobial

therapeutics. Part of this work focuses on identification and further characterization of

peptide therapeutic that target the major virulence factor TcdA/TcdB. Towards

development of mechanistic-based anti-toxin agent, phage display was …

Single-Stranded Dna Scanning And Deamination With Single-Molecule Resolution, Padhuk Gamarala Senavirathne

Wayne State University Dissertations

SINGLE-STRANDED DNA SCANNING AND DEAMINATION WITH SINGLE-MOLECULE RESOLUTION

by

GAYAN SENAVIRATHNE

December 2013

Advisor: Dr. David Rueda & Dr.Ashok Bhagwat

Major: Chemistry (Analytical)

Degree: Doctor of Philosophy

APOBEC3G (Apo3G) and Activation-Induced cytidine Deaminase (AID) are the most notable members of APOBEC enzymes, a family of cytidine (C) deaminases with crucial functions in the immune system. In T cells, Apo3G deaminates C in viral cDNA to halt the replication of HIV 1 strains lacking viral infectivity factor (vif). In B cells, AID is required for the diversification of antibodies through initiation of somatic hypermutation (SHM), and class switch recombination (CSR), by …

Applications Of Electronic Structure Theory To Problems In Strong-Field Chemistry, Inorganic Chemistry, And Nanomaterial Systems, Jason Anthony Sonk

Wayne State University Dissertations

This dissertation covers research performed on applications of electronic structure theory to various fields of chemistry and is divided into eight chapters. Chapters 2 through 4 describe a series of related works which explore applications of excited state electronic structure methods to problems in strong field chemistry. Chapters 5, 6, and 7 discuss the application of electronic structure theory methods to solving problems in inorganic chemistry. Finally, Chapter 8 looks at an application of electronic structure theory to nanomaterials.

Chapter 2 covers the modeling of electron dynamics of butadiene interacting with a short, intense laser pulse in the absence of …

Metal Complexes Of Non-Heme Ligands: Biological Applications, Jai Prakash

Wayne State University Dissertations

Oxidative inactivation of proteins (carbonic anhydrase–I, trypsin, chymotrypsin and 20S proteasome) by non–heme iron complexes, and glutathionylation of non–heme cobalt complexes mimicking the N5 coordination environment like that of biologically important cofactor cobalamin or B₁₂ (Cbl) are reported. Different non–heme ligand sets or inhibitors were used to inactivate different proteins. Carbonic anhydrase–I (CA–I) and 20S proteasome were inactivated by iron complexes in the presence of O₂ and a reductant (DTT), consistent with a pathway involving the reductive activation of O₂, whereas serine proteases trypsin and chymotrypsin were inactivated by ferryls (single turnover), and by an iron …

"Fine-Tuning" Of Ribosomal Structure And Functions By Pseudouridylation And Rna-Protein Interactions, Jun Jiang

Wayne State University Dissertations

ABSTRACT

"Fine-tuning" of ribosomal structure and functions by pseudouridylation and RNA-protein interactions

by

JUN JIANG

AUGUST 2012

Advisor: Prof. John SantaLucia Jr.

Major: Chemistry (Biochemistry)

Degree: Doctor of Philosophy

Ribosomal structure and functions appear to be "fine-tuned" by pseudouridylation and RNA-protein interactions. Pseudouridylation may promote base stacking interactions by mediating the base stacking between residues on both sides. In the RNA duplex region, this enhanced stacking interaction contributes to stabilization of duplex folding. In the loop region, enhanced stacking in one structural motif may destabilize the conformation of adjacent structural residues. This hypothesis is supported by both UV-melting experiments, where …

State-Resolved Slice Imaging Of Photochemical Dynamics, Herath Mudiyans Nuradhika Herath

Wayne State University Dissertations

This dissertation focuses on the understanding the unimolecular photochemistry and dynamics

utilizing state-resolved slice imaging approach combined with the quantum-state selective

spectroscopy technique called resonance enhanced multi photon ionization (REMPI)

method. This powerful technique allows selecting the initial quantum states of the reactants

and determining the nal quantum states, energy, the orientation and alignments of

the products. In the investigations of photodissociation dynamics of acetone at 230 nm,

a bimodal distribution for the resulting CO photoproduct is identied. This observation

indicated the presence of unimolecular dissociation mechanism analogues to the roaming

dynamics reported in formaldehyde photodissociation. Moreover, another type of …

Development Of An Electrospary Ionization Source And Vacuum Interface For Guided Ion Beam Tandem Mass Spectrometry Experiments: Structural And Energetic Effects In The Molecular Recognition Of Amino Acids By 18-Crown-6, Yu Chen

Wayne State University Dissertations

Absolute 18-crown-6 (18C6) binding affinities of the side chains of AAs in peptides and proteins were determined in a step by step fashion using guided ion beam tandem mass spectrometry techniques. Firstly, 18C6 binding affinities of several peptidomimetic bases (B) that serve as mimics of the side chains of Lys, Arg, and His and n-terminal amino group have been examined to provide initial estimates of the 18C6 binding affinities of the side chains of AAs. The Bs were extended to natural occurring AAs and further extended to acetylated AAs (AcAA) to determine the binding affinities of the side chains of …

The Structural Requirements Of Histone Deacetylase (Hdac) Inhibitors: Suberoylanilide Hydroxamic Acid (Saha) Analogues Modified At C3, C6, And C7 Positions Enhance Selectivity, Sun Ea Choi

Wayne State University Dissertations

Histone deacetylase (HDAC) proteins are targets for drug design towards the treatment of cancers since overexpression of HDAC is linked to cancer. Several HDAC inhibitors, including the FDA approved drug suberoylanilide hydroxamic acid (SAHA, Vorinostat), have cleared clinical trials and emerged as anti-cancer drugs. However, SAHA inhibits all of the 11 metal ion-dependent HDAC proteins. Therefore, we synthesized several libraries of small molecule HDAC inhibitors based on SAHA to help understand the structural requirements of inhibitory potency and isoform selectivity.

In previous work, SAHA analogues functionalized at the C2 position (C2-SAHA analogues) near the metal binding hydroxamic acid displayed decreased …

Metal Chalcogenide Nanoparticle Gel Networks: Their Formation Mechanism And Application For Novel Material Generation And Heavy Metal Remediation Via Cation Exchange Reactions, Irina Ramona Pala

Wayne State University Dissertations

METAL CHALCOGENIDE NANOPARTICLE GEL NETWORKS: THEIR FROMATION MECHANISM AND APPLICATION FOR NOVEL MATERIAL GENERATION AND HEAVY METAL REMEDIATION VIA CATION EXCHANGE REACTIONS

by

IRINA R. PALA

February 2012

Advisor: Dr. Stephanie L. Brock

Major: Chemistry

Degree: Doctor of Philosophy

The dissertation research is focused on (1) uncovering the mechanism of metal chalcogenide nanoparticle gel formation; (2) extending the cation exchange reaction protocol to zinc sulfide gel networks, with the goal of accessing new aerogel chemistries and understanding the factors that drive the process; and (3) conducting a quantitative analysis of the ability of ZnS aerogels to remove heavy metal ions …

Synthesis, Spectroscopic, And Electrochemical Properties Of 3d Metal And Ruthenium Complexes With Phenolate And Catecholate Ligands, Frank Donald Lesh

Wayne State University Dissertations

The integration of amphiphilic properties into transition metal coordination systems is a pertinent step toward the development of candidate metallosurfactant precursors for the formation of responsive monolayer films. This concept is intended to preserve the solution-observed redox, spectroscopic, and magnetic responses onto solid surfaces for potential application. Selected metal ions and various ligand designs are investigated to address the effect of coordination and protonation preferences on amphiphilic behavior, the aspects of new modular approaches for Langmuir film precursors of differentiated topologies to extend amphiphilicity and redox behavior, and the introduction of photosensitizing properties into electroactive metallosurfactant precursors. In an attempt …

Probing The Dynamics Of Radical Reactions With Polyatomic Hydrocarbons By Crossed-Beam Dc Slice Imaging, Armando Dura Estillore

Wayne State University Dissertations

This work presents results of crossed molecular beam imaging studies on the reaction of radicals (Cl and CN) with polyatomic hydrocarbons of different functionalities such as pentane isomers, deuterated alkanes, alkenes, and alcohols. The reactively scattered alkyl radicals are probed as a function of collision energy using single photon ionization. The scattering results for pentane are quite similar for all reactants, suggesting that the nature of the abstraction site has surprisingly little influence on the dynamics studied at ~5 and ~9 kcal/mol. The angular distributions are broad with a backscattered peak at low collision energy and a sharp forward peak …

New Precursors And Chemistry For The Growth Of Transition Metal Films By Atomic Layer Deposition, Thomas Joseph Knisley

Wayne State University Dissertations

The advancing complexity of advanced microelectronic devices is placing rigorous demands on currently used PVD and CVD deposition techniques. The ALD deposition method is proposed to meet the film thickness and conformality constraints needed by the semiconductor industry in future manufacturing processes. Unfortunately, there is a limited number of chemical precursors available that have high thermal stability, reactivity, and vapor pressure suitable for ALD film growth to occur. These properties collectively contribute to the lack of suitable transition metal precursors available for use in ALD. In this thesis, we report the discovery of a series of novel transition metal diazadienate …

Genetic And Biochemical Studies Of Human Apobec Family Of Proteins, Priyanga Wijesinghe

Wayne State University Dissertations

The AID/APOBEC family of proteins in higher vertebrates converts cytosines in DNA or RNA into uracil. These proteins have essential roles in either innate immunity or adaptive immunity. Recently, AID has also been implicated in DNA demethylation in the context of early embryogenesis in mammals. This is partly based on the reported ability of AID to deaminate 5-methyl cytosine to thymine (5mC to T). I reexamined this proposed new role of AID (5mC deamination) with two members of the APOBEC family in a novel Escherichia coli based genetic system. My results confirmed that while all three enzymes are strong cytosine …

Synthesis And Characterization Of Size Controlled Transitionmetal Phosphide Nanoparticles And Their Hydrodesulfurization Catalytic Activity, Galbokka Hewage Layan Savithra

Wayne State University Dissertations

Transition metal phosphides are promising catalysts for hydrodesulfurization (HDS). The size-dependent catalytic activity of these metal phosphides for hydrodesulfurization (HDS) remains unstudied because the traditional temperature programmed reduction (TPR) method used in catalyst preparation results in highly polydisperse particles.

The main goals of this dissertation research are (1) synthesize metal phosphide nanoparticles (Ni²P, Rh²P, and Pd⁵P²) with control of size and morphology using a solution based arrested precipitation method; (2) develop large scale synthesis of mesoporous silica encapsulated nanoparticles (Ni²P and Pd⁵P²) with controlled loading to …

Synthesis And Á-Stereoselective Sialylation Of Kdn And Late Stage Modification Of Neuraminic Acid Sialosides, Chandra Sekhar Navuluri

Wayne State University Dissertations

ABSTRACT

SYNTHESIS AND á-STEREOSELECTIVE SIALYLATION OF KDN AND LATE STAGE MODIFICATIONS OF NEURAMINIC ACID SIALOSIDES

by

CHANDRA SEKHAR NAVULURI

December 2012

Advisor: Prof. David Crich

Major: Chemistry

Degree: Doctor of Philosophy

Keto deoxy nonulosonic acid has gained prominence in the recent years after the discovery of its presence in humans and the consequent appreciation of its role in human development and disease, and because of its potential as a marker of disease states. The development of efficient á-KDN sialylation methodology, an investigation of the mechanistic aspects of such sialylations, and the synthesis of this sparsely occurring sialic acid are the …

Synthesis And Characterization Of Group 5 Metal Complexes Containing Pyrazolate, Amidate, And Related Ligands As Potential Precursors For Thin Film Growth By Atomic Layer Deposition, Thuduwage Hiran Perera

Wayne State University Dissertations

Atomic Layer Deposition (ALD) is an advanced variant of Chemical Vapor Deposition (CVD) and is used to deposit smooth and conformal thin films for applications in the microelectronics industry. ALD requires metal precursors that are sufficiently volatile and thermally stable at elevated temperatures. Several group 5 ALD and CVD precursors were reported in the literature, which have been used to deposit TaN, NbN, Nb2O5, and Ta2O5 thin films. Synthesis of low and mid valent group 5 metal ALD precursors might give us access to deposit NbO2, Nb2O3, Ta2O3, and TaO2 thin films by low temperature ALD pathways upon applying mild …

Development Of A Cargo Delivery System And Inhibition Studies Focused On Clostridium Difficile Toxin A, Stephanie Marie Kern

Wayne State University Dissertations

Virulence factors of pathogenic bacteria are to be blamed for life-threatening infections such as diphtheria, anthrax, botulism, and tentanus. In the case of enzymatic exotoxins, disease arises from cytotoxic proteins, and cytotoxicity is acheived only after cell entry. This intrinsic mechanism for cell entry is intriguing from research and medical views. Along with a review on existing cargo delivery systems utilizing protein toxins and the usefulness of such a system, here is described the first reported Clostridium difficile toxin A fusion protein, luciferase-TcdA, and evidence of the successful transport of an active enzyme, luciferase, into the cytosol of vero cells. …

New Adaptations Of Analytical Tools For The Study Of Dynamic Interactions Of Lanthanide-Based Catalysis In Aqueous Media, Prabani Lakmanthi Dissanayake

Wayne State University Dissertations

Lewis acid catalyzed carbon-carbon bond-forming reactions are of great interest in organic synthesis. However, many conventional Lewis acids, and almost all enantioselective Lewis acid catalysts, must be used under strictly anhydrous conditions to avoid hydrolysis and the difficulties associated with recovery and reuse of the catalysts. Due to these drawbacks of conventional Lewis acids, there is a growing desire to perform many organic transformations using more environmentally friendly aqueous-stable catalysts. The advantages of using aqueous-stable catalysts include the ability to use unprotected functional groups, ease of product separation and catalyst recovery, and avoidance of costly solvent drying procedures. Lanthanide trifluoronmethanesulfonates …

Exploring Conformational Variability Of An Rna Domain In The Ribosome: From Structure And Function To Potential Antibiotic Targeting, Yogo Sakakibara

Wayne State University Dissertations

RNA in nature is modified at many specific sites to order to gain extra functions or to expand the genetic code. One of such RNAs is ribosomal RNA (rRNA), which contains several modified bases, particularly around the functionally significant sites. We have focused on understanding the influences of modified base on RNA structure and function by employing helix 69 (H69), which is a good region to evaluate the roles of modified bases since it contains three pseudouridines in the loop region and exists at the core of the ribosome.

Previous model studies using small hairpin H69 showed the conformational differences …

Drug Resistance Mechanisms And Drug Design Strategies For Human Immunodeficiency Virus And Hepatitis C Virus Proteases, Yong Wang

Wayne State University Dissertations

The antiviral drug development has improved steadily to treat the infections of human immunodeficiency virus (HIV) and hepatitis C virus (HCV) which represent heavy public health burdens. The viral protease plays an indispensable role in viral maturation and therefore becomes one of the most important targets for drug design. Nine HIV-1 protease inhibitors and two HCV protease inhibitors have been developed and approved by the U.S. Food and Drug Administration. However, mutations in the protease decrease reduce the efficacy the drugs. In this study, the enzyme assays indicate that darunavir and tipranavir exhibit the most potent inhibition against the multi-drug …

Single Molecule Studies Of Rna-Target Interactions, Sharla Leann Wood

Wayne State University Dissertations

We have used FRET, single molecule spectroscopy, and several other biophysical techniques to study how the folding of RNA allows it to perform its various functions by recognizing and binding a target ligand. We have shown that the c-di-GMP riboswitch undergoes a large, global conformational change upon binding of the ligand. The folding dynamics of the c-di-GMP riboswitch upon Mg2+ binding help to pre-organize the aptamer for efficient ligand binding and ultimately efficient gene expression. We have also investigated two instances, a fluorophore-binding aptamer and molecular beacon, where the folding of RNA can be used to detect an analyte. We …

Synthesis Of Oligosaccharide Mimetics By The Desulfurative Rearrangement Of Allylic Disulfides And Stereoelectronic Influence Of C-O Bonds On C- And O-Glycosylation, Myriame Moume-Pymbock

Wayne State University Dissertations

This dissertation focuses on two different problems. The first part of this manuscript presents the application of a novel methodology to access the synthesis of oligosaccharide mimetics while the second part focuses on the study of the stereoelectronic effects of proximal C-O bonds in C- and O-glycosylation reactions.

The first chapter provides a brief overview of the important roles that oligosaccharides and glycoconjugates play in biological processes and sets out the major advances that have been made in the past few decades in the synthesis of such complex structures while bringing out the ongoing challenges and the limitations that impede …

Effect Of Low Endogenous Brain-Derived Neurotrophic Factor Levels On Striatal Dopamine Dynamics, Francis Kabui Maina

Wayne State University Dissertations

Many neurological diseases and disorders are a result of alterations with neurotransmitters, neuromodulators, and/or proteins. Specifically, one protein that has been linked to numerous neurological diseases and disorders such as Parkinson's disease, Huntington's disease, addiction, attention deficit hyperactivity disorder (ADHD), and depression is brain-derived neurotrophic factor (BDNF). As a trophic factor, BDNF role is to assist in the growth, survival, and differentiation of neurons. However, there is increasing evidence that BDNF may mediate neurotransmitter dynamics. Our goals were to understand how endogenous BDNF levels and aging modulate the dopamine (DA) dynamics in the mouse striatum. Two complementary neurochemical techniques, slice …

Determination Of Descriptors By Liquid-Liquid Partition And Chromatographic Methods, Thushara Namal Karunasekara

Wayne State University Dissertations

ABSTRACT

DETERMINATION OF DESCRIPTORS BY LIQUID-LIQUID PARTITION AND CHROMATOGRAPHIC METHODS

by

THUSHARA KARUNASEKARA

September 2012

Advisor: Prof. Colin F. Poole

Major: Chemistry (Analytical)

Degree: Doctor of Philosophy

Partition coefficients for varied compounds were determined for several totally organic biphasic systems using formamide, propylene carbonate, ethylene glycol or dimethyl sulfoxide as the base solvent and n-heptane, 1,2-dichloroethane, 1-octanol or isopentyl ether as the counter solvent. These partition coefficient databases are analyzed using the solvation parameter model facilitating a quantitative comparison of these systems with other totally organic and water-based partition systems. These totally organic biphasic solvent systems offer a complementary approach …

Techniques For Sensor-Integrated Robotic Systems: Raman Spectra Analysis, Image Guidance, And Kinematic Calibration, Luke Anthony Reisner

Wayne State University Dissertations

Robotics and sensor technology have made impressive advancements over the years. There are now robotic systems that help perform surgeries or explore the surface of Mars, and there are sensors that detect trace amounts of explosives or identify diseased human tissue. The most powerful systems integrate robots and sensors, which are natural complements to each other. Sensors can provide information that might otherwise be unavailable due to indirect robotic manipulation (e.g., images of the target environment), and robots can provide suitably precise positioning of an analytical sensor.

To have an effective sensor-integrated robotic system, multiple capabilities are needed in the …

Nmr Solution Structures Of Two Hairpins Of E. Coli 16s Rrna: The Effects Of Mutations And Chemical Modifications On Structure And Function Of Rrna, Yu Liu

Wayne State University Dissertations

The structures of two functional mutants, the UC (G690U, U697C) and the QM mutants (G690A, G693C, A695C, U697A) of the 690 hairpin of E. coli 16S ribosomal RNA were determined by NMR. The UC mutant and the QM mutant with high biological function are able to fold into structures that are isomorphous with the wild-type 690 hairpin sequence. The structural comparisons among the functional mutants and the wild-type provides structural validation for previously identified specific functional groups that are crucial for maintaining function of the 690 hairpin. The key groups for maintaining the structure and function of the 690 loop …

Exploring Potential Drug Target Sites In The Ribosome Using Cisplatin And Its Analogues, Keshab Rijal

Wayne State University Dissertations

Cis-diamminodichloridoplatinum (II), cisplatin, is an antitumor drug that has been used to treat several types of cancers. The reaction of cisplatin with DNA has been studied and discussed extensively in the literature; however, the effects of cisplatin on RNA function are poorly understood. In this thesis, two aspects of cisplatin, its preferred sites of interaction with RNA and its use as a chemical probe to gain accessibility information, were explored.

To understand the site-selectivity of cisplatin with RNA, model RNA constructs and full-length 16S rRNA were employed. The binding studies revealed a cisplatin preference for guanosine-rich sequences. Primer extensions in …

Synthesis Of N-Acetyl And C-Tert-Butyl Natural Amino Acid Substrates That Mimic Residues Of Polypeptides And Their Reactivity With [Feiv(O)(N4py)]2+: Kinetic And Mechanistic Investigations, Ashley Ann Campanali

Wayne State University Dissertations

This dissertation is divided into two chapters, the first chapter includes an introduction to reactive oxygen species and their reactions with proteins. The introduction also covers metal-based oxidants, including both heme and non-heme enzymes that activate dioxygen as well as complexes that mimic these enzymes. The work discussed in chapter one concerns the synthesis of amino acid substrates that mimic amino acid residues. Substrates synthesized were derived from Gln, Asn, Ile, Cys and Tyr. Once synthesized, these substrates were reacted with [FeIV(O)(N4Py)]2+ under pseudo-first order conditions. The mechanisms for the reactions of the most reactive substrates were investigated. Electron-transfer proton-transfer …

Study Of Protein-Rna Interactions Using Fluorescence Resonance Energy Transfer (Fret) And Single-Molecule Fret, Rajan Lamichhane

Wayne State University Dissertations

In the cell, RNA and protein, interact to form ribonucleoprotein complexes (RNPs) that have vital structural, catalytic and regulatory roles. Despite their functional importance, the mechanistic details and dynamics of RNPs are poorly understood. Single-molecule Fluorescence Resonance Energy Transfer (smFRET) techniques that provide information about heterogeneity and dynamic behaviors of molecules have been developed to investigate inter- and intra-molecular interactions. Here we have used FRET in combination with smFRET to study three very different RNP systems.

Alternative splicing is a highly regulated biological process that plays a crucial role in proteomic diversity in eukaryotes. One splicing regulator, PTB, has been …