Biochemistry Commons^™

Role Of Small Molecules In Rescuing Protein Folding Under Oxidative Stress, Mahmoud Fawzi Megahed Helal Khalil

Open Access Theses & Dissertations

Increased levels of nitrosative stress intracellularly within the endoplasmic reticulum is a key factor involvled in the pathogenesis of both Parkinson's (PD) and Alzheimer's (AD) diseases. Previous in-vitro studies in our lab showed that increased levels of nitrosative stress lead to aggregation of misfolded proteins and formation of Lewy Bodies, the main biomarker of PD and AD diseases. Although this was mainly through nitrosylation of Protein Disulfide Isomerase (PDI), the chief endoplasmic reticulum (ER) resident oxidoreductase chaperone responsible for maturation of disulfide-bond-containing proteins, we demonstrate in this project that increased levels of nitrosative stress has an additional direct effect on …

Chemoenzymatic Studies To Enhance The Chemical Space Of Natural Products, Jhong-Min Chen

Theses and Dissertations--Pharmacy

Natural products provide some of the most potent anticancer agents and offer a template for new drug design or improvement with the advantage of an enormous chemical space. The overall goal of this thesis research is to enhance the chemical space of two natural products in order to generate novel drugs with better in vivo bioactivities than the original natural products.

Polycarcin V (PV) is a gilvocarcin-type antitumor agent with similar structure and comparable bioactivity with the principle compound of this group, gilvocarcin V (GV). Modest modifications of the polyketide-derived tetracyclic core of GV had been accomplished, but the most …

Sharp Rna Recognition Motif Optimizations, Extensions, And Mutations For Use In 2d And 3d Nmr Experiments, Shaun M. Christie

Williams Honors College, Honors Research Projects

SMRT/HDAC Associated Repressor Protein interacts with the long noncoding RNA, produced by SRA, by binding at the RRMs. Three projects were done to prepare the truncated proteins for use in 2D and 3D NMR experiments. The first focuses on RRM 3 and its optimization during the purification process. The second focuses on RRM 2-4, which was found to be missing two alpha helices that may be important for protein stability. These helices can also interact with RRM 3 as well due to the tight association of RRMs 3 and 4. The two step PCR extension of RRM 2-4 was assumed …

On The Protective Properties Of Glycine Based Osmolytes In A Thiol Reducing Environment, John Michael Hausman

Dissertations, Master's Theses and Master's Reports - Open

The protective properties of osmolytes have been studied intently for decades. Originally used to aid in the crystallization of proteins in x-ray diffraction studies, these cosolvents have been shown to reverse protein denaturation and aggregation. Osmolytes aid extremophiles in surviving harsh environments by preferentially excluding themselves from the surface of the protein, thus directing water molecules to the protein’s surface. These osmolytes are naturally found in many health foods and also in many daily use products such as shampoo. Due to their osmoprotective effect their use in everyday consumer product is increasing. Consumers also supplement their diets with thiol-based antioxidants …

Evaluation Of Small Molecules On The Excitatory Amino Acid Transporter 3 (Eaat3) For The Treatment Of Ocd, Emmanuel Zubia

Open Access Theses & Dissertations

We seek to discover new drug candidates for the excitatory amino acid transporter 3 (EAAT3) for the treatment of Obsessive Compulsive Disorder (OCD). We hypothesize that decreasing the glutamatergic transmission via EAAT3 intervention will create an amelioration of the symptoms of OCD. For this we have prepared in-silico binding calculations to identify a better compound that can stimulate EAAT3 and decrease glutamatergic transmission. This research will help us further understand and elucidate the role of glutamate in the neural mechanisms of this illness, which to date remain inconclusive. Those areas of study are significant because, until now, there is no …

Inhibition Of Toxic Iapp Amyloid By Extracts Of Common Fruits, David A. Moffet, Pei-Yu Kao, Evangeline Green, Catalina Pereirab, Shauna Ekimura, Dennis Juarez, Travis Whyte, Taylor Arhar, Bianca Malaspina, Luiza A. Nogaj

Chemistry and Biochemistry Faculty Works

The aggregation of the 37-amino acid polypeptide islet amyloid polypeptide (IAPP, amylin), as either insoluble amyloid or as small oligomers, appears to play a direct role in the death of pancreatic β-islet cells in type 2 diabetes. It is believed that inhibiting the aggregation of IAPP may slow down, if not prevent entirely, the progression of this disease. Extracts of thirteen different common fruits were analyzed for their ability to prevent the aggregation of amyloidogenic IAPP. Thioflavin T binding, immuno-detection and circular dichroism assays were performed to test the in vitro inhibitory potential of each extract. Atomic force microscopy was …

Dynamic Motions Of The Hiv-1 Frameshift Site Rna, Kathryn Mouzakis

Chemistry and Biochemistry Faculty Works

The HIV-1 frameshift site (FS) plays a critical role in viral replication. During translation, the HIV-1 FS transitions from a 3-helix to a 2-helix junction RNA secondary structure. The 2-helix junction structure contains a GGA bulge, and purine-rich bulges are common motifs in RNA secondary structure. Here, we investigate the dynamics of the HIV-1 FS 2-helix junction RNA. Interhelical motions were studied under different ionic conditions using NMR order tensor analysis of residual dipolar couplings. In 150 mM potassium, the RNA adopts a 43°(±4°) interhelical bend angle (β) and displays large amplitude, anisotropic interhelical motions characterized by a 0.52(±0.04) internal …

Global Shape Mimicry Of Trna Within A Viral Internal Ribosome Entry Site Mediates Translational Reading Frame Selection, Kathryn Mouzakis

Chemistry and Biochemistry Faculty Works

The dicistrovirus intergenic region internal ribosome entry site (IRES) adopts a triple-pseudoknotted RNA structure and occupies the core ribosomal E, P, and A sites to directly recruit the ribosome and initiate translation at a non-AUG codon. A subset of dicistrovirus IRESs directs translation in the 0 and +1 frames to produce the viral structural proteins and a +1 overlapping open reading frame called ORFx, respectively. Here we show that specific mutations of two unpaired adenosines located at the core of the threehelical junction of the honey bee dicistrovirus Israeli acute paralysis virus (IAPV) IRES PKI domain can uncouple 0 and …

Regional-Scale Simulations Of Fungal Spore Aerosols Using An Emission Parameterization Adapted To Local Measurements Of Fluorescent Biological Aerosol Particles, Matthias Hummel, Corinna Hoose, M. Gallagher, D. A. Healy, J. Alex Huffman, D. O'Connor, U. Pöschl, C. Pöhlker, N. H. Robinson, M. Schnaiter, J. R. Sodeau, M. Stengel, E. Toprak, H. Vogel

Chemistry and Biochemistry: Faculty Scholarship

Fungal spores as a prominent type of primary biological aerosol particles (PBAP) have been incorporated into the COSMO-ART (Consortium for Small-scale Modelling- Aerosols and Reactive Trace gases) regional atmospheric model. Two literature-based emission rates for fungal spores derived from fungal spore colony counts and chemical tracer measurements were used as a parameterization baseline for this study. A third, new emission parameterization for fluorescent biological aerosol particles (FBAP) was adapted to field measurements from four locations across Europe. FBAP concentrations can be regarded as a lower estimate of total PBAP concentrations. Size distributions of FBAP often show a distinct mode at …

Fluorescence Imaging Of Analyte Profiles In An Inductively Coupled Plasma With Laser Ablation As A Sample Introduction Source, Lance Moses

Theses and Dissertations

Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) has risen to among the top tier techniques for the direct analysis of solid samples. However, significant problems remain that must be solved to achieve the full analytical potential of LA-ICP-MS. Inefficient conversion of aerosol to ions within the ICP or transmission through the MS interface may decrease precision, sensitivity, and/or accuracy. Although fundamental mechanisms that govern ion production and transmission have been studied extensively in solution-nebulization (SN) ICP-MS instruments, significant gaps in our understanding remain. Furthermore, it is unclear to what extent differences between the aerosols generated during SN and LA …

Constitutive Activity In Orphan G Protein Coupled Receptors, Adam Lee Martin

Doctoral Dissertations

"The goal of this research was to use a distal signaling pathway analysis to evaluate the extent of agonist independent constitutive signaling among orphan class-A G protein coupled receptors (GPCRs). These receptors translate extracellular signals via conformational change into intracellular activation of different G proteins and subsequent second messenger synthesis. These small molecules regulate cellular biochemistry, eventually leading to nuclear signaling that results in changes in gene expression. Some GPCRs are capable of signaling in the absence of an activating ligand, a phenomenon called constitutive activity that is inhibited via an "inverse-agonist". The use of cAMP dependent Luciferase expression is …

Effects Of N-Acetylcysteine Amide In Preventing/Treating Cataracts, Sri Krishna Yasaswi Maddirala

Doctoral Dissertations

"Cataract, the opacification of an eye lens, is a common pathological abnormality of the lens accounting for approximately 50% of all blindness. The only effective treatment currently available for a cataract is the surgical removal of the affected lens and replacement with an artificial lens for the restoration of vision. Although, cataract surgery is considered to be a very successful procedure in terms of visual outcome, the cost of surgery, need for trained personnel and surgeons, and postsurgical complications, limit the worldwide availability and accessibility of this procedure. Hence, alternative preventive and treatment procedures are worthy of investigation. The lens …

Biosynthesis Of Long-Chain Fatty Acid Amides, Kristen A. Jeffries

USF Tampa Graduate Theses and Dissertations

The vast variety of long-chain fatty acid amides identified in biological systems is intriguing. The general structure of a fatty acid amide is R-CO-NH-X, where R is an alkyl group and X is derived from an immense variety of biogenic amines. Although structurally simple, the bioactivities of these molecules as signaling lipids are very diverse and have just recently begun to emerge in the literature. Interest in the long-chain fatty acid amides dramatically increased following the identification and characterization of one specific N-acylethanolamine, N-arachidonoylethanolamine (anandamide), as the endogenous ligand for the cannabinoid receptors in the mammalian brain. Since …

Real-Time Kinetic Studies Of Bacillus Subtilis Oxalate Decarboxylase And Ceriporiopsis Subvermispora Oxalate Oxidase Using Luminescent Oxygen Sensor, Laura Molina, Thomas Goodall, Umar Twahir, Ellen W. Moomaw

Faculty Articles

Oxalate decarboxylase (OxDC), an enzyme of the bicupin superfamily, catalyzes the decomposition of oxalate into carbon dioxide and formate at an optimal pH of 4.3 in the presence of oxygen. However, about 0.2% of all reactions occur through an oxidase mechanism that consumes oxygen while producing two equivalents of carbon dioxide and one equivalent of hydrogen peroxide. The kinetics of oxidase activity were studied by measuring the consumption of dissolved oxygen over time using a luminescent oxygen sensor. We describe the implementation of and improvements to the oxygen consumption assay. The oxidase activity of wild type OxDC was compared to …

Investigating The Links Between Ozone And Organic Aerosol Chemistry In A Biomass Burning Plume From A Prescribed Fire In California Chaparral, M. J. Alvarado, C. R. Lonsdale, Robert Yokelson, S. K. Akagi, H. Coe, J. S. Craven, E. V. Fischer, G. R. Mcmeeking, J. H. Seinfeld, T. Soni, J. W. Taylor, D. R. Weise, C. E. Wold

Chemistry and Biochemistry Faculty Publications

Within minutes after emission, rapid, complex photochemistry within a biomass burning smoke plume can cause large changes in the concentrations of ozone (O₃) and organic aerosol (OA). Being able to understand and simulate this rapid chemical evolution under a wide variety of conditions is a critical part of forecasting the impact of these fires on air quality, atmospheric composition, and climate. Here we use version 2.1 of the Aerosol Simulation Program (ASP) to simulate the evolution of O₃ and secondary organic aerosol (SOA) within a young biomass burning smoke plume from the Williams prescribed burn in chaparral, …

Synthesis And Characterization Of Polymer (Sulfonated Poly-Ether-Ether-Ketone) Based Nanocomposite (H-Boron Nitride) Membrane For Hydrogen Storage, Naresh Muthu, S. Rajashabala, R. Kannan

Chemistry and Biochemistry Faculty Publications

The development of light weight and compact hydrogen storage materials is still prerequisite to fuel-cell technology to be fully competitive. The present experimental study reports the hydrogen storage capability of sulfonated poly-ether-ether-ketone (SPEEK)-hexagonal boron nitride (h-BN) (SPEEK-h-BN) nanocomposite membranes. The nanocomposite membranes are prepared by considering various amount of h-BN (0, 1, 3 and 5 wt. %) by phase inversion technique. The degree of sulfonation of the PEEK (SPEEK) is found to be 65% by Proton Nuclear Magnetic Resonance (¹H NMR) spectroscopy. Hydrogen adsorption studies have been carried out using a Seiverts-like hydrogenation setup. The membranes are characterized …

Antifungal Amphiphilic Aminoglycoside K20: Bioactivities And Mechanism Of Action, Sanjib K. Shrestha, Cheng-Wei Tom Chang, Nicole Meissner, John Oblad, Jaya P. Shrestha, Kevin N. Sorensen, Michelle M. Grilley, Jon Y. Takemoto

Chemistry and Biochemistry Faculty Publications

K20 is a novel amphiphilic antifungal aminoglycoside that is synthetically derived from the antibiotic kanamycin A. Reported here are investigations of K20′s antimicrobial activities, cytotoxicity, and fungicidal mechanism of action. In vitro growth inhibitory activities against a variety of human and plant pathogenic yeasts, filamentous fungi, and bacteria were determined using microbroth dilution assays and time-kill curve analyses, and hemolytic and animal cell cytotoxic activities were determined. Effects on Cryptococcus neoformans H-99 infectivity were determined with a preventive murine lung infection model. The antifungal mechanism of action was studied using intact fungal cells, yeast lipid mutants, and small unilamellar lipid …

Microchip Thermal Gradient Gas Chromatography, Anzi Wang

Theses and Dissertations

Although the airbath oven is a reliable heating method for gas chromatography (GC), resistive heating is needed for higher analytical throughput and on-site chemical analysis because of size, heating rate and power requirements. In the last thirty years, a variety of resistive heating methods were developed and implemented for both benchtop and portable GC systems. Although fast heating rates and low power consumption have been achieved, losses in column efficiency and resolution, complex construction processes and difficulties experienced in recovering damaged columns have also become problematic for routine use of resistively heated columns. To solve these problems, a new resistively …

Fabrication, Characterization, Optimization And Application Development Of Novel Thin-Layer Chromatography Plates, Supriya Singh Kanyal

Theses and Dissertations

This dissertation describes advances in the microfabrication of thin layer chromatography (TLC) plates. These plates are prepared by the patterning of carbon nanotube (CNT) forests on substrates, followed by their infiltration with an inorganic material. This document is divided into ten sections or chapters. Chapter 1 reviews the basics of conventional TLC technology. This technology has not changed substantially in decades. This chapter also mentions some of the downsides of the conventional approach, which include unwanted interactions of the binder in the plates with the analytes, relatively slow development times, and only moderately high efficiencies. Chapter 2 focuses primarily on …

Synthesis And Characterization Of Complex Molecular Assemblies On Surfaces, Nitesh Madaan

Theses and Dissertations

The research presented in this dissertation is focused on the construction of complex molecular structures on planar gold and silicon dioxide surfaces using a variety of surface modification techniques, along with thorough surface characterization at each modification step. The dissertation is structured into six separate chapters. In Chapter 1, an introduction to the importance and implications of molecular level surface modification, commonly employed surface modification methods, and available surface characterization techniques is presented. Chapter 2 shows applications of novel methodologies for the functionalization of gold surfaces using alkane dithiol self-assembled monolayers and thiol-ene click chemistry. The resulting functionalized gold substrates …

Chaperone-Mediated Folding And Assembly Of Β-Propeller Proteins Into Cellular Signaling Complexes, Rebecca L. Plimpton

Theses and Dissertations

G protein signaling depends on the ability of the individual subunits of the G protein heterotrimer to assemble into a functional complex. Formation of the G protein βγ (Gβγ) dimer is particularly challenging because it is an obligate dimer in which the individual subunits are unstable on their own. Recent studies have revealed an intricate chaperone system that brings the Gβ and Gγ subunits together. This system includes the cytosolic chaperonin containing TCP-1 (CCT) and a co-chaperone phosducin-like protein 1 (PhLP1). Two key intermediates in the Gβγ assembly process, the Gβ-CCT and the PhLP1-Gβ-CCT complexes, were isolated and their structures …

Ultrafast Interfacial Electron Transfer Across Molecule-Tio2 Nanocomposites: Towards Solar Cells And Two Photon Absorption, Edwin Mghanga

Dissertations

Interfacial charge transfer (ICT) across the molecule-TiO2 nanoparticle interface has gained enormous research attention for applications in dye sensitized solar cells (DSSC), photo-catalysis, water splitting and nonlinear optics. DSSCs are promising clean alternative energy sources. However, current DSSCs suffer from lower efficiencies and higher cost. Better understanding of the ICT processes in DSSCs can help solve these problems. We have used two strategies to understand ICT in the context of DSSCs. Firstly, we used a computationally validated anchor group, acetylacetonate (acac) to bind molecules to the semiconductor surface and facilitate charge separation. Secondly, we used natural dye sensitizers, …

Cold Magnetically Trapped 2DG Scandium Atoms. I. Interaction Potential, Tijs Karman, Xi Chu, Gerrit C. Groenenboom

Chemistry and Biochemistry Faculty Publications

We present a first principles description of the interaction of two ground-state scandium atoms. Scandium has a ²D_g ground state. Thirty molecular states correlate to the lowest dissociation limit of the dimer. In the short range, potential energy curves are calculated using second-order n-electron valence state perturbation theory. The first-order long-range interaction is calculated at the complete active space self-consistent field level. We determine the second-order long-range dispersion interaction from atomic dynamic polarizabilities at imaginary frequencies. These polarizabilities are calculated using time-dependent density functional theory. We merge the short-range approach with the long-range model to obtain a physical …

Cross-Disciplinary Sciences At Gettysburg College: Second Annual Poster Presentation, X-Sig

Student Publications

This booklet includes Biology student presentations by: Taylor Bury, Abigail Dworkin-Brodsky, Mary Pearce, Jasper Leavitt, Morgan Panzer, Ellen Petley, Kalli Qutub, Taylor Randell, Samantha Eck, Lana McDowell, Jenn Soroka, Celina Harris, Natalie Tanke, Alexandra Turano, and Caroline Garliss.

This booklet includes Biochemistry & Molecular Biology student presentations by: Matthew Dunworth, Andrew Sydenstricker, Brianne Tomko, Albert Vill, Warren Campbell, David Van Doren, Kevin Mrugalski, Stacey Heaver, Alecia Achimovich, and Katherine Boas.

This booklet includes Chemistry student presentations by: Kristen Baker, Laura Lee, Kathryn Fodale, Daniel Ruff, Michael Counihan, Ida DiMucci, Joshua Sgroi, Celina Harris, and Natalie Tanke.

This booklet include Health …

Aerosol Emissions From Prescribed Fires In The United States: A Synthesis Of Laboratory And Aircraft Measurements, A. A. May, G. R. Mcmeeking, T. Lee, J. W. Taylor, J. S. Craven, I. R. Burling, A. P. Sullivan, Sheryl Kashi Akagi, J. L. Collett Jr., M. Flynn, H. Coe, S. P. Urbanski, J. H. Seinfeld, Robert Yokelson, S. M. Kreidenweis

Chemistry and Biochemistry Faculty Publications

Aerosol emissions from prescribed fires can affect air quality on regional scales. Accurate representation of these emissions in models requires information regarding the amount and composition of the emitted species.Wemeasured a suite of submicron particulatematter species in young plumes emitted from prescribed fires (chaparral and montane ecosystems in California; coastal plain ecosystem in South Carolina) and from open burning of over 15 individual plant species in the laboratory. We report emission ratios and emission factors for refractory black carbon (rBC) and submicron nonrefractory aerosol and compare field and laboratory measurements to assess the representativeness of our laboratory-measured emissions. Laboratory measurements …

New Experimental And Theoretical Tools For Studying Protein Systems With Elements Of Structural Disorder, Tairan Yuwen

Open Access Dissertations

Disordered proteins are one class of proteins which do not possess well-folded three-dimensional structures as their native conformations. Many eukaryotic proteins have been found to be fully disordered or contain certain disordered regions. Disordered proteins usually display several characteristic properties, such as increased motional freedom and the conformational heterogeneity caused by that. The elements of structural disorder are commonly involved in many important biological functions and are implicated in many diseases. Therefore, the study of disordered proteins has become one of the most important research topics in recent years. This thesis presents results from three different research projects; the common …

Airborne Characterization Of Smoke Marker Ratios From Prescribed Burning, A. P. Sullivan, A. A. May, T. Lee, G. R. Mcmeeking, S. M. Kreidenweis, S. K. Akagi, Robert Yokelson, S. P. Urbanski, J. L. Collett Jr.

Chemistry and Biochemistry Faculty Publications

A Particle-Into-Liquid Sampler – Total Organic Carbon (PILS-TOC) and fraction collector system was flown aboard a Twin Otter aircraft sampling prescribed burning emissions in South Carolina in November 2011 to obtain smoke marker measurements. The fraction collector provided 2 min time-integrated offline samples for carbohydrate (i.e., smoke markers levoglucosan, mannosan, and galactosan) analysis by high-performance anion-exchange chromatography with pulsed amperometric detection. Each fire location appeared to have a unique 1levoglucosan /1water-soluble organic carbon (WSOC) ratio (RF01/RF02/RF03/RF05 = 0.163± 0.007 μg C μg−1 C, RF08 = 0.115 ± 0.011 μg C μg−1 C, RF09A = 0.072 ± 0.028 μgC μg−1 C, …

New Strategies To Reveal Protein Candidates In Protein-Protein Interactome Study, Meng-Chieh Chen

Open Access Theses

Comprehensive protein-protein interaction network analysis can help reveal protein functions in a system-wide manner. A reliable knowledgebase of interaction networks is not only important for selecting the candidates for drug therapies, but also for evaluating the disease risk. In current interaction databases, 322579 interactions comprised of 56460 proteins have been reported (statistical analysis from APID: Agile Protein Interaction DataAnalyzer; http://bioinfow.dep.usal.es/apid/index.htm). The huge datasets are contributed mainly by yeast -two -hybrid (Y2H) screening and affinity-purification followed by mass spectrometry (AP-MS). High false positive rates and failing to cover certain interaction categories are the limitations of these two methods. Here, we developed …

Towards A Paradigm Shift In The Modeling Of Soil Organic Carbon Decomposition For Earth System Models, Yujie He

Open Access Dissertations

Soils are the largest terrestrial carbon pools and contain approximately 2200 Pg of carbon. Thus, the dynamics of soil carbon plays an important role in the global carbon cycle and climate system. Earth System Models are used to project future interactions between terrestrial ecosystem carbon dynamics and climate. However, these models often predict a wide range of soil carbon responses and their formulations have lagged behind recent soil science advances, omitting key biogeochemical mechanisms. In contrast, recent mechanistically-based biogeochemical models that explicitly account for microbial biomass pools and enzyme kinetics that catalyze soil carbon decomposition produce notably different results and …

The Modification Of Brucine Derivatives As Chiral Ligands And Its Application In The Asymmetric Synthesis, Jian-Yuan Li

Open Access Dissertations

The modification of brucine derivatives as chiral ligands and the use of a multifaceted chiral ligand, brucine diol, under different reaction conditions to produce various optical isomers is described. In Chapter 1, the generation of a number of brucine derivatives is described. Taking the advantage of brucine-diol's excellent molecular recognition capability for multiple organic functional groups, we focused on the synthetic modifications of brucine-diol and the synthesis of brucine N-oxide. We also produced various brucine derivatives with different functional moieties in good yields and selectivities. ^ In Chapter 2, we described the investigation of brucine N-oxide catalyzed Morita-Baylis-Hillman …