Physical Sciences and Mathematics Commons^™

Contributions Of Tunneling In 8Π-6Π Electrocyclic Cascade Reactions Of Bicyclo[4.2.0]Octa-2,4-Diene Moieties, Ishika Jain, Claire Castro, William L. Karney

Featured Student Work

Six-electron electrocyclic reactions usually require relatively high temperatures; however recent research has shown that such reactions can occur at significantly lower temperatures in biosynthetic and biomimetic pathways. Pathways resulting in bicyclo[4.2.0]octa-2,4-diene moieties arise from thermally allowed 8π-6π electrocyclization cascade reactions of 1,3,5,7-octatetraenes, as in the biosynthesis of endiandric acids, elysiapyrones, and numerous other natural products. We report multidimensional tunneling calculations to explore the possible contribution of heavy-atom tunneling (e.g. by carbon) to biosynthetic pathways and biomimetic syntheses, and thus to provide a more complete picture of biochemical kinetics. M06-2X/cc-pVDZ calculations on the 8π-6π cascade cyclizations of methylated octatetraene model systems …

Potential Interactions Between Diatoms And Bacteria Are Shaped By Trace Element Gradients In The Southern Ocean, Alexa R. Sterling, Laura Z. Holland, Randelle M. Bundy, Shannon M. Burns, Kristen N. Buck, P. Dreux Chappell, Bethany D. Jenkins

OES Faculty Publications

The growth of diatoms in the Southern Ocean, especially the region surrounding the West Antarctic Peninsula, is frequently constrained by low dissolved iron and other trace metal concentrations. This challenge may be overcome by mutualisms between diatoms and co-occurring associated bacteria, in which diatoms produce organic carbon as a substrate for bacterial growth, and bacteria produce siderophores, metal-binding ligands that can supply diatoms with metals upon uptake as well as other useful secondary compounds for diatom growth like vitamins. To examine the relationships between diatoms and bacteria in the plankton (diatom) size class (> 3 mu m), we sampled both …

A Study Of Cannabigerolic Acid And Its Derivatives Via Raman Spectroscopy And Density Functional Theory, Trevor Wolfe

Honors Theses

The cannabinoids are a class of molecules endogenous to the cannabis plant. Their scientific relevance has increased in recent years due to the mercurial legal status of marijuana across the United States. Some of the most known are cannabidiol (CBD), δ9-tetrahydrocannabinol (δ9-THC), and δ8-THC due in large part to their widespread use, especially in states where marijuana and related products are legal. However, cannabigerolic acid (CBGA) is arguably the most important cannabinoid; it is enzymatically converted into other acidic cannabinoids, which subsequently undergo non-enzymatic processes (isomerization, thermal decarboxylation, oxidation, etc.) to synthesize further cannabinoids. Although there is a wealth of …

Synthesis Of 6,6- And 7,7-Difluoro-1-Acetamidopyrrolizidines And Their Oxidation Catalyzed By The Nonheme Fe Oxygenase Lolo, Nabin Panth

Theses and Dissertations--Chemistry

One of the remarkable steps in loline alkaloid biosynthesis is the installation of an ether bridge between two unactivated C atoms in 1-exo-acetamidopyrrolizidine (AcAP). LolO, a 2-oxoglutarate-dependent nonheme Fe oxygenase, catalyzes both the hydroxylation of AcAP and the resulting alcohol's cycloetherification to give N-acetylnornoline (NANL). The mechanism of hydroxylation is well understood, but the mechanism of the oxacyclization is not. I synthesized difluorinated analogs of AcAP in an attempt to further understand the mechanism of the unusual cycloetherification step.

I prepared 6,6-F₂-AcAP in eight steps from N,O-protected 4-oxoproline. The key step was a Dieckmann …

Biomedical Applications Of Chasmanthera Dependens Stem Extract Mediated Silver Nanoparticles As Antimicrobial, Antioxidant, Anticoagulant, Thrombolytic, And Larvicidal Agents, Daniel Ayandiran Aina, Oluwafayoke Owolo, Agbaje Lateef, Folasade O. Aina, Abbas Saeed Hakeem, Morenike Adeoye-Isijola, Victor Okon, Tesleem B. Asafa, Joseph Adetunji Elegbede, Olumide D. Olukanni, Isaac Adediji

Karbala International Journal of Modern Science

The stem extract of Chasmanthera dependens was used in the biofabrication of silver nanoparticles (AgNPs) in this study. The AgNPs was characterised using UV-visible spectroscopy, Field Emission Scanning Electron Microscope (FESEM), EDX, and the Fourier Transform Infrared Spectroscopy (FTIR). Antibacterial, antioxidant, anticoagulant, thrombolytic and larvicidal activities of the biosynthesised nanoparticles were carried out. There was a peak at 418 nm with a strong silver peak observed around 2.7KeV when the EDX analysis was carried out. The FESEM showed a large number of cubically shaped nanoparticles with sizes ranging from 24.53 to 92.38 nm. CDE-AgNPs was effective against Klebsiella pneumoniae at …

Green Synthesis/Biosynthesis Of Silver Nanoparticles By Using Orange Peel Extract, Leela Joshi

Theses and Dissertations

Joshi, Leela, Green Synthesis/Biosynthesis of Silver Nanoparticles by Using Orange Peel Extract. Master of Science (MS), December, 2018, 40 pages, 23 figures, references, 36 titles. In this work, we report synthesis of silver nanoparticles (AgNPs) with an average size of ~6 nm. The aqueous solution of Ag+ ions is reduced using an aqueous extract from orange peel (Citrus Sinensis) at varying pHs. Reduction of Ag+ ions in solution was monitored using UV-visible absorption spectroscopy, and the corresponding surface plasmon resonance of AgNPs at 435 nm. The solution changed color from yellow to reddish-brown upon bioreduction of silver nitrate in orange …

An Integrated Approach To Studying And Engineering Bacterial Type Ii Polyketide Core Structure Biosynthesis, Xuechen Zhu

Chemistry and Chemical Biology ETDs

Natural products including alkaloids, phenylpropanoids, polyketides, terpenoids and antibiotics provide abundant resources for drugs and drug leads. Type II polyketides (PK-IIs) are a large array of aromatic polyketides that have exhibited various bioactivities including anti-tumor, anti-cancer, anti-fungal and anti-bacteria. Based on the lengths of carbon chains and the cyclization patterns in their core structures, most bacterial PK-IIs have been classified into 6 typical classes: benzoisochromanequinone (BIQ), anthracycline (ANT), angucycline (ANG), tetracycline (TET), tetracenomycin (TCM) and pentangular (PEN). Bioengineering for diversification of PK-II core structures will generate libraries of bioactivities, which can serve the drug discovery in this family of compounds. …

Investigation In To The Stabilizing Effects Of The Modified Base Archaeosine In Trna And The Identification Of The Fluorescent Product Of Base Treatment Of Nad(P)+ Cofactors, Ben Turner

Dissertations and Theses

This dissertation covers two projects linked by their involvement in the modification of tRNA bases.

The first project focused on an investigation of a role for the modified base Archaeosine, the ubiquitous modification in tRNA in the archaeal domain. Initial work was performed on a set of in vitro prepared tRNA modified to feature either the canonical guanine base at position 15, preQ₀ (TGT product) or Archaeosine (ArcS product). There was very little difference in the thermal stability of tRNAs containing these modifications in the halophilic H. volcanii tRNA^Ser or E. coli tRNA^Gln. In tRNA^{Gln …}

Quef-Like, A Non-Homologous Archaeosine Synthase From The Crenarchaeota, Adriana Bon Ramos, Lide Bao, Ben Turner, Valérie De Crécy-Lagard, Dirk Iwata-Reuyl

Chemistry Faculty Publications and Presentations

Archaeosine (G+) is a structurally complex modified nucleoside ubiquitous to the Archaea, where it is found in the D-loop of virtually all archaeal transfer RNA (tRNA). Its unique structure, which includes a formamidine group that carries a formal positive charge, and location in the tRNA, led to the proposal that it serves a key role in stabilizing tRNA structure. Although G+ is limited to the Archaea, it is structurally related to the bacterial modified nucleoside queuosine, and the two share homologous enzymes for the early steps of their biosynthesis. In the Euryarchaeota, the last step of the archaeosine biosynthetic pathway …

Formation Of The Ether Bridge In The Loline Alkaloid Biosynthetic Pathway, Minakshi Bhardwaj

Theses and Dissertations--Chemistry

Lolines are specialized metabolites produced by endophytic fungi, such as Neotyphodium and Epichloë species, that are in symbiotic relationships with cool-season grasses. Lolines are vital for the survival of the grasses because their insecticidal and antifeedant properties protect the plant from insect herbivory. Although lolines have various bioactivities, they do not have any concomitant antimammalian activities.

Lolines have complex structures that are unique among naturally occurring pyrrolizidine alkaloids. Lolines have four contiguous stereocenters, and they contain an ether bridge connecting C(2) and C(7) of the pyrrolizidine ring. An ether bridge connecting bridgehead C atoms is unusual in natural products and …

Quef And Quef-Like: Diverse Chemistries In A Common Fold, Adriana Bon Ramos

Dissertations and Theses

The tunneling fold (T-Fold) superfamily is a small superfamily of enzymes found in organisms encompassing all kingdoms of life. Seven members have been identified thus far. Despite sharing a common three-dimensional structure these enzymes perform very diverse chemistries.

QueF is a bacterial NADPH-dependent oxidoreductase that catalyzes the reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ₀) to a primary amine (preQ₁) in the queuosine biosynthetic pathway. Previous work on this enzyme has revealed the mechanism of reaction but the cofactor binding residues remain unknown. The experiments discussed herein aim to elucidate the role of residues lysine 80, …

Discovery And Characterization Of The Proteins Involved In The Synthesis Of N⁶-Threonylcarbamoyl Adenosine, A Nucleoside Modification Of Trna, Christopher Wayne Deutsch

Dissertations and Theses

N6-threonylcarbamoyl adenosine (t⁶A) is a universally conserved tRNA modification found at position 37 of tRNAs which decode ANN codons. Structural studies have implicated its presence as a requirement for the disruption of a U-turn motif in certain tRNAs, leading to the formation of properly structured anticodon stem loop. This structure is proposed to enhance the base pairing between U₃₆ of tRNA and A₁ of the codon which aids in translational frame maintenance.

Despite significant effort since its discovery in the 1970s the enzymes involved in its biosynthesis remained undiscovered. Bioinformatic analysis identified two proteins as likely …

Synthetic Methods Development Towards The Total Synthesis Of Chlorosulfolipids, Andres Villalpando

LSU Doctoral Dissertations

The focus of this dissertation is the development of a novel chlorination reaction utilizing a triphosgene-amine based mixture towards the total synthesis of chlorosulfolipids, a subclass of naturally occurring organohalogen natural products. This novel, mild chlorination reaction will be utilized under a global chlorination strategy to chlorinate multiple alcohol substituents in one synthetic operation. Chapter one details the history of chlorosulfolipids from the early stages of their isolation, relevant structural elucidation techniques, appropriate biosynthetic discoveries, and their biological relevance to a thorough investigation of the total syntheses completed to date. These compounds demonstrate a range of biological activities and have …

The Dape-Encoded N-Succinyl-L,L-Diaminopimelic Acid Desuccinylase From Haemophilus Influenzae Contains Two Active-Site Histidine Residues, Danuta M. Gillner, David L. Bienvenue, Boguslaw P. Nocek, Andzrej Joachimiak, Vincentos Zachary, Brian Bennett, Richard C. Holz

Richard C. Holz

The catalytic and structural properties of the H67A and H349A dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) from Haemophilus influenzae were investigated. On the basis of sequence alignment with the carboxypeptidase from Pseudomonas sp. strain RS-16, both H67 and H349 were predicted to be Zn(II) ligands. The H67A DapE enzyme exhibited a decreased catalytic efficiency (180-fold) compared with wild-type (WT) DapE towards N-succinyldiaminopimelic acid. No catalytic activity was observed for H349A under the experimental conditions used. The electronic paramagnetic resonance (EPR) and electronic absorption data indicate that the Co(II) ion bound to H349A-DapE is analogous to that of WT DapE after the …

Promiscuous And Adaptable Enzymes Fill “Holes” In The Tetrahydrofolate Pathway In Chlamydia Species, Nancy E. Adams, Jennifer J. Thiaville, James Proestos, Ana L. Juárez-Vázquez, Andrea J. Mccoy, Francisco Barona-Gómez, Dirk Iwata-Reuyl, Valérie De Crécy-Lagard, Anthony T. Maurelli

Chemistry Faculty Publications and Presentations

Folates are tripartite molecules comprising pterin, para-aminobenzoate (PABA), and glutamate moieties, which are essential cofactors involved in DNA and amino acid synthesis. The obligately intracellular Chlamydia species have lost several biosynthetic pathways for essential nutrients which they can obtain from their host but have retained the capacity to synthesize folate. In most bacteria, synthesis of the pterin moiety of folate requires the FolEQBK enzymes, while synthesis of the PABA moiety is carried out by the PabABC enzymes. Bioinformatic analyses reveal that while members of Chlamydia are missing the genes for FolE (GTP cyclohydrolase) and FolQ, which catalyze the initial …

Synthesis And Evaluation Of Unnatural Hpaa, Norcoclaurine, And Tyramine Analogues, Sean Crowe

College of Science and Health Theses and Dissertations

There are several approaches to obtaining unnatural analogues of natural products. One of these approaches is precursor-directed biosynthesis (PDB), which is the process of using natural biosynthetic machinery to transform unnatural analogues of precursor compounds to produce an unnatural analogue of a target natural product. Berberine and galanthamine are chosen as model systems for the evaluation of PDB for the production of aromatic alkaloids in plants. Several approaches to the synthesis of unnatural 4 hydroxyphenylacetaldehyde (HPAA), norcoclaurine, and tyramine analogues are explored. 3-chloro-, 3-bromo-, and 3-iodoHPAA are all synthesized in good yields via and oxidative decarboxylation of tyrosine. These analogues …

Biosynthesis Of Marineosin, A Spiroaminal Undecylprodiginine Natural Product, Shaimaa Mohamed Salem

Dissertations and Theses

Marineosins A and B are two spiroaminal-ring containing tripyrrole compounds isolated from the marine actinomycete, Streptomyces CNQ-617, and were found to possess potent and selective cytotoxic activity against leukemia and melanoma. Marineosins belong to the prodiginines class of natural products, examples of which are undecylprodiginine and streptorubin B. Unlike marineosins, prodiginines structures are characterized by the presence of fully conjugated tripyrrole nucleus linked to an alkyl chain (that lacks any oxygen). Cyclic prodiginines arise from an oxidative cyclization of the alkyl chain onto the tripyrrole, a step catalyzed by Rieske-oxygenase like enzymes such as RedG. The biosynthesis of prodiginines is …

Transformation Of Fusarium Verticillioides With A Polyketide Gene Cluster Isolated From A Fungal Endophyte Activates The Biosynthesis Of Fusaric Acid, Yunxuan Xie, Wei Zhang, Yaoyao Li, Mingzi Wang, Ronald Cerny, Yue Shen, Liangcheng Du

Liangcheng Du Publications

A large number of bioactive natural products have been isolated from plant endophytic fungi. However, molecular mechanisms for the biosynthesis of these metabolites have lagged behind because genetic and biochemical studies are difficult to perform within many of the endophytes. In this work, we describe our attempt to express a putative mycoepoxydiene (MED) biosynthetic gene cluster in Fusarium verticillioides, which has a well-developed genetic system for the study fungal polyketide biosynthesis. MED was isolated from Phomopsis sp. A123, a fungal endophyte of the mangrove plant, Kandelia candel. It has several unusual structural features and interesting biological activities. Integration of …

Absolute Configuration And Biosynthesis Of Pahayokolide A From Lyngbya Sp. Strain 15-2 Of The Florida Everglades, Li Liu

FIU Electronic Theses and Dissertations

Pahayokolides A-D are cytotoxic cyclic polypeptides produced by the freshwater cyanobacterium Lyngbya sp. strain 15-2 that possess an unusual β-amino acid, 3-amino-2,5,7,8-tetrahydroxy-10-methylundecanoic acid (Athmu). The absolute configuration of pahayokolides A-D was determined using advanced Marfey’s method. It was also confirmed that a pendant N-acetyl-N-methyl leucine moiety in pahayokolide A was absent in pahayokolides B and pahayokolides C-D were conformers of pahayokolide A. Feeding experiments indicated that the biosynthesis of the Athmu sidechain arises from leucine or α-ketoisovalerate, however could not be further extended by three rounds of condensation with malonate units. Putative four peptide and one unique polyketide synthetases in …

Halothiobacillus Neapolitanus Carboxysomes Sequester Heterologous And Chimeric Rubisco Species, Balaraj B. Menon, Zhicheng Dou, Sabine Heinhorst, Jessup M. Shively, Gordon C. Cannon

Faculty Publications

Background: The carboxysome is a bacterial microcompartment that consists of a polyhedral protein shell filled with ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), the enzyme that catalyzes the first step of CO(2) fixation via the Calvin-Benson-Bassham cycle. Methodology/Principal Findings: To analyze the role of RubisCO in carboxysome biogenesis in vivo we have created a series of Halothiobacillus neapolitanus RubisCO mutants. We identified the large subunit of the enzyme as an important determinant for its sequestration into alpha-carboxysomes and found that the carboxysomes of H. neapolitanus readily incorporate chimeric and heterologous RubisCO species. Intriguingly, a mutant lacking carboxysomal RubisCO assembles empty carboxysome shells of …

Functional Replacement Of The Ketosynthase Domain Of Fum1 For The Biosynthesis Of Fumonisins, A Group Of Fungal Reduced Polyketides, Xiangcheng Zhu, Fengan Yu, R. S. Bojja, K. Zaleta-Rivera, Liangcheng Du

Liangcheng Du Publications

The genetic manipulation of the biosynthesis of fungal reduced polyketides has been challenging due to the lack of knowledge on the biosynthetic mechanism, the difficulties in the detection of the acyclic, non-aromatic metabolites, and the complexity in genetically manipulating filamentous fungi. Fumonisins are a group of economically important mycotoxins that contaminate maize-based food and feed products worldwide. Fumonisins contain a linear dimethylated C₁₈ chain that is synthesized by Fum1p, which is a single module polyketide synthase (PKS). Using a genetic system that allows the specific manipulation of PKS domains in filamentous fungus Fusarium verticillioides, we replaced the KS domain …

Regulation And Localization Of Endogenous Human Tristetraprolin, Anna-Marie Fairhurst, John E. Connolly, Katharine A Hintz, Nicolas J Goulding

Dartmouth Scholarship

Tumor necrosis factor (TNF) has been implicated in the development and pathogenicity of infectious diseases and autoimmune disorders, such as septic shock and arthritis. The zinc-finger protein tristetraprolin (TTP) has been identified as a major regulator of TNF biosynthesis. To define its intracellular location and examine its regulation of TNF, a quantitive intracellular staining assay specific for TTP was developed. We establish for the first time that in peripheral blood leukocytes, express

The Biosynthetic Gene Cluster For The Anticancer Drug Bleomycin From Streptomyces Verticillus Atcc15003 As A Model For Hybrid Peptide–Polyketide Natural Product Biosynthesis, B. Shen, Liangcheng Du, C. Sanchez, D. J. Edwards, M. Chen, J. M. Murrell

Liangcheng Du Publications

The hybrid peptide–polyketide backbone of bleomycin (BLM) is assembled by the BLM megasynthetase that consists of both nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) modules. BlmIX/BlmVIII/BlmVII constitute a natural hybrid NRPS/PKS/NRPS system, serving as a model for both hybrid NRPS/PKS and PKS/NRPS systems. Sequence analysis and functional comparison of domains and modules of BlmIX/BlmVIII/BlmVII with those of nonhybrid NRPS and PKS systems suggest that (1) the same catalytic sites appear to be conserved in both hybrid NRPS–PKS and nonhybrid NRPS or PKS systems, with the exception of the KS domains in the hybrid NRPS/PKS systems that are unique; (2) …