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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 …

Chemistry & Biochemistry Newsletter, Department Of Chemistry & Biochemistry, South Dakota State University

Chemistry & Biochemistry Newsletter: 2002-2015

Inside:

Page 2-3 BioSNTR Funding Boosts Biotechnology in South Dakota

Page 3 New Student Club Decorates Tree

Page 4-5 New Graduate Students

Page 5 Arts & Sciences contributes 2,875 items to food pantry

Page 6-7 New Faculty and Staff

Page 7 Recent Faculty Publications

Page 8 Student Engineers (and a biochemist) Without Borders

Determination Of Disulfide Bond Connecting Patterns Via Tandem Mass Spectrometry (Msn) And Biomolecular Ion/Radical Reactions, Kirt Lenroy Durand

Open Access Dissertations

Disulfide bond formation is one of the most common post translational modifications to occur in proteins and naturally occurring peptides. Disulfide bond formation plays a critical role in stabilizing their three-dimensional structure; therefore, it is very important to pinpoint the correct disulfide bond connecting pattern in order to fully understand the biological functions of these proteins and peptides. To fully characterize an analyte containing disulfide bonds, the sequence must first be known followed by the disulfide bond connecting pattern. This presents an analytical challenge as there are very few methodologies that can produce those essential pieces of information. The gold …

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, …

Folate Targeted Agents For Diagnostic And Therapeutic Uses, Mekeda Carr

All Capstone Projects

Folic acid has been frequently exploited for target therapies geared toward overexpressed folate receptors on malignant cells. The folic acid/folate-receptor high affinity interaction can be used to not only target but image cancer cells. Folate-linked nanoparticles represent a potential new drug carrier for tumor cell-selective therapeutics. Folate targeting, nanoparticles in therapeutics, and cancer cell imaging will be outlined in this literature report.

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 …

Identifying Conditions To Optimize Lactic Acid Production From Food Waste, Raymond M. Redcorn

Open Access Theses

There is an increased demand for lactic acid for the production of biopolymers and to aid nutrient removal in wastewater treatment. Food waste offers a source of soluble sugars to produce lactic acid, which does not increase land demand, but digestion conditions have yet to be optimized when co-digested with primary sludge. Food waste was collected from cafeteria waste bins, homogenized and seeded with primary sludge. A Box Behnken Response surface design was used to optimize lactic acid production based on pH, temperature, loading rate, and retention time. Subsequent experiments verified and refined those conditions to optimize for both yield …

Elucidating The Mechanism Of Phenylpropanoid Regulation By The Arabidopsis Mediator Complex, Wenjie Zeng

Open Access Theses

The Mediator complex is a multi-protein co-regulator of eukaryotic transcription which plays a role in the expression of many, if not most, genes of the cell. Two Mediator subunits, REF4 and RFR1, were demonstrated to be important for the normal regulation of phenylpropanoid metabolism in Arabidopsis. Phenylpropanoids are a family of specialized plant metabolites derived from the amino acid phenylalanine and are involved in defense against pathogens, UV protection and structural support. In order to understand how Mediator regulates phenylpropanoid metabolism through REF4 and RFR1, a better basic understanding of this protein complex is required. Here I provide data on …

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 …

Quantum Mechanics In Complex Systems, Ross Douglas Hoehn

Open Access Dissertations

This document should be considered in its separation; there are three distinct topics contained within and three distinct chapters within the body of works. In a similar fashion, this abstract should be considered in three parts. Firstly, we explored the existence of multiply-charged atomic ions by having developed a new set of dimensional scaling equations as well as a series of relativistic augmentations to the standard dimensional scaling procedure and to the self-consistent field calculations. Secondly, we propose a novel method of predicting drug efficacy in hopes to facilitate the discovery of new small molecule therapeutics by modeling the agonist-protein …

How Do Metalloenzymes Propagate And Control Chemical Reactions?, Whitney F Kellett

Open Access Dissertations

Enzymes control and propagate a dizzying array of chemical reactions, including radical reactions and reactions cleaving carbon-carbon bonds. Metalloenzymes, which contain a metal cofactor, are particularly adept at propagating these reactions. This thesis focuses on several metalloenzymes; each an example of a different unique reaction control strategy. Both experimental and computational methodologies have been employed in order to identify specific residues or features which contribute to each enzyme's ability to control the reaction. Emphasis is made on special properties of the metal Manganese. Controlling residues include not only first shell or active site residues, but also residues more distant from …

Development Of Novel Strategies To Combat Multidrug Resistance Mediated By Efflux Transporters And Intracellular Bacteria, Jerrin Kuriakose

Open Access Dissertations

Multidrug resistance (MDR) is the condition where cancer cells or microorganisms cease to respond to multiple drugs. MDR conferred by efflux transporters, that deprive the bioavailability of drugs at their site of action, are a threat to cancer and malarial chemotherapy. Specifically, the mammalian ABC transporter Pglycoprotein (P-gp) has undermined many drugs in treatment of cancer and other disease states. Mutations in the parasitic transporter Plasmodium falciparum chloroquine resistance transporter (PfCRT) have given rise to strains unsusceptible to the aminoquionoline family of antimalarials. Using the very drug substrates, we have developed bivalent inhibitors of P-gp. Here, click chemistry has been …

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 …

Excited States Of Chromophores And Vibronic Interactions, Benjamin T. Nebgen

Open Access Dissertations

The main focus of my Ph.D. work has been on building a vibronic coupling model for multichromophores and extending that model to more general systems. This Dissertation serves as both a summary of this work as well as a manual for the two vibronic coupling programs I have written. It is my hope that the instructions written here are complete enough for any who would like to replicate my work on vibronic coupling on other systems. ^ Additionally, I have also worked on a few purely computational projects not directly related to the vibronic coupling work. The status of these …

Transformation Of Biomass Carbohydrates By Transition Metal Catalysts, Christine M Bohn

Open Access Dissertations

By selectively removing functional groups from biomass derived carbohydrates, valuable platform chemicals can be generated from renewable sources. Through dehydration chemistry glucose can be upgraded into 5-(Hydroxymethyl)-2-furfuraldehyde (HMF) and levulinic acid. Iron (III) chloride hexahydrate has shown moderate activity to transform glucose into HMF and has also shown high yields and selectivity for the production of levulinic acid. Typically synthesized from acidic solutions made with mineral acids, levulinic acid has now been produced in high yields with a metal salt. The difference between maximizing production for HMF or levulinic acid from the same catalyst relies on the control of the …

Supersonic Jet Spectroscopy Of Synthetic Foldamers, Multichromophores, And Their Water Containing Clusters, Evan Gardner Buchanan

Open Access Dissertations

A central theme specific to this dissertation concerns the conformation-specific spectroscopy of flexible molecules in an effort to bridge the complexity gap. Generally, molecules in the complexity gap have several flexible coordinates yet conformational isomerization still occurs along a simple reaction coordinate on the potential energy surface. Molecules in this regime benefit greatly from experiments probing the potential energy surfaces and provide a means to develop and test new theories in an effort to explain more complex system. These measurements are possible through the utilization of a supersonic jet expansion to collisionally cool molecules into their vibrational zero-point levels, collapsing …

Aircraft-Based Measurements For The Identification And Quantification Of Sources And Sinks In The Carbon Cycle, Dana R Caulton

Open Access Dissertations

Improved quantification of carbon-cycle sources and sinks is an important requirement for determining mitigation strategies and modeling future climate interactions. Analytically robust measurements require high-precision instrumentation and thoughtful experimental design to produce rigorous and reproducible results despite complex and quickly changing meteorological and environmental conditions. Here, an aircraft platform equipped with a high-precision cavity ring-down spectrometer for CO₂, CH₄ and H₂O quantification was used to acquire data from previously un-sampled sources. The aircraft mass-balance technique was used to quantify CH4 emissions from natural gas well pads in the drilling stage, which were 2-3 orders of …

Synthesis And Evaluation Of Sensitizer Drug Photorelease Chemistry: Micro-Optic Method Applied To Singlet Oxygen Generation And Drug Delivery, Goutam Ghosh

Dissertations, Theses, and Capstone Projects

This thesis summarizes a new micro-optic method for singlet oxygen generation and sensitizer drug delivery, which include i) synthesis and evaluation of a first generation device for drug delivery from native and fluorinated silica probe tips, ii) synthesis of PEG conjugated sensitizers to study phototoxicity in ovarian cancer cells, and iii) synthesis and evaluation of tris-PEGylated chlorin conjugated fluorinated silica for its future integration into the device to use as a 2nd generation device. A first generation micro-optic device was developed that works by sparging O2 gas and light generating cytotoxic singlet oxygen that cleaves the covalently attached drug (sensitizer) …

Carbon And Nitrogen Dynamics From Slow Pools Of Soil Organic Matter In A Temperate Forest: Pyrogenic Organic Matter And And Root Litter, Fernanda Dos Santos

Dissertations, Theses, and Capstone Projects

Soil organic matter (SOM) is the dominant reservoir of organic carbon (OC) in terrestrial ecosystems, storing approximately three times the size of the C pool in the atmosphere. In temperate forests, a major fraction of the SOM consists of slowly decaying soil organic C (SOC) pools. While slowly cycling C pools constitute a large reservoir of stable C in soils, the dominant environmental factors controlling this C pool remain unresolved. This research investigates two significant, but poorly characterized slowly decaying C pools: fine root litter (< 2mm) and thermally altered plant biomass (pyrogenic organic matter, PyOM). Specifically, I used compound-specific stable isotope analysis (¹³C and ¹⁵N) as my main methodological approach to examine the (1) …

Development Of Cell-Active Inhibitors And Activity-Based Probe Of Cysteine Cathepsins, Dibyendu Dana

Dissertations, Theses, and Capstone Projects

Cysteine cathepsins are an important class of enzymes that coordinate a variety of important cellular processes, and are implicated in various types of human diseases. Still however, many of their cellular function remain poorly understood. Chemical biology approaches employing small molecules can be utilized for this purpose. Unfortunately small molecule probes that are cell-permeable and non-peptidyl in nature are scarcely available.

In this work, first a library of sulfonyloxiranes is synthesized. From this library, 2-(2-ethylphenylsulfonyl)oxirane is identified as a selective inhibitor of cysteine cathepsins. Cell-based study reveals that 2-(2-ethylphenylsulfonyl)oxirane is a cell-permeable, covalent, and irreversible inhibitor of cathepsin B with …

Development And Applications Of Mass Spectrometric Methods For Phosphorylation Analysis, Hsin-Pin Ho

Dissertations, Theses, and Capstone Projects

Protein phosphorylation modification regulates numerous cellular functions by a reversible and selective control of kinases and phosphatases. To understand the entire dynamic network of phosphorylation requires sensitive and reliable quantification of phosphorylation, measurements that can be achieved by mass spectrometry. In this research, we established efficient MALDI-mass spectrometric methods as strategies for single- or multi-site phosphorylation quantification without the use of isotopes, chromatography and calibration curves. The methods were assessed by analyzing peptide standards with different single-multiple phosphorylation sites, showing a wide dynamic range, good accuracy and reproducibility. This is the first label-free MALDI method without using a calibration methodology …

Syntheses Of Aminyl Diradicals And Nitroxide Tetra- And Octaradicals, Arnon Olankitwanit

Department of Chemistry: Dissertations, Theses, and Student Research

This dissertation comprises of two main research projects: aminyl diradicals and calix[4]arene nitroxide tetra- and octaradicals. The design, multi-step synthesis and characterization, including NMR, EPR spectroscopy, magnetic measurements and X-ray crystallography of precursors and target compounds will be discussed.

Aminyl radicals, nitrogen-centered radicals, are typically short-lived and considered as reactive intermediates. Because of their unique magnetic properties, aminyls are attractive building blocks for high-spin di-and polyradicals. The challenge is in the design and synthesis of aminyls with increased stability. In this chapter, we have prepared triplet (S = 1) ground state aminyl diradicals, which are derivatives of aza-m …

Crystal Structure Of (E)-13-{4-[(Z)-2-Cyano-2-(3,4,5-Trimethoxyphenyl)Ethenyl]Phenyl}Parthenolide Methanol Hemisolvate, Narsimha Reddy Penthala, Shobanbabu Bommagani, Venumadhav Janganati, Sean Parkin, Peter A. Crooks

Chemistry Faculty Publications

The title compound, C₃₃H₃₅NO₆ [systematic name: (Z)-3-(4-{(E)-[(E)-1a,5-dimethyl-9-oxo-2,3,7,7a-tetra­hydro­oxireno[2′,3′:9,10]cyclo­deca­[1,2-b]furan-8(1aH,6H,9H,10aH,10bH)-yl­idene]meth­yl}phen­yl)-2-(3,4,5-tri­meth­oxy­phen­yl)acrylo­ni­trile methanol hemisolvate], C₃₃H₃₅NO₆·0.5CH₃OH, was prepared by the reaction of (Z)-3-(4-iodo­phen­yl)-2-(3,4,5-tri­meth­oxy­phen­yl)acrylo­nitrile with parthenolide [systematic name: (E)-1a,5-dimethyl-8-methyl­ene-2,3,6,7,7a,8,10a,10b-octa­hy­dro­oxireno[2′,3′:9,10]cyclo­deca­[1,2-b]furan-9(1aH)-one] under Heck reaction conditions. The mol­ecule is built up from fused ten-, five- (lactone) and three-membered (epoxide) rings with a {4-[(Z)-2-cyano-2-(3,4,5-tri­meth­oxy­phen­yl)ethen­yl]phen­yl}methyl­idene group as a substituent. The 4-[(Z)-2-cyano-2-(3,4,5-tri­meth­oxy­phen­yl)ethen­yl]phenyl group on the parthenolide exocyclic double bond is …

Oxocarbenium Ion And Alkene Metathesis Strategies For The Synthesis Of Complex Cyclohexanes, Clayton Errol Mattis

Dissertations, Theses, and Capstone Projects

Highly oxygenated cyclohexanes comprise the structures of a number of pharmacologically interesting molecules, including potently bioactive natural products and carbapyranosides. The latter, which are unnatural analogues of carbohydrates in which the ring oxygen of the parent sugar is replaced with a methylene group, have attracted interest as hydrolytically stable mimetics of their parent O-glycosides. This research reports the development of two general methodologies for the synthesis of highly oxygenated cyclohexanes: (1) Oxocarbenium Ion Cyclization (OCC) and (2) Ring Closing Metathasis (RCM).

Chapter one gives a review of the literature on the synthesis for highly oxygenated cyclohexanes.

Previous results from this …

Synthesis Of Biologically Important C-Glycosides From Simple C-Glycosyl Alkenes, Ahmad Sabri Altiti

Dissertations, Theses, and Capstone Projects

C-Glycosides are carbohydrate analogues in which the glycosidic oxygen is replaced with a methylene substituent. Because of their stability under acidic hydrolysis or enzymatic cleavage, they are widely used as mimetics of their parent O-glycosides in medicinal chemistry. This thesis describes the development of new synthetic methods for C-glycosides, which center on the use of readily available, simple C-allyl glycosides as precursors. C- glycosides of three structurally distinct and pharmacologically interesting carbohydrates, the immunostimulatory glycolipid C-KRN700, the insulin mimetic glycoinositol β-galactosamine-(1→4)-3-O-methyl-D-chiro-inositiol (INS-2), and α-mannose-(1→6)-D-myo-inositiol, a subunit of the cell wall in Mycobacterium tuberculosis, will be used as test cases for …

Sorption Of Cr(Iii) And Cr(Vi) To High And Low Pressure Synthetic Nano-Magnetite (Fe3o4)Particles, Jason Parsons, Jeffrey Hernandez, Christina M. Gonzalez, J. L. Gardea-Torresdey

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

The binding of Cr(III) and Cr(VI) to synthetic nano-magnetie particles synthesized under open vessel conditions and a microwave assisted hydrothermal synthesis techniques was investigated. Batch studies showed that the binding of both the Cr(III) and Cr(VI) bound to the nano-materials in a pH dependent manner. The Cr(III) maximized at binding at pH 4 and 100% binding. Similarly, the Cr(VI) ions showed a maximum binding of 100% at pH 4. The data from the time dependency studies showed for the most part the majority of the binding occurred within the first 5 minutes of contact with the nanomaterial and remained constant …

Supramolecular Biopolymeric Composite Materials: Green Synthesis, Characterization And Applications, Tamutsiwa Moven Mututuvari

Dissertations (1934 -)

Macrocycles, such as crown ethers (CRs) and resorcinarenes (RESs), exhibit selective complexation of heavy metal ions and organic pollutants respectively. Consequently, they have been investigated for their suitability in adsorbing these aqueous pollutants. However, they are difficult to handle and recycle for reuse because, by themselves, they can only be fabricated in powder form. To alleviate this challenge, we developed a method to encapsulate these macrocycles into film-forming polysaccharides--cellulose (CEL) and chitosan (CS). This was achieved by using a green and recyclable solvent, an ionic liquid, to dissolve both macrocycles and polysaccharides and regenerate corresponding composites in water. Resultant composites …

Resonant Two-Photon Ionization Studies Of Non Covalent Interactions In Halo Aromatic Clusters And Spin-Orbit Coupling Modeling In Mono-Halocarbenes, Silver Nyambo

Dissertations (1934 -)

Non-covalent interactions in halobenzenes (PhX) (X=F, Cl, Br) and phenylamine (C₆ H₅ NH₂ ) have been studied here using resonance two-photon ionization (R2PI) spectroscopy combined with a linear TOF-mass spectrometer. Their interaction with polar molecules in form of ammonia (NH ₃ ) and trifluorohalomethanes (CF₃ X) has also been studied. DFT and TD-DFT calculations using M06-2X functionals were carried out on different cluster conformations to compliment experimental results. A general trend of broadness in homogenous dimers (PhX)₂ , has been attributed to mainly the presence of multiple cluster isomers and Frank-Condon activity in the low …

Endothelial Nitric Oxide Synthase Is Regulated By Erk Phosphorylation At Ser602, John C. Salerno, Dipak K. Ghosh, Raj Razdan, Katy A. Helms, Jonathan L. Mcmurry, Emily A. Rye, Carol A. Chrestensen

Faculty Articles

eNOS (endothelial nitric oxide synthase) contains a MAPK (mitogen-activated protein kinase)-binding site associated with a major eNOS control element. Purified ERK (extracellular-signal-regulated kinase) phosphorylates eNOS with a stoichiometry of 2–3 phosphates per eNOS monomer. Phosphorylation decreases NO synthesis and cytochrome c reductase activity. Three sites of phosphorylation were detected by MS. All sites matched the SP and TP MAPK (mitogen-activated protein kinase) phosphorylation motif. Ser602 lies at the N-terminal edge of the 42-residue eNOS AI (autoinhibitory) element. The pentabasic MAPK-binding site lies at the opposite end of the AI, and other critical regulatory features are between them. Thr46 and Ser58 …

An Expeditious Green Route Toward 2-Aryl-4- Phenyl-1h-Imidazoles, Debasish Bandyopadhyay, Lauren C. Smith, Daniel R. Garcia, Ram Naresh Yadav, Bimal K. Banik

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Background: Azaheterocycles are an important class of compounds because of their highly potent medicinal activities, and the imidazole subcategory is of special interest in regard to drug discovery research.

Findings: An expeditious synthetic protocol of 2-aryl-4-phenyl-1H-imidazoles has been accomplished by reacting phenylglyoxal monohydrate, ammonium acetate, and aldehyde under sonication. Following this green approach a series of 2-aryl-4-phenyl-1H-imidazoles has been synthesized using diversely substituted aldehydes.

Conclusions: A rapid and simple synthetic procedure to synthesize diversely substituted 2-aryl-4-phenyl-1H-imidazoles has been reported. Other salient features of this protocol include milder conditions, atom-economy, easy extraction, and minimum wastes. The present procedure may find application …