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Mutagenic And Spectroscopic Investigation Of Ph Dependent Cooa Dna Binding, Brian R. Weaver

Chemistry Honors Papers

The carbon monoxide (CO) sensing heme protein, CooA, is a transcription factor which exists in several bacteria that utilize CO as an energy source. CooA positively regulates the expression of coo genes in the presence of CO such that the corresponding proteins may metabolize CO. The present studies have yielded the unexpected result that Fe(III) CooA binds DNA tightly at pH < 7, deviating from all previously reported work which indicate that CooA DNA binding is initiated only when the exogenous CO effector reacts with the Fe(II) CooA heme. This observation suggests that the disruption of one or more salt bridges upon effector binding may be a critical feature of the normal CooA activation mechanism. To test this possibility, several protein variants that eliminated a selected salt bridge for the CooA homolog from Rhodospirillum rubrum were prepared via site-directed mutagenesis. Samples of these variant proteins, which were overexpressed in Escherichia coli, were then characterized by spectroscopic methods and functional assays to investigate the impact these mutations had on CooA heme coordination …

Protein Engineering Of Cota Laccase By Using Bacillus Subtilis Spore Display, Silu Sheng

Dissertations

Spore display offers advantages over more commonly utilized microbe cell-surface display systems. For instance, protein-folding problems associated with the expressed recombinant polypeptide crossing membranes are avoided. Hence, a different region of protein space can be explored that previously was not accessible. In addition, spores tolerate many physical/chemical extremes. The aim is to improve pH stability using spore display. The maximum activity of CotA is between pH 4 and 5 for the substrate ABTS (ABTS = diammonium 2, 2’-azino-bis(3-ethylbenzothiazoline-6-sulfonate)). However, the activity dramatically decreases at pH 4. The activity is not significantly altered at pH 5. CotA is used as a …

Synthesis And Detection Of Dna Damage, Xun Gao

Dissertations

The biological effects of DNA alkyl adducts are difficult to evaluate at the cellular level due to their instability. Synthesis of oligonucleotides that contain a single N7-alkylguanine has become a vital tool to achieve the above goal. However, the instability of N7-alkyguanines is not compatible with the phosphoramidite chemistry used by solid-phase oligonucleotide synthesis either. Development of chemically stable analogues of unstable DNA lesions enables accurate study of polymerase bypass. The design and successful synthesis of N7-hydroxyethyl-9-deaza-2′-deoxyguanosine and N7-oxoethyl-9-deaza-2′-deoxyguanosine as the stable analogues of N7-hydroxyethyl- 2'-deoxyguanosine and N7-oxoethyl-2′-deoxyguanosine, respectively, are reported. The synthesis of these two nucleosides whose N7 side …

An Expedited, Regiospecific Para-Bromination Of Activated Aryls, Kathryn E. Dudley

Masters Theses & Specialist Projects

Electrophilic Aromatic Substitution (EAS) is one of the most frequently used aryl substitution methods. Aside from the fact that most EAS reactions require an acid and an oxidizer to proceed, the reactions involving activated aryls typically produce a mixture of ortho- and para- products as well as an ortho-/para- disubstituted product. Regiospecificity in aromatic substitution is key in the production of many compounds in a variety of disciplines. Since EAS is one of the most often used substitution methods, it is extremely important to develop an efficient method for regiospecific substitutions. Previous research developed a method of ortho-substitution by using …

The Effects Of Carrier Ligands On Cisplatin Binding To Cysteine And Methionine, Adam C.R Smith

Masters Theses & Specialist Projects

We have reacted several derivatives of the anticancer drug cisplatin with N-acetyl-Lcysteine (N-AcCys) and N-acetyl-L-methionine (N-AcMet), which are two of the primary amino acid targets of platinum. NMR spectroscopy was used to monitor the reactions and determine the effect the different ligands would have on the platinum reactivity. Several of the platinum compounds were tested at pH of 4 and 7, and with platinum:amino acid ratios of 1:1, 2:1 and 1:2. Competition reactions between cysteine and methionine were done to confirm which would react with the platinum compound first. [Pt(dien)(NO3)]+ reacts faster with methionine than with cysteine at both pH …

Environmentally Friendly Synthesis Of Transition Metalorganic Hybrid Nanocomposites, Aubrey N. Penn

Masters Theses & Specialist Projects

Research on metal nanoparticles (MNPs) synthesis and their applications for optoelectronic devices has been a recent interest in the fields of nanoscience and nanotechnology Photovoltaics are one of such systems in which MNPs have shown to be quite useful, due to unique physical, optical, magnetic, and electronic properties, including the metal nanoparticles synthesized in this research.

Owing to the challenges with the most common physical and chemical methods of preparing MNPs, including the use of high temperatures, toxic reducing agents, and environmentally hazardous organic solvents, there is a critical need for a benign synthesis procedure for MNPs. In this work, …

Regiospecific P-Bromination Of Activated Aromatic Systems – Greener Approach, Elnaz Jalali

Masters Theses & Specialist Projects

The halogenated derivatives of heterocyclic compounds (haloarenes) are highly utilized in many fields of chemistry, including drug discovery, medicinal, and material chemistry. There are a variety of ways to functionalize an aromatic system and introduce halogen substituent into the ring. However, electrophilic aromatic substitution (EAS) has been the focus of growing attention, particularly for electronrich substrates.

Electrophilic aromatic bromination protocols are one of the most important electrophilic aromatic substitution reactions. However, preparation of bromoarenes classically recommends the use of highly oxidative agents along with utilizing various metal catalysts in a halogenated solvent. The corrosive and toxic nature of these reagents …

Tio2/Pdms Buoyant Photocatalyst For Water Remediation And Cu‑Rbs Organic/Inorganic Hybrid For Thermoelectric Applications, John R. Bertram

Masters Theses & Specialist Projects

Two novel materials have been developed: TiO2/poly(dimethylsiloxane) (PDMS) beads as buoyant photocatalyst materials for water remediation, and copper rhodamine‑B silane (Cu‑RBS) as an n ‑type organic/inorganic hybrid for thermoelectric applications. The approach to incorporate TiO2 into low‑density PDMS beads addresses many of the challenges traditionally encountered when creating buoyant photocatalysts, an area which is crucial for wide‑spread remediation of water resources, including natural bodies of water. The performance and reusability of the buoyant photocatalyst materials, demonstrated by using methylene blue as a model degradation target, is strong enough for environmental application. The use of a kinetic model and the introduction …

Investigating The Effects Of Pre-Laboratory Videos With Associated Questions On The Performance And Overall Laboratory Experience Of Organic Chemistry Students, Shareef Gamal Mohamed Kotb

Health Sciences Student Work

Background: Teachers struggle communicating ideas to students (Moreno et al, 2001). One of the aspects of teaching that’s most concerning is when students experience cognitive overload: the total effort exerted by working memory to grasp new information (Mayer, et al, 2002). The educational community found that introducing multimedia in learning minimizes cognitive overload (Mayer, et al, 2002). Little research has related to undergraduate chemistry classes, specifically the relationship between organic chemistry pre-laboratory multimedia and student learning. Purpose: The purpose of this capstone is to investigate the subjective efficacy of integrating pre-laboratory videos for lab preparation in an undergraduate organic chemistry …

Special Elements Of Excellence: Spring 2017, Department Of Chemistry

Chemistry News

• Chair's Welcome
• The Science Behind Crafting Beer
• 10 Year Chemistry Building Celebration 8th Annual Research Chemistry Research Day & Spring 2017 Awards
• KALSEC Tour - An Insider's Look
• New Faculty Specialist!
• 2017 Million Dollar Club
• Frontiers in Chemistry Lectureship
• Recent Awards received by Students and Faculty of the WMU Department of Chemistry
• Examples of Published Research from the Faculty of WMU Department of Chemistry

Correlated Mutation In The Evolution Of Catalysis In Uracil Dna Glycosylase Superfamily, Bo Xia, Yinling Liu, Jose Guevara, Jing Li, Celeste Jilich, Ye Yang, Liangjiang Wang, Brian N. Dominy, Weiguo Cao

Publications

Enzymes in Uracil DNA glycosylase (UDG) superfamily are essential for the removal of uracil. Family 4 UDGa is a robust uracil DNA glycosylase that only acts on double-stranded and single-stranded uracil-containing DNA. Based on mutational, kinetic and modeling analyses, a catalytic mechanism involving leaving group stabilization by H155 in motif 2 and water coordination by N89 in motif 3 is proposed. Mutual Information analysis identifies a complexed correlated mutation network including a strong correlation in the EG doublet in motif 1 of family 4 UDGa and in the QD doublet in motif 1 of family 1 UNG. Conversion of EG …

The Coastal Monitor: Vol 2. No 1., John Tanacredi Ph.D.

The Coastal Monitor

There is something enchanting and vibrant about viewing the coast. Every day at CERCOM we are welcomed by either a vivid sunrise, a view of the barrier island Fire Island and a blending of the sky across the horizon, ultimately flooding the Great South Bay with either clouds or sunshine that reveals the Bay’s surface as either shimmering with sunlight, or an integration of sky and water as an endless ocean. I don’t normally wax poetic but the varying sights along the near shore ocean and this embayment beckon our scientific inquisitiveness. What’s below the surface water? How do animals …

Ruthenium-Catalyzed Dehydrogenative And Dehydrative C-H Coupling Reactions Of Arenes With Alcohols And Carbonyl Compounds, Hanbin Lee

Dissertations (1934 -)

Despite their outstanding achievements, the requirement of preformed functional groups and wasteful byproduct formation are inherent disadvantages associated with the transition metal catalyzed cross-coupling methods. Inspired by the needs for green and sustainable chemistry, transition metal catalyzed dehydrogenative and dehydrative coupling methods have been recognized as environmentally sustainable and atom economical synthetic routes for the new C-C bond formation. The catalytic activation of C-H and C-O bonds allows the formation of coupling products from ubiquitous hydrocarbon substrates by releasing hydrogen or water byproduct. However, these novel protocols require relatively harsh conditions due to their low reactivity of C-H and C-O …

Synthesis, Kinetic And Catalytic Studies Of Manganese Complexes With Corrole And Porphyrin Ligands, Haleh Jeddi

Masters Theses & Specialist Projects

High-valent transition metal-oxo intermediates play a significant role in the catalytic cycle of the ubiquitous cytochrome P450 enzymes and in biomimetic catalytic systems. In this work, manganese(III) porphyrin and corrole systems (2) were synthesized and characterized by UV-vis absorbance and 1H-NMR, matching literaturereported spectroscopic data. Manganese(V)-oxo corroles (3) and a manganese(IV)-oxo porphyrin (4) were successfully generated by chemical oxidation using mchloroperoxybenzoic acid (m-CPBA), and their oxidation reactions with organic reductants were comparatively investigated. Results from single-turnover kinetic studies indicate that in the tris(pentafluorophenyl)corrole system (3a), the active oxidizing intermediate differs in different solvents. The active oxidizing intermediate in acetonitrile is …

Effects Of Binding Affinity Between Bovine Serum Albumin And Platinum Drugs, Nathan Puckett

Masters Theses & Specialist Projects

Platinum complex drugs such as cisplatin have been used as highly successful chemotherapy drugs since the 1970s. We are interested in how the ligands attached to cisplatin analogs influences their reactivity with biologically relevant targets along with time and amount. For this study, reactions were conducted to determine the reactivity between different platinum compounds and the protein bovine serum albumin. Various platinum compounds with different ligands were reacted in varying amounts with albumin in ammonium acetate buffer for either 1 hour, 4 hours, or 24 hours. Each reaction was quenched after the designated reaction time by dialysis and the platinum …

Antimicrobial Activities Of Tea-Derived Flavonoids Against Skin Staphylococci, Ahyun Hong

CUP Undergraduate Research

This thesis investigates the antimicrobial activities of tea-derived flavonoids against skin Staphylococci. Four hypotheses were tested: (1) Teas that contain high polyphenolic contents possess higher antimicrobial activity against skin bacteria (e.g. S. aureus and S. epidermidis); (2) Different tea infusions and tea-derived individual catechins show differential inhibition of S. aureus and S. epidermidis; (3) Different tea infusions and tea-derived individual catechins show differential inhibition of S. aureus isolated from individuals with and without chronic atopic dermatitis; (4) EGCg, the most abundant polyphenols found in tea, possess the highest anti-staphylococcal activity. We employed multiple methods such as Folin-Ciocalteau colorimetric …

Synthesis Of Bis(Quinoxalino) Ligand For The Removal Of Transition Metal Contamination, Alexander J. Farmer

Honors Theses

Transition metal contamination is a constant concern both in the environment and in chemical reaction mixtures. One proposed solution, is the use of peraza-crown macrocycles to selectively bind and remove transition metals. The aim of our project is to determine the novel synthesis of bis(quinoxalino) peraza-crown macrocycles for use as ligands to bind to transition metals. Our proposed molecules incorporate the rigid quinoxaline subunit into an aza-crown macrocycle which can improve binding properties. The synthesis route is novel and overcomes several limitations of the existing methods of aza-crown macrocycle preparation. We have designed the synthesis in such a way that …

The Effects Of Structural Modification Of The Wing Helix Domain Of Pria On Bacterial Dna, Erich Auer

Honors Theses

During a cell’s life it must copy itself or face death. For the cell to form a new copy it must replicate its DNA, this DNA is the blueprint for the essential components of the cell. The replication process does not always go to completion, which is necessary for the cell to survive, so there are mechanisms to keep the replication process running smoothly. In bacteria, PriA is used to restart replication after damage to the DNA. By looking at the structure of PriA we can start to determine how exactly it works with the damaged DNA and restart the …

Oxygen Activation By Mononuclear Mn, Co, And Ni Centers In Biology And Synthetic Complexes, Adam T. Fiedler, Anne A. Fischer

Chemistry Faculty Research and Publications

The active sites of metalloenzymes that catalyze O₂-dependent reactions generally contain iron or copper ions. However, several enzymes are capable of activating O₂ at manganese or nickel centers instead, and a handful of dioxygenases exhibit activity when substituted with cobalt. This minireview summarizes the catalytic properties of oxygenases and oxidases with mononuclear Mn, Co, or Ni active sites, including oxalate-degrading oxidases, catechol dioxygenases, and quercetin dioxygenase. In addition, recent developments in the O₂ reactivity of synthetic Mn, Co, or Ni complexes are described, with an emphasis on the nature of reactive intermediates featuring superoxo-, peroxo-, or …

Nmr Line Shape Analysis Of A Multi-State Ligand Binding Mechanism In Chitosanase, Shoko Shinya, Mariana G. Ghinet, Ryszard Brzezinski, Kyoko Furuita, Chojiro Kojima, Sneha Shah, Evgenii L. Kovrigin, Tamo Fukamizo

Chemistry Faculty Research and Publications

Chitosan interaction with chitosanase was examined through analysis of spectral line shapes in the NMR HSQC titration experiments. We established that the substrate, chitosan hexamer, binds to the enzyme through the three-state induced-fit mechanism with fast formation of the encounter complex followed by slow isomerization of the bound-state into the final conformation. Mapping of the chemical shift perturbations in two sequential steps of the mechanism highlighted involvement of the substrate-binding subsites and the hinge region in the binding reaction. Equilibrium parameters of the three-state model agreed with the overall thermodynamic dissociation constant determined by ITC. This study presented the first …

A Program Aimed Toward Inclusive Excellence For Underrepresented Undergraduate Women In The Sciences, Laura A. Katz, Kathryn M. Aloisio, Nicholas J. Horton, Minh Ly, Sara B. Pruss, Kate Queeney, Cate Rowen, Patricia Marten Dibartolo

Biological Sciences: Faculty Publications

Created to foster inclusive excellence, Smith College’s Achieving Excellence in Mathematics, Engineering, and Science (AEMES) Scholars program provides early faculty-mentored research opportunities and other programming as a way to foster success in academic outcomes for underrepresented women in science. Using academic record data, we compared Scholars’ outcomes over time with those of underrepresented students before program launch and to relevant peer comparison groups. Since its launch, AEMES Scholars have achieved significantly higher gateway life sciences course grade point averages (GPAs), rates of persistence in life and natural sciences, and participation in natural sciences advanced research relative to baseline. Gains for …

Emerging Antimicrobial Research Against Superbugs: Perspectives From A Polymer Laboratory, Mitra S. Ganewatta, Md Anisur Rahman, Chuanbing Tang

Journal of the South Carolina Academy of Science

Infectious diseases caused by drug-resistant microorganisms have become a major contributor for human morbidity and mortality. To overcome such threats, we have developed various antimicrobial agents using natural product derivatives and metallopolymers. Abundant biomass such as resin acids can be utilized to prepare cationic polymers for inhibiting a variety of bacteria. These polymers have been used in solution as well as surfaces as antimicrobial materials with low cytotoxicity. In addition, a class of charged metallopolymers have been developed to kill superbugs such as MRSA.

Table Of Contents

Journal of the South Carolina Academy of Science

No abstract provided.

Antitumor Activity Of Selected Derivatives Of Pyrazole- Benzenesulfonamides From Dilithiated C(Α), N-Phenylhydrazones And Lithiated Methyl 2-(Aminosulfonyl)Benzoate, N. Dwight Camper [Deceased], James M. Gum, Darby E. Lyles, William T. Pennington, Charles F. Beam, Clyde R. Metz

Journal of the South Carolina Academy of Science

Several pyrazole-benzenesulfonamides were subjected to biological evaluation involving tumor formation on potato discs caused by Agrobacterium tumefaciens. This assay led to some excellent and promising initial results with three of the pyrazole compounds showing increased tumor inhibition when compared to a recognized standard, camptothecin. The select pyrazole-benzenesulfonamides were prepared by condensation-cyclization of several dilithiated C(α),N-phenylhydrazones with lithiated methyl 2-aminosulfonyl-benzoate.

Differential Response Of Coral Symbiotic Dinoflagellates To Bacterial Toxins That Produce Bleaching In Stony Corals, Diego L. Gil-Agudelo, Yael Ban-Haim, Eugene Rosenberg, Garriet W. Smith

Journal of the South Carolina Academy of Science

Bleaching of corals and other organisms with symbiotic zooxanthellae is a worldwide phenomenon with increasing importance due to global warming scenarios. Bleaching has been historically related to changes in the environment, especially water temperature increase, that stress corals and provoke the release of zooxanthellae. The discovery of Vibrio shilonii, a bacterium causing bleaching under thermal stress in corals of the Mediterranean Sea has changed our thinking about the cause (or explanation) for bleaching of corals worldwide. During this study, we evaluated the effect of a proline rich toxin, extracted from Vibrio shilonii, on zooxanthellae obtained from: Oculina patagonica from the …

Biosorption Of Pharmaceuticals And Noble Metals Nanoparticles By Algal Turf Communities, Haider Abid Faraj

Dissertations

Pharmaceuticals and nanoparticles are increasingly released into the aquatic ecosystem, while removing these contaminants from waters can be challenging. This study explores the use of periphytic algal turf communities to remove these contaminants. Initially algal turfs from different locations and aquatic systems were analyzed for pharmaceuticals commonly observed in wastewater outflows. Lab-grown turfs were exposed to a mixture of six representative pharmaceuticals of different functionality (acid, base, neutral and steroidal). Analysis of water column and the algal biomass showed pharmaceutical removal rates varied, specific to each pharmaceutical. Caffeine and estradiol had the highest removal rates while carbamazepine was not removed. …

Sdsl-Epr Of Residues 60-70 Of Influenza M2 Protein Reveals Structural Properties Of A Region Involved In Viral Budding, Grace Kim , '17

Senior Theses, Projects, and Awards

The M2 protein is a 97-residue multifunctional transmembrane homotetrameric protein. It is found in the viral coat of the Influenza A virus, which is responsible for approximately 250,000 to 500,000 deaths annually worldwide.¹ Extensive research has elucidated M2's role as an ion channel, which plays a critical role in the uncoating of the viron once it has entered the host cell. The C-terminal tail of M2 has also been shown to play a crucial role in generating curvature in the cell membrane to mediate viral budding.²³ Deletions in the C-terminal tail of the M2 protein lead to impaired viral infectivity.⁴ …

Combination Therapy Of Prostate Cancer Utilizing Functionalized Iron Oxide Nanoparticles Carrying Tnf-A And Lactonic Sophorolipids, James Beach, Tuhina Banerjee, Jyothi Kallu, Ryan Higginbotham, Richard Gross

Paper and Posters Presentations

Prostate cancer is one of the most prevalent forms of cancer afflicting men in the United States. In recent years, advances in the field of nanotechnology have allowed for new and innovative ways to treat various types of cancer and various other diseases. Our research focuses on the treatment of the LNCaP line prostate cancer utilizing iron oxide nanoparticles (IONPs) loaded with soluble TNF-a and lactonic sophorolipids (LSLs). TNF-a is a cytokine responsible for apoptosis initiation, while LSLs are naturally-glycolipids shown to alleviate inflammation and improve immune response in certain diseases. We hypothesized that this combination may possess a synergistic …

On The Structure And Properties Of S-Nitrosated Cysteine Models: A Computational Study, Dmitry Khomyakov

Dissertations (1934 -)

S-Nitrosation of cysteine (Cys) residues, a covalent modification of its S atom by NO group, is a major post-translational modification of proteins. Despite the importance of S-nitrosoproteins in numerous physiological processes, lability of the S-nitrosothiol (-SNO) group hinders the research progress. In this work, computational chemistry methods were applied to S-nitrosated cysteine (CysNO) models to gain a deeper insight into its structure and properties. First, we obtained the most accurate at the moment computational estimation of the molecular structure and properties of CH3SNO model molecule using Feller-Peterson-Dixon (FPD) ab initio protocol. The S–N bond length in cis- CH3SNO is calculated …

Computational Modeling Of S-Thiolation Reaction: Toward Discovering The Enzymatic Mechanisms Of Endogenous Hno Formation, Elena Ivanova

Dissertations (1934 -)

S-nitrosothiols (RSNOs) have long been proposed as potential sources of the elusive endogenous nitroxyl (HNO) via S-thiolation reaction with thiols. It is however not clear how S-thiolation can compete with the trans-S-nitrosation pathway commonly observed in vitro. Based on the insights into the highly unusual, antagonistic chemical nature of RSNO molecules, we hypothesize that, while difficult in vitro, S-thiolation could easily lend itself to enzymatic catalysis. To explore this possibility, we adopted a bottom-up computational approach that aims to identify possible catalytic mechanisms able to steer the RSNO + thiol reaction toward HNO production. Inspired by recent discovery of small …