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Identification Of The Nad(P)H Binding Site Of Eukaryotic Udp-Galactopyranose Mutase, Richa Dhatwalia, Harkewal Singh, Luis M. Solano, Michelle Oppenheimer, Reeder M. Robinson, Jacob F. Ellerbrock, Pablo Sobrado, John J. Tanner

Chemistry Faculty Research & Creative Works

UDP-galactopyranose mutase (UGM) plays an essential role in galactofuranose biosynthesis in microorganisms by catalyzing the conversion of UDP-galactopyranose to UDP-galactofuranose. The enzyme has gained attention recently as a promising target for the design of new antifungal, antitrypanosomal, and antileishmanial agents. Here we report the first crystal structure of UGM complexed with its redox partner NAD(P)H. Kinetic protein crystallography was used to obtain structures of oxidized Aspergillus fumigatus UGM (AfUGM) complexed with NADPH and NADH, as well as reduced AfUGM after dissociation of NADP+. NAD(P)H binds with the nicotinamide near the FAD isoalloxazine and the ADP moiety extending toward the mobile …

A New Random Walk Simulation Model For Study Of Diffusion Behavior Of Single Particle Within Two-Dimensional Space, Jianwei Zhao, Lili Chen, Yingqiang Fu, Shaohong Li, Tiannan Chen, Shijie Zhang

Journal of Electrochemistry

Research on diffusion behaviors is of significant value in that it is closely related to transport phenomena in micro-chemistry. However, the effects of variables on diffusion are still unclear. Here, we developed and programmed a simulation methodology along with data analysis, which was capable to simulate the diffusion of a particle within twodimensional heterogeneous space in large timescale; the effects of periodically arranged impenetrable barriers of specific shape and lateral drifting velocity on diffusion behavior were studied. As well as standard mean square displacement analysis, a new method, the appearance probability distribution method, was introduced, which revealed whether the particle …

In Situ Pm-Irras Studies Of A Floating Bilayer Lipid Membrane At Au(111) Electrode Surface, Su Zhangfei, Kycia Annia, Jay Leitch J., Lipkowski Jacek

Journal of Electrochemistry

In situ Polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) was used to study the structure of a DMPC + cholesterol + GM1 floating bilayer lipid membrane (fBLM) at a Au(111) surface. 1-thio-beta-D-glucose (beta-Tg) was self-assembled onto the Au electrode to increase the overall hydrophilicity of the surface. The fBLM was deposited on the beta-Tg self-assembled monolayer (SAM) using a combination of Langmuir-Blodgett/Langmuir-Schaefer (LB/LS) techniques. The carbohydrate headgroups of the GM1 molecules were physically adsorbed to the beta-Tg SAM forming a water rich cushion between the fBLM and the modified gold substrate. The PM-IRRAS spectra indicate that the DMPC molecules within …

Foreword, Bin Ren

Journal of Electrochemistry

On the request of Prof. Shi-Gang Sun, Editor-in-Chief of Journal of Electrochemistry, I served as the guest editor for this International Special Issue on Current Electrochemistry. The Journal of Electrochemistry was founded in 1995 associated to the Chinese Chemical Society just before the 46^th Annual meeting of the International Society of Electrochemistry (ISE). Prof. Zhao-Wu Tian was the founder of the journal and had been serving as the Editor-in-Chief until 2010. The journal is known for high quality scientific papers related to the electrochemical science, techniques and engineering, and is well-known in Electrochemistry Community in China. However, the journal …

Electrochemical Detection Of Ammonia In Aqueous Solution Using Fluorescamine: A Comparison Of Fluorometric Versus Voltammetric Analysis, Panchompoo Janjira, G. Compton Richard

Journal of Electrochemistry

Fluorescamine is a non-fluorescent reagent widely used for the quantitative determination of primary amines by fluorescence spectroscopy as it reacts readily with primary amines to form a fluorescent product. In this work, a new sensitive voltammetric method for the detection of ammonia in aqueous solution by the reaction with fluorescamine has been developed. First, the electrochemical behaviour of fluorescamine in the absence and presence of ammonia was investigated in 0.1 mol L^-1 borate buffer solution (pH 9.0) by cyclic voltammetry using a glassy carbon (GC) electrode. As for fluorescamine itself, a well-defined irreversible oxidation peak could be observed at …

The Oxidation Of Hydrogen Peroxide On Nanostructured Rhodium Microelectrodes, N. Bartlett Philip, F. Esterle Thomas

Journal of Electrochemistry

Mesoporous Rh films were deposited onto platinum microelectrodes from the H₁ lyotropic liquid crystalline phase of C₁₂EO₈ (octaethyleneglycol monododecyl ether). The electrodes show well defined voltammetry for the oxidation and the reduction of hydrogen peroxide at low concentrations (<10 mmol•L-1) with excellent stability for operation at neutral pH. Based on the hysteresis in the current and the potential dependence the oxidation of hydrogen peroxide occurs through a CEE mechanism involving Rh(OH)₃ on the mesoporous Rh electrode surface. At higher hydrogen peroxide concentrations the current reaches a plateau that is due to either saturation of the binding sites for hydrogen peroxide or limitation of the reaction due to acidification of the solution within the pores. For the thin films (below 200 nm) the hydrogen peroxide calibration curves we …

Organics In Environmental Ices: Sources, Chemistry, And Impacts, V. F. Mcneill, A. M. Grannas, J. P. D. Abbatt, M. Ammann, P. Ariya, T. Bartels-Rausch, F. Domine, D. J. Donaldson, Marcelo I. Guzman, D. Heger, T. F. Kahan, P. Klán, S. Masclin, C. Toubin, D. Voisin

Chemistry Faculty Publications

The physical, chemical, and biological processes involving organics in ice in the environment impact a number of atmospheric and biogeochemical cycles. Organic material in snow or ice may be biological in origin, deposited from aerosols or atmospheric gases, or formed chemically in situ. In this manuscript, we review the current state of knowledge regarding the sources, properties, and chemistry of organic materials in environmental ices. Several outstanding questions remain to be resolved and fundamental data gathered before an accurate model of transformations and transport of organic species in the cryosphere will be possible. For example, more information is needed regarding …

One-Pot Three-Step Thioconjugate Addition-Oxidation-Diels–Alder Reactions Of Ethyl Propiolate, C. Wade Downey, Smaranda Craciun, Christina A. Vivelo, Ana M. Neferu, Carly J. Mueller, Stephanie Corsi

Chemistry Faculty Publications

Ethyl propiolate undergoes one-pot three-step thioconjugate addition-oxidation-Diels–Alder cycloaddition when treated with a variety of thiols in the presence of catalytic base, meta-chloroperbenzoic acid, lithium perchlorate, and cyclopentadiene. The reaction of S‑aryl thiols is catalyzed by trialkylamines, and the reaction of aliphatic thiols requires catalytic alkoxide base. Yields of the major diastereomer of the conveniently functionalized bicyclic products range from 47 to 81% depending upon the thiol reactant, which compares favorably to yields observed when the entire synthesis is performed step by step.

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

Chemistry & Biochemistry Newsletter: 2002-2015

Inside:

Page 2 Jing wins Avera/SDSU Collaborative Research Funding; Teaching Assistants complete Certification of Excellence Program; Ron Utecht Issued Two Patents

Page 3 Tille is 2012 Education and Research Grant Recipient; Biochem Student Summit League Male Cross Country Athlete of the Year

Page 4 Zhang receives Board of Regents Grant

Page 5 MLS Receives National Clinical Pathology Scholarship

Page 6 Alumni Updates; Faculty Updates; Recent Publications

A Novel Microfluidic Enrichment Technique For Carbonylated Proteins, Bryant C. Hollins

Doctoral Dissertations

Proteins are the building blocks of cells in living organisms, and are composed of amino acids. The expression of proteins is regulated by the processes of transcription and translation. Proteins undergo post-translational modifications in order to dictate their role physiologically within a cell.

Not all post-translational modifications are beneficial for the protein or the cell. One type of post-translational modification, called carbonylation, irreversibly places a carbonyl group onto an amino acid residue, most commonly proline, lysine, arginine, and threonine. This modification can have severe consequences physiologically, including loss of solubility, loss of function, and protein aggregation.

Carbonylated proteins have commonly …

The Association Of Elevated 2′,5′-Oligoadenylate-Dependent Rnase L With Lung Cancer Correlated With Deficient Enzymatic Activity And Decreased Capacity Of Rnase L Dimerization, Huijing Yin, Aimin Zhou, Yalei Dai

Chemistry Faculty Publications

RNase L mediates critical cellular functions including antiviral, proapoptotic, antiproliferative and tumor suppressive activities. In this study, the expression and function of RNase L in lung cancer cells were examined. Interestingly we have found that the expression of RNase L in lung cancer cells was 3- and 9-fold higher in its mRNA and protein levels, but a significant decrease of its enzymatic activity when compared to that in corresponding normal lung cells. Further investigation revealed that 2-5A-induced dimerization of the RNase L protein, a necessary prerequisite for activation of RNase L, was inhibited, as a result of that RLI, a …

Method For Arsenic Detection In Mine Samples From The Upper Peninsula Of Michigan, Vinay Babu Yalamanchili

All Capstone Projects

Arsenic is the 20th abundant element in the earth crust. High concentrations of Arsenic is seen in mine operating countries which can affect public health and biological environment. This may reach to drinking water through ground or surface run-off water. Long term exposure to arsenic causes cancer of bladder, skin, and lungs. So detecting the amount of arsenic in soil and drinking has been an analytical challenge. Arsenic is found in variety of chemical forms in organic and inorganic compounds which results in chemical and physical interferences in the analysis. Graphite Furnace Atomic Absorption Spectroscopy (GFAAS) was used to measure …

Evaluation And In Vitro Studies Of Folate Peg Biotin And Other Peg Agents, Syed Zahid Hussain

All Capstone Projects

Folate is a member of vitamin B family and plays an essential role in cell survival by participating in the biosynthesis of nucleic and amino acids. Receptors folic acid are frequently over expressed on epithelial cancer cells. These receptors are believed to serve as a receptor-mediated transport system of folic acid into cancer cells and cells associated with inflammation. Interesting, most normal cells in the body have lower frequency of these receptors. Based on these attributes, folate based drug delivery, imaging systems, and diagnostic systems are in several stages of development worldwide.

In this current project, we have characterized the …

Literature Search On Using Dendrimer Nanoparticles As Drug Delivery Vehicles, Sivateja Kasaraneni

All Capstone Projects

The architectural design of dendrimers, multivalency, well-defined molecular weight and higher degree of branching differentiates them as unique and excellent nanocarriers in therapeutic applications such as drug delivery, gene transfection, tumor therapy, imaging and diagnostics. Nanoparticle drug-delivery systems are well known to increase the stability and selectivity of therapeutic agents. However immunogenicity, reticuloendothelial system uptake, drug leakage, cytotoxicity, hemolytic toxicity, poor aqueous solubility restrict the use of these drug delivery systems. These defects are overcame by surface engineering of the dendrimer molecule.

Drug molecule can be efficiently conjugated or encapsulated into the interior of the dendrimer or physically adsorbed onto …

Purification And Analysis Of Folate-Dye Conjugate, Sravya Mothe

All Capstone Projects

Folate receptor has achieved great importance for use in targeted drug delivery and in vitro and in vivo diagnostic assays. Folate receptor (FR) is over expressed on several cancer cell types and activated macrophages, but exists in relatively low abundance on the surface of non-cancerous tissue and non-inflammatory cells. This unique attribute is the hallmark of folate – targeted methodologies allowing the diagnostic agent and/or drug to be ferried to the specific disease sites while preventing “off target” effects in normal tissues. Although several folate-based dyes have been reported, simple and detailed synthetic and purification methods for these conjugates have …

Quality Assurance Plan Project For Copper Determination Using Flame Atomic Absorption Spectroscopy, Bharath Raparthi

All Capstone Projects

This study developed a method for determination of Copper by flame atomic absorption spectrometry (FAAS) from the soil samples and mine tailings using Perkin Elmer AAnalyst 800 atomic absorption spectrometer. A detailed procedure has been developed with a detection limit of 0.12 mg/L. In the recent decades, pollution from heavy metals has been increased. Copper is one of the trace metals that has a significant impact and carries risk to the human health. Calibration curve was established with working range 0.1 ppm to 5 ppm with a correlation coefficient of 0.9994. Over 50 environmental samples from the historic Copper mining …

Cox Inhibitors Indomethacin And Sulindac Derivatives As Antiproliferative Agents: Synthesis, Biological Evaluation, And Mechanism Investigation, Snigdha Chennamaneni, Bo Zhong, Rati Lama, Bin Su

Chemistry Faculty Publications

Cyclooxygenase (COX) inhibitors Indomethacin and its structural analogs Sulindac exhibit cell growth inhibition and apoptosis inducing activities in various cancer cell lines via COX independent mechanisms. In this study, the molecular structures of Indomethacin and Sulindac were used as starting scaffolds to design novel analogs and their effects on the proliferation of human cancer cells were evaluated. Compared to Indomethacin and Sulindac inhibiting cancer cell proliferation with IC50s of more than 1 mM, the derivatives displayed significantly increased activities. Especially, one of the Indomethacin analogs inhibited the growth of a series of cancer cell lines with IC50s around 0.5 μM–3 …

Liposome Encapsulation Of A Photochemical No Precursor For Controlled Nitric Oxide Release And Simultaneous Fluorescence Imaging, Alexis D. Ostrowski, Brian F. Lin, Matthew V. Tirrell, Peter C. Ford

Chemistry Faculty Publications

Described are photochemical studies of the nitric oxide precursors, trans-Cr(L)(ONO)(2)(+) (L = cyclam = 1,4,8,11-tetraazacyclotetradecane, CrONO, or L = mac = 5,7-dimethyl-6-anthracenylcyclam, mac-CrONO) encapsulated in phosphatidylcholine liposomes. The liposomes provide a means to maintain a localized high concentration of NO releasing complexes and are easily modified for in vivo targeting through self-assembly. Steady, controlled release of NO is seen after photolysis of the liposome-encapsulated CrONO as compared to the burst of NO release seen by the unencapsulated complex in oxygenated solutions. The quantum yields for photochemical NO release from liposome-encapsulated CrONO and mac-CrONO were determined in both oxygenated and anoxic …

The Influence Of Auxiliary Ligands On The Photophysical Characteristics Of A Series Of Ruthenium (Ii) Polypyridyl Complexes, Luke O'Neill, Laura Perdisatt, Christine O'Connor

Articles

A series of ruthenium polypyridyl complexes were studied using UV/Vis absorption and luminescence spectroscopy as well as luminescence lifetime determination by time correlated single photon counting (TCSPC). The complexes were characterised with regard to the variation in the electronic band-gap as a result of the sequential variation of the auxiliary ligand 2,2’-bipyridine (bpy), 1,10-phenanthroline (phen) and 2,2’-biquinoline (biq) ligands while the main ligand remained constant for three different main ligand types. Luminescence yields were calculated and correlated with structural and electronic variation. It was found that both the absorption and emission characteristics could be tailored through the systematic variation of …

Probing The Role Of Asn 152 In The Class C Β-Lactamase Ampc, Brianne Docter, Mujahid Anwar, David Leonard, Rachel Powers, Bradley Wallar

Student Summer Scholars Manuscripts

AmpC, a class C β-lactamase, is a main cause of antibiotic resistance to cephalosporins in many species of bacteria. The current proposed mechanism of action involves an acyl-intermediate, where the enzyme becomes covalently attached to the drug at serine-64, before an activated water hydrolyzes the bond and regenerates the enzyme. Although this mechanism is generally accepted, the exact roles that the other active site residues play in recognition and breakdown of the substrate are not fully understood. Here, we investigate the role of the active site residue asparagine-152 (Asn152) in E. coli AmpC by mutating it to a glycine, serine, …

Spectral Characterization Of Cytochromes P450 Active Site And Catalytic Intermediates, Daniel Kaluka

Dissertations (1934 -)

Cytochromes P450 (P450s) have been the subject of intense research for over six decades. Though it is widely accepted that a highly reactive Fe(IV)=O π-cation radical, or the so called compound I, facilitates the oxidation of relatively inert hydrocarbons, spectroscopic characterization of this putative intermediate has eluded detection under turnover conditions, presumably due to its very short lifetime. In this work, chemically inert substrates of P450s have been utilized in a new approach to capture and stabilize this transient intermediate and characterize it with resonance Raman (RR) spectroscopy, which is a well established tool for studying heme proteins. Specifically, perfluorodecanoic …

Photochemical Eilmination Reactions Via Zwitterionic Intermediates Generated By Electrocyclic Ring Closures, Majher Ibna Mannan Sarker

Dissertations (1934 -)

The research focuses on the design of photoremovable protecting groups that can be used to deprotect biological substrates of an organic compound by photolysis. The deprotection of the protecting group via photolysis requires heterolysis of a bond to the substrate. Heterolysis of a C-O or C-S σ-bonds in a zwitterionic intermediate is proposed. The photochemical electrocyclic reactions studied involve acrylanilides, benzothiophene carboxanilides, and N-(9-oxothioxanthenyl) benzothiophene carboxamides. α,β-Unsaturated anilides bearing leaving groups at the allylic position of the α-methylacrylamide group undergo photochemical electrocyclic ring closure with release of leaving group which could occur directly from a photochemically produced zwitterionic intermediate or …

Rat Brain Pro-Oxidant Effects Of Peripherally Administered 5 Nm Ceria 30 Days After Exposure, Sarita S. Hardas, Rukhsana Sultana, Govind Warrier, Mo Dan, Rebecca L. Florence, Peng Wu, Eric A. Grulke, Michael T. Tseng, Jason M. Unrine, Uschi M. Graham, Robert A. Yokel, D. Allan Butterfield

Chemistry Faculty Publications

The objective of this study was to determine the residual pro-or anti-oxidant effects in rat brain 30 days after systemic administration of a 5 nm citrate-stabilized ceria dispersion. A ∼4% aqueous ceria dispersion was iv-infused (0 or 85 mg/kg) into rats which were terminated 30 days later. Ceria concentration, localization, and chemical speciation in the brain was assessed by inductively coupled plasma mass spectrometry (ICP-MS), light and electron microscopy (EM), and electron energy loss spectroscopy (EELS), respectively. Pro- or anti-oxidant effects were evaluated by measuring levels of protein carbonyls (PC), 3-nitrotyrosine (3NT), and protein-bound-4-hydroxy-2-trans-nonenal (HNE) in the hippocampus, cortex, and …

An Expeditious Iodine-Catalyzed Synthesis Of 3-Pyrrole-Substituted 2-Azetidinones, Debasish Bandyopadhyay, Jessica Cruz, Ram N. Yadav, Bimal K. Banik

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

2-Azetidinones and pyrroles are two highly important classes of molecules in organic and medicinal chemistry. A green and practical method for the synthesis of 3-pyrrole-substituted 2-azetidinones using catalytic amounts of molecular iodine under microwave irradiation has been developed. Following this method, a series of 3-pyrrole-substituted 2-azetidinones have been synthesized with a variety of substituents at N-1 and at C-4. The procedure is equally effective for mono-as well as polyaromatic groups at the N-1 position of the 2-azetidinone ring. The C-4 substituent has no influence either on the yield or the rate of the reaction. Optically pure 3-pyrrole-substituted 2-azetidinones have also …

Project Synthesis Of N Acetyl L Histidine Ethyl Amide And Standard Operating Procedure For Fractional Collector, Maneesha Jakkampudi

All Student Theses and Dissertations

Photo oxidation of proteins leads to the formation of cross links of the amino acids in the proteins and leads to induction of cataracts, photo aging of the skin and in the Photodynamic therapy of tumors.

Oxidation of proteins involves significant modification of particular amino acids residues with consequent photodynamic damage. Studies show that tryptophan, tyrosine and histidine side chains gives rise to semi stable peroxides on exposure to singlet oxygen these oxidized structures are studied with low temperature NMR. These peroxides or species derived from them have been postulated as key intermediates in subsequent reactions such as cross linking …

Chemical Proteomics-Based Analysis Of Off-Target Binding Profiles For Rosiglitazone And Pioglitazone: Clues For Assessing Potential For Cardiotoxicity, Brian R. Hoffmann, Mohamed F. El-Mansy, Daniel S. Sem, Andrew S. Greene

Chemistry Faculty Research and Publications

Drugs exert desired and undesired effects based on their binding interactions with protein target(s) and off-target(s), providing evidence for drug efficacy and toxicity. Pioglitazone and rosiglitazone possess a common functional core, glitazone, which is considered a privileged scaffold upon which to build a drug selective for a given target—in this case, PPARγ. Herein, we report a retrospective analysis of two variants of the glitazone scaffold, pioglitazone and rosiglitazone, in an effort to identify off-target binding events in the rat heart to explain recently reported cardiovascular risk associated with these drugs. Our results suggest that glitazone has affinity for dehydrogenases, consistent …

Experimental Documentation Of The Structural Consequences Of Hydrogen-Bonding Interactions To The Proximal Cysteine Of A Cytochrome P450, Piotr J. Mak, Yuting Yang, Sangchoul Im, Lucy A. Waskell, James R. Kincaid

Chemistry Faculty Research and Publications

Resonance Raman spectroscopy is used to document, for the first time, a 6 cm−1 decrease of the Fe-S stretch by introducing an H-bond donor into the proximal pocket of a cytochrome P450, which interacts with the key cysteine thiolate axial ligand. The anticipated trans-effect on bound exogenous ligands is also confirmed and evidence is obtained supporting intimate interaction of the new histidyl-imidazole fragment with the heme periphery.

Cop1 Mediates The Coordination Of Root And Shoot Growth By Light Through Modulation Of Pin1- And Pin2-Dependent Auxin Transport In Arabidopsis, Massimiliano Sassi, Yanfen Lu, Yonghong Zhang, Juan Wang, Pankaj Dhonukshe, Ikram Blilou, Minqiu Dai, Juan Li, Ximing Gong, Yvon Jaillais, Xuhong Yu, Jan Traas, Ida Ruberti, Haiyang Wang, Ben Scheres, Teva Vernoux, Jian Xu

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

When a plant germinates in the soil, elongation of stem-like organs is enhanced whereas leaf and root growth is inhibited. How these differential growth responses are orchestrated by light and integrated at the organismal level to shape the plant remains to be elucidated. Here, we show that light signals through the master photomorphogenesis repressor COP1 to coordinate root and shoot growth in Arabidopsis. In the shoot, COP1 regulates shoot-to-root auxin transport by controlling the transcription of the auxin efflux carrier gene PIN-FORMED1 (PIN1), thus appropriately tuning shoot-derived auxin levels in the root. This in turn directly influences root elongation and …

Exploring The Role Of A Conserved Class A Residue In The Ω-Loop Of Kpc-2 Β-Lactamase: A Mechanism For Ceftazidime Hydrolysis

Chemistry Faculty Publications

Gram-negative bacteria harboring KPC-2, a class A β-lactamase, are resistant to all β-lactam antibiotics and pose a major public health threat. Arg-164 is a conserved residue in all class A β-lactamases and is located in the solvent-exposed Ω-loop of KPC-2. To probe the role of this amino acid in KPC-2, we performed site-saturation mutagenesis. When compared with wild type, 11 of 19 variants at position Arg-164 in KPC-2 conferred increased resistance to the oxyimino-cephalosporin, ceftazidime (minimum inhibitory concentration; 32→128 mg/liter) when expressed in Escherichia coli. Using the R164S variant of KPC-2 as a representative β-lactamase for more detailed analysis, we …

Restricted Access Media And Methods For Making Restricted Access Media, David S. Hage, Chunling Wa, Abby Jackson, Hai Xuan

David Hage Publications

The present invention is directed to restricted access media (RAM), methods for preparing restricted access media, and kits for preparing restricted access media that contain protected ligand binding agents or protected enzymes. Certain RAM provided contain a plurality of protected regions of the Support that contain ligand binding agents that are protected by blocking agents. Certain RAM provided contain a plurality of protected regions of the support that contain unbound ligand binding agents or enzymes that are retained in the protected regions by a capping agent. Methods of making the RAM of the invention and associated kits are also provided.