VTechWorks Repository :: Browsing by Author "Bevan, David R."

Browsing by Author "Bevan, David R."

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Albumin Adsorption: Inferences of Protein Interactions Measured by Sedimentation both Between Species and Induced by Denaturing
McKeon, Kristin Dianne (Virginia Tech, 2008-04-18)
Biological development and progression are managed by a diverse macromolecular group called proteins. Protein structure results from a complex folding process that leads to a final active form. This protein state is susceptible to changes in the surrounding environment and an incorrect structure can be produced. Changes in the protein conformation can lead to the formation of protein aggregates. Adsorption of proteins onto surfaces is utilized in many research analyses, but is capable of irreversibly changing the protein structure and causing aggregation. Albumin is a plasma protein that adsorbs on many different surfaces because the structure easily rearranges. The structure of albumin once adsorbed has been shown to deteriorate; however, outcomes of both stabilization and aggregation have been found. A dynamic laser light scattering instrument will be utilized to measure the differences in size and determine the amount of aggregation. Our lab has developed a z-axis translating laser light scattering device (ZATLLS) that has been used to measure the sedimentation velocity of several different materials in solution. In this case, bovine serum albumin (BSA) will be adsorbed onto polystyrene particles and the particle settling velocity determined. The settling solution viscosity and density will also be ascertained, so Stoke's law can infer the average aggregate size of each experiment. BSA-coated polystyrene particles displayed a more controlled settling behavior compared to non-coated polystyrene particles. Although the BSA-coated particles had a smaller sedimentation velocity, a larger aggregate size was found due to the greater solution viscosity. Therefore, the ZATLLS instrument can be employed to measure sedimentation velocities of multiple interactions and the aggregation level inferred. Although most albumin molecules are remarkably similar, there are subtle differences in amino acid residues, length, and charge. Sedimentation velocities for human serum albumin (HSA) coated polystyrene particles and BSA-coated polystyrene particles only had a small difference. However an almost 50% higher solution viscosity was measured in BSA experiment solutions, and resulted in the slower settling of the larger aggregates compared to HSA-coated particles. Viscosity calibration curves for each albumin species were used to determine the amount of protein desorbed from the particles during the settling process. The larger solution viscosity for BSA-coated particle experiments led to a much larger degree of desorption. HSA was shown to be the more stable albumin species when adsorbed onto polystyrene particles. Temperature denaturing was performed to aid in the determination of the stability of BSA. Reversible and irreversible conformational changes in BSA were produced at 46ºC and 76ºC respectively. The solutions were cooled to room temperature before adsorption ontopolystyrene particles and the sedimentation velocities measured. A 50% difference in average viscosity between the reversibly and irreversibly changed BSA was found. This caused the larger aggregates formed in the 76ÂºC BSA experiments to have an almost equivalent sedimentation velocity to those in the reversibly denatured BSA experiments. Average aggregate size for reversibly denatured BSA was well within the ranges found for non-denatured BSA. In conclusion, irreversibly denatured BSA formed larger aggregates and was more likely to desorb from the polystyrene particles than reversibly changed BSA.
Algorithms for Reconstructing and Reasoning about Chemical Reaction Networks
Cho, Yong Ju (Virginia Tech, 2013-01-24)
Recent advances in systems biology have uncovered detailed mechanisms of biological processes such as the cell cycle, circadian rhythms, and signaling pathways. These mechanisms are modeled by chemical reaction networks (CRNs) which are typically simulated by converting to ordinary differential equations (ODEs), so that the goal is to closely reproduce the observed quantitative and qualitative behaviors of the modeled process. This thesis proposes two algorithmic problems related to the construction and comprehension of CRN models. The first problem focuses on reconstructing CRNs from given time series. Given multivariate time course data obtained by perturbing a given CRN, how can we systematically deduce the interconnections between the species of the network? We demonstrate how this problem can be modeled as, first, one of uncovering conditional independence relationships using buffering experiments and, second, of determining the properties of the individual chemical reactions. Experimental results demonstrate the effectiveness of our approach on both synthetic and real CRNs. The second problem this work focuses on is to aid in network comprehension, i.e., to understand the motifs underlying complex dynamical behaviors of CRNs. Specifically, we focus on bistability---an important dynamical property of a CRN---and propose algorithms to identify the core structures responsible for conferring bistability. The approach we take is to systematically infer the instability causing structures (ICSs) of a CRN and use machine learning techniques to relate properties of the CRN to the presence of such ICSs. This work has the potential to aid in not just network comprehension but also model simplification, by helping reduce the complexity of known bistable systems.
Analysis of the Allergenic Potential of the Ubiquitous Airborne Fungus Alternaria Using Bioinformatics
Babiceanu, Mihaela (Virginia Tech, 2011-06-15)
Among the environmental airborne fungi one of the most common is Alternaria alternata. From a clinical perspective Alternaria has long been associated with IgE-mediated, histamine-dependent mold allergy, allergic rhinitis, chronic rhinosinusitis (CRS) and asthma. Recently it has been proven that an abnormal immunological response to Alternaria most likely contributes to the pathogenesis of upper respiratory airway disorders. In this body of work, we present for the first time results of several sets of experiments including, 1) the analysis of A. alternata spore germination expressed sequence tags (ESTs), 2) the survey of global allergen homologues in fungal genomes, and 3) the first microarray experiment investigating airway epithelial cell responses to this fungus. In the first project, the analyses of the EST dataset offered a first look into the gene content of A. alternata and represents the beginning of future research of this ubiquitous fungus. Annotation and classification of ESTs revealed a number of genes that could be involved in the immunomodulation process of the human immune response toward fungi. We also discovered that the majority of known allergens are expressed during the spore germination phase of A. alternata. For investigating the allergenic potential of fungi we developed a whole genome approach by querying fungal genome sequences (A. alternata, A. brassicicola, and Aspergillus fumigatus) with a database of all known allergenic proteins from a taxonomically diverse group of organisms. Interestingly, we identified homologues of diverse types of allergens in these fungal genomes and also many homologues of allergens from other organisms including those from pollen, insects, and venoms. Finally, we investigated global gene expression changes of human airway cells in response to A. alternata and an ∆alt a 1 deletion mutant. We found that wild type Alternaria spores induced significant changes in gene expression patterns in human airway epithelial cells, especially known immune response genes. Furthermore, results of these analyses revealed that Alt a 1 is a major factor in inducing epithelial inflammatory responses.
Antioxidant activity of Mn-salophen complex and its effects on antioxidant enzymes in Escherichia coli
Liu, Zheng-Xian (Virginia Tech, 1994-11-05)
Mn-salophen complex with superoxide-scavenging activity was prepared from manganese(III) acetate dihydrate and salophen in ethanol. Visible absorption spectrum of the red-brown solution exhibited a broad absorption band at 430 - 450 nm with two shoulders between 500 and 600 nm which were absent with either salophen or manganic acetate alone. Titration of salophen with manganese(III) was consistent with a 1:1 Mn to salophen stoichiometry of the complex based on changes in the absorbance at 500 nm or of superoxide scavenging activity. The SOD-like activity of the complex in the xanthine-xanthine oxidase/cytochrome c assay was 1450 units/mg salophen. The SOD activity of the complex was suppressed 50% in the presence of EDTA (1 mM), but was not altered in the presence of bovine serum albumin (1 mg/ml) or crude protein extract of E. coli QC779 sodA sodB (1 mg/ml). E. coli QC779 sodA sodB grew scantily after an 8 hour lag phase in aerobic M63 glucose minimal medium.
Antioxidant Intervention With manganese(Iii)-Salophen in the Selenite Cataract Model: Implications for Cataract Disease
Dell, Kevin David (Virginia Tech, 1998-05-04)
Cataract disease affects millions of people worldwide. It is characterized by the accumulation of light-scattering bodies within the lens that reduce visual acuity. Cataracts are effectively treated surgically, but at great expense, costing Medicare $3.4 billion in 1997. Development of an alternative therapy for this disease would provide medical and economic benefits. We have investigated a novel antioxidant, the superoxide scavenger Mn(III)-salophen, as a therapeutic agent in the selenite cataract model. Mn(III)-salophen has been shown to protect E. coli colonies against oxidative stress but was untested in a eukaryotic system. A total dose of 300 mmol/kg, given IP in four equal 75 mmol/kg doses spaced four hours apart, protects 75% of neonatal rats from nuclear cataract development five days after selenite injection. Selenite is toxic through its reaction with the endogenous antioxidant glutathione (GSH). The reduction of selenite to selenide through an intermediate, selenodiglutathione (GSSeSG) leads to generation of superoxide radical, one of several toxic oxygen species that can damage the lens. Mn(III)-salophen causes an in vitro preservation of the lifetime of GSSeSG by interrupting the reduction of selenite. We have established that the reduction of GSSeSG to selenide does not use GSH as a reducing agent, but rather depends upon electrons generated in the earlier reduction of selenite to selenodiglutathione. These electrons can be intercepted by known one-electron scavengers, arresting the metabolism of GSSeSG. Extensive proteolysis of lens crystallins and loss of calcium homeostasis occur in cataractous lenses from a rat treated with sodium selenite. The visual protection with Mn(III)-salophen is accompanied by a partial loss of the calcium homeostasis, a net increase in sodium, and calpain-mediated proteolysis of Ã -crystallins similar to lenses from animals treated with selenite alone. Although preservation of alpha-crystallins may contribute to the greater transparency in the protected lens, generalized Ã -crystallin proteolysis is insufficient for cataract formation. From these experiments we propose that Mn(III)-salophen minimizes the oxidative stress imposed upon the cell by interfering with the metabolism of selenodiglutathione. This allows the cell to compensate for the loss of cation homeostasis and prevents aggregation of proteolyzed crystallins into cataracts.
Assembly of Iron-Sulfur Clusters In Vivo
O'Carroll, Ina Puleri (Virginia Tech, 2009-02-03)
Iron-sulfur [Fe-S] clusters are protein cofactors that facilitate various life-sustaining biological processes. Their in vivo assembly is accomplished by three different systems known to date. These are: the NIF system which provides [Fe-S] clusters for nitrogenase and other nitrogen-fixing proteins, the SUF system which is induced during conditions of oxidative stress and iron starvation in E. coli, and the ISC system which serves as the housekeeping assembly apparatus. The latter is the focus of this dissertation and includes the proteins IscR, IscS, IscU, IscA, HscB, HscA, Fdx, and IscX. IscU is purified in its cluster-less (apo) form, but can serve as a scaffold to assemble [Fe-S] clusters in vitro in the presence of excess iron and sulfide. To test the scaffold hypothesis and gain insight into the events that occur during [Fe-S] cluster assembly and delivery, we developed two methods that allow the isolation of IscU and other ISC proteins in vivo. In the first method, Azotobacter vinelandii IscU is isolated from its native host, whereas in the second, it is isolated recombinantly from E. coli using a vector that allows expression of the entire isc operon. We found that IscU exists in vivo in two forms: apo-IscU and [2Fe-2S]2+ cluster-loaded IscU which are believed to be conformationally distinct. Both transient and stable IscU-IscS complexes were identified, indicating that the two proteins interact in vivo in a manner that involves their association and dissociation. The [2Fe-2S]2+-IscU species was present as a single entity, whereas significant amounts of apo-IscU were found associated with IscS, suggesting that IscU-IscS dissociation is triggered by the completion of [2Fe-2S] clusters. Both apo and [2Fe-2S]2+-IscU were predominantly monomeric whereas IscU-IscS complexes were determined to have an Î±2Î²2 composition. IscU was purified in the absence of the chaperones HscA and HscB and was also shown to accommodate a [2Fe-2S]2+ cluster similar to the one bound to IscU isolated from wild type cells. The findings suggest that [2Fe-2S]2+-IscU exists in one conformation in vivo and that any conformational changes on IscU are exerted after [2Fe-2S] cluster formation. In silico studies showed that a flexible loop containing the conserved LPPVK motif, which is responsible for interactions with HscA, may facilitate cluster exposure to either mediate its delivery to acceptor proteins or participation in the construction of [4Fe-4S] clusters. Experiments with NfuA, a protein similar to the C-terminal domain of NifU, demonstrated that NfuA and similar proteins might serve as [Fe-S] cluster carriers to accomplish the efficient delivery of nascent cofactors to the various recipient proteins.
Baculovirus-directed expression of the phosphorylase kinase catalytic subunit: pseudosubstrate and calmodulin regulation
Lanciotti, Robert Arthur (Virginia Tech, 1994-08-05)
Phosphorylase kinase (EC 2.7.1.38) is a key enzyme involved in the regulation of the glycogenolysis pathway. It catalyzes the Ca²⁺-dependent phosphorylation and activation of the enzyme glycogen phosphorylase to make the active form glycogen phosphorylase. Phosphorylase kinase is composed of 4 subunits with a stoichiometry of (αβγδ)₄. The γ subunit is the catalytic subunit. The regulatory domain (residues 277-387) of γ contains a sequence resembling the sites phosphorylated in known γ substrates with the exception that a valine₃₃₂ occurs at the analogous position of the phosphorylated serine or threonine residue.
Binding properties of adaptor proteins Tollip and Tom1
Brannon, Mary Katherine (Virginia Tech, 2015-07-02)
Adaptor proteins, like Tollip and Tom1, facilitate cellular cargo sorting through their ubiquitin-binding domains. Tollip and Tom1 bind to each other through their TBD and GAT domains, respectively, whereas Tollip interacts with phosphatidylinositol-3-phosphate (PtdIns(3)P)-containing endosomal membranes. Tom1 and Tollip interaction and association with endosomes is proposed to be involved in the lysosomal degradation of polyubiquitinated cargo. Through cellular, biochemical, and biophysical techniques, we have further characterized the association of Tom1 with Tollip. Mutations in the binding interface of the Tom1 GAT and Tollip TBD complex leads to a subcellular mis-localization of both proteins, indicating that Tom1 may serve to direct Tollip to specific cellular pathways. It was determined that Tom1 inhibits the binding of Tollip to PtdIns(3)P and inhibition was reversed when mutations in the binding interface of the Tom1 GAT and Tollip TBD were present. Furthermore, it was established that, upon the binding of Tollip TBD to Tom1 GAT, ubiquitin is inhibited from binding to Tom1 GAT. It was also demonstrated that Tom1 GAT, but not Tollip TBD, can weakly bind to PtdIns(3)P. Consequently, we propose that association of Tom1 may serve to direct Tollip for involvement in specific cell signaling pathways. Gaining insight into the function of Tom1 and Tollip may lead to their use as therapeutic targets for increasing the efficiency of cargo trafficking and also for patients recovering from various cardiac injuries.
A biochemical and physiological characterization of coenzyme F420-reducing hydrogenase from Methanobacterium formicicum
Baron, Stephen Francis (Virginia Polytechnic Institute and State University, 1988)
The coenzyme F₄₂₀-reducing hydrogenase of Methanobacterium formicicum was purified 87-fold to electrophoretic homogeneity. The enzyme formed aggregates (1,000 kd) of a coenzyme F₄₂₀-active monomer (109 kd) composed of 1 each of a, β, and γ subunits (43.6, 36.7, xy and 28.8 kd, respectively). It contained 1 mol of FAD, 1 mol of nickel, 12-14 mols of iron, and 11 mols of acid-labile sulfide per mol of the 109 kd species, but no selenium. The amino acid sequence I---P--R-EGH-----EV was conserved in the N-terminus of a subunit of the enzyme and the largest subunits of nickel-containing hydrogenases from Methanobacterium thermoautotrophicum, Desulfovibrio baculatus, and Desulfovibrio gigag. FAD dissociated from the coenzyme F42O-reducing hydrogenase during reactivation with H2 and coenzyme F₄₂₀, unless KCl was present, yielding coenzyme F₄₂₀-inactive apoenzyme. The hydrogenase catalyzed H₂ production at a rate 3-fold less than that for H2 uptake. Specific antiserum inhibited the coenzyme F₄₂₀ dependent activity but not the methyl viologen-dependent activity of the purified enzyme. Cell extract of M. formicicum contained a coenzyme F₄₂₀-mediated formate hydrogenlyase system. Formate hydrogenlyase activity was reconstituted with coenzyme F₄₂₀-reducing hydrogenase, coenzyme F₄₂₀-reducing formate dehydrogenase, and coenzyme F₄₂₀, all purified from M. formicicum. The reconstituted system required FAD for maximal activity (kinetic Kd= 4 μM). without FAD, the formate dehydrogenase and hydrogenase rapidly lost coenzyme F₄₂₀-dependent activity relative to methyl viologen-dependent activity. Immunoadsorption of the formate dehydrogenase or hydrogenase from cell extract greatly reduced formate hydrogenlyase activity; addition of the purified enzymes restored activity. Formate hydrogenlyase activity of cell extract and the reconstituted system was reversible. The coenzyme F₄₂₀-reducing hydrogenase and formate dehydrogenase of M. formicicum were shown to be located at the cytoplasmic membrane using immunogold labeling of thin sectioned, Lowicryl-embedded cells. Neither enzyme was released from whole cells by osmotic shock treatment.
Biochemical Studies of Aromatic Amino Acid Decarboxylases and Acetaldehyde Synthases
Liang, Jing (Virginia Tech, 2018-07-09)
Pyridoxal 5'-phosphate (PLP)-dependent enzymes widely exist in most living organisms from bacteria to human. Among different types of PLP-dependent enzymes, aromatic amino acid decarboxylases play critical physiological roles because many aromatic amines are essential neurotransmitters. This dissertation concerns the biochemical characterization of several PLP-dependent decarboxylases and aims to understand the structure-function relationships, especially critical residues involved in their catalysis. We first present an overview of the current opinions and recent advances in structure-function relationships of several PLP-dependent enzymes with the first reaction step at substrate Cα position, including decarboxylase and acetaldehyde synthase. L-3, 4-dihydroxyphenylalanine (L-dopa) decarboxylase (DDC) is a model enzyme we use as a reference because the structures and functions of DDC are relatively well established. We previously identified two annotated DDC-like proteins from Drosophila indeed catalyzing a decarboxylation-oxidative deamination reaction of L-dopa to form 3,4-dihydroxyphenylacetaldehyde (DHPA), CO2, NH3, and H2O2 and we named these proteins as DHPA synthases due to the physiological importance of DHPA for cuticle protein crosslinking. Our results provide an efficient way to identify more DHPA synthase enzymes from DDC based on sequence identity and the signature residues we identified (Asn192 in DHPA synthase versus His192 in DDC), and we also propose a reasonable explanation of the mechanism. The results that H2O2 produced by the reaction can be reused in the reaction as an oxidizing agent suggest a way to avoid the oxidative stress of H2O2. We then compared tyrosine decarboxylase (TyDC) with DDC. As the enzyme catalyzing the first step of insect neurotransmitter tyramine/octopamine synthesis, the biochemical characteristics of insect TyDC have not been thoroughly elucidated yet because of the expression difficulty. We expressed one insect TyDC and analyzed its biochemical properties. Our enzyme analyses reveal that insect TyDC prefers tyrosine as a substrate, but it also displays some activity to L-dopa. Spectral analysis also shows that the absorbance spectra of insect TyDC have major differences as compared to those of DDC. Site-directed mutagenesis indicates that the interactions between residue Asn304 with PLP is primarily responsible for its spectra differences of TyDC as compared to those of DDC and also is involved in higher substrate affinity to L-tyrosine. Another active site residue (Ser353) has the main effect on substrate selectivity. Our results show the biochemical properties of TyDC for the first time and also provide some insights into the mechanism of its substrate selectivity.
Biochemical studies of enzymes in insect cuticle hardening
Liu, Pingyang (Virginia Tech, 2013-03-28)
In insects, the cuticle provides protection against physical injury and water loss, rigidness for muscle attachment and mechanical support, and flexibility in inter-segmental and joint areas for mobility. As most insects undergo metamorphosis, they need to shred off old cuticle and synthesize new cuticle to fit the body shape and size throughout their life cycles. The newly formed cuticle, mainly composed of cuticular proteins, chitin, and sclerotizing reagents, needs to be hardened through the crosslinks between cuticular proteins and sclerotizing reagents. This dissertation concerns the biochemical activities of several pyridoxal 5-phosphate (PLP)-dependent decarboxylases with most of them involved in insect cuticle hardening. Herein, we first present a detailed overview of topics in reactions and enzymes involved in insect cuticle hardening. Aspartate 1-decarboxylase (ADC) is at the center of this dissertation. beta-alanine, the product of ADC-catalyzed reaction from aspartate, is the component of an important sclerotizing reagent, N-beta-alanyldopamine; the levels of beta-alanine in insects regulate the concentrations of dopamine, therefore affecting insect sclerotization and tanning (collectively referred as cuticle hardening in this dissertation). Biochemical characterization of insect ADC has revealed that this enzyme has typical mammalian cysteine sulfinic acid decarboxylase (CSADC) activity, able to generate hypotaurine and taurine. The result throws lights on research in the physiological roles of insect ADC and the pathway of insect taurine biosynthesis. Cysteine was found to be an inactivator of several PLP-dependent decarboxylases, such as ADC, glutamate decarboxylase (GAD) and CSADC. This study helps to understand symptoms associated with the abnormal cysteine concentrations in several neurodegenerative diseases. A mammalian enzyme, glutamate decarboxylase like-1 (GADL1), has been shown to have the same substrate usage as insect ADC does, potentially contributing to the biosynthesis of taurine and/or beta-alanine in mammalian species. Finally, the metabolic engineering work of L-3, 4-dihydroxyphenylalanine decarboxylase (DDC) and 3, 4-dihydroxylphenylacetaldehyde (DHPAA) synthase has revealed that the reactions of these enzymes could be determined by a few conserved residues at their active site. As both enzymes have been implicated in the biosynthesis of sclerotizing reagents, it is of great scientific and practical importance to understand the similarity and difference in their reaction mechanisms. The results of this dissertation provide valuable biochemical information of ADC, DDC, DHPAA synthase, and GADL1, all of which are PLP-dependent decarboxylases. ADC, DDC, DHPAA synthase are important enzymes in insect cuticle hardening by contributing to the biosynthesis of sclerotizing reagents. Knowledge towards understanding of these enzymes will promote the comprehension of insect cuticle hardening and help scientists to search for ideal insecticide targets. The characterization of GADL1 lays groundwork for future research of its potential role in taurine and beta-alanine metabolism.
The Biosynthesis and Function of Nitrogenase Metalloclusters
Dos Santos, Patricia C. (Virginia Tech, 2004-11-29)
Nitrogenase catalyzes the biological reduction of N2 to ammonia (nitrogen fixation). The metalloclusters associated with the nitrogenase components include the [4Fe-4S] cluster of the Fe protein, and the P-cluster [8Fe7S] and FeMo-cofactor [7Fe-9S-Mo-X-homocitrate], both contained within the MoFe protein. These metal-complexes play a vital role in enzyme activity during electron transport and substrate reduction. It is known that the FeMo-cofactor provides the site of substrate reduction, but the exact site of substrate binding remains a topic of intense debate. Some models for the substrate binding location favor the molybdenum atom, while other models favor one or more iron atoms within FeMo-cofactor. We have shown that the a-70 residue of the MoFe protein plays a significant role in defining substrate access to the active site: a-70 approaches one 4Fe-4S face of the FeMo-cofactor. Substitutions at this position alter enzyme specificity for reduction of alternative alkyne substrates. These altered MoFe proteins and alternative alkyne substrates, such as propargyl alcohol, were used to trap an intermediate during substrate reduction. Further studies involving the effect of pH on substrate reduction of these altered MoFe proteins pinpointed the location of the bound substrate-derived intermediate on the FeMo-cofactor to a specific Fe atom, designated Fe6. In addition to understanding how substrates are bound and reduced at the active site, understanding how these clusters are biologically assembled is a second point of interest. Inactivation of NifU or NifS has been shown to affect the activity of both nitrogenase components. NifS is a cysteine desulfurase that provides the sulfur for cluster formation and NifU serves as a molecular scaffold during [Fe-S] cluster assembly. Genetic and biochemical experiments involving amino acid substitutions within the N-terminal and C-terminal domains of NifU indicate that both domains can separately participate in nitrogenase-specific [Fe-S] cluster formation. Furthermore, the NifU and NifS protein appear to have specialized functions in the maturation of metalloclusters of nitrogenase and cannot functionally replace the isc [Fe-S] cluster system used for the maturation of other [Fe-S] proteins. These results indicate that, in certain cases, [Fe-S] cluster biosynthetic machineries have evolved to perform only specialized functions.
Biosynthesis of Caldariellaquinone in Sulfolobus acidocaldarius
Zhou, Dan (Virginia Tech, 1991)
The biosynthesis of caldariellaquinone (CQ) has been studied in Sulfolobus acidocaldarius using a variety of methods. By growing cells with a series of tyrosines labeled with deuterium or ¹³C and measuring the extent and position at which label was incorporated into the CQ by mass spectrometry, it was concluded that the benzo[b]thiophen-4,7-quinone ring of CQ is derived as an intact unit from all of the carbons of tyrosine except C-1. Additional work, using (3S)-L-(2-²H, 3-²H]-, (3R)-D-[2-²H, 3-²H]-, (3S)-D-[3-²H]-, and (3R)-L-[3-²H]- tyrosine, demonstrated that the pro-3S hydrogen of either D- or L-tyrosine is the origin of the C-3 proton of the benzo[b]thiophene ring. Considering the above information and the structure of CQ, it was concluded that CQ was most likely biosynthesized by the condensation of farnesylfarnesyl pyrophosphate with homogentisic acid (HA) in a reaction analogous to that found in the biosynthesis of ubiquinone. The possibility of this reaction being involved in the biosynthesis of CQ was supported by the identification of farnesylfarnesol, a hydrolytic breakdown product of farnesylfarnesyl pyrophosphate, by gas chromatography-mass spectrometry (GC-MS) of purified lipid extracts. The possible involvement of HA in CQ biosynthesis, however, could not be confirmed by five independent methods. The possible formation of CQ by the condensation of benzo[b]thiophen-4,7-quinone with farnesylfarnesyl pyrophosphate was eliminated by the inability to detect benzo[b]thiophen-4,7-quinone in S. acidocaldarius. Attempts to identify the tyrosine metabolites leading to CQ by studing the metabolisms of tyrosine, 2-fluorotyrosine, and 3-fluorotyrosine in S. acidocaldarius lead to the identification of two previously undescribed pathways for tyrosine metabolism. These two pathways branch after the conversion of tyrosine to 4-hydroxyphenylacetic acid (pHPA). The ability of labeled pDHPA to be incorporated into these metabolites, but not into CQ, indicates that the first committed step in the biosynthesis of CQ occurs at either tyrosine or a metabolite very closely related to tyrosine, e.g., 4-hydroxyphenylpyruvate (pHPP). Analysis of the extract of the cells grown with 3-fluorotyrosine showed two fluorine-containing compounds, which are likely to be fluoro-analogues of the intermediates in the biosynthesis of CQ. However, because of the small amount of these two compounds found (24 nmoles/g of wet weight), structural characterization was not possible. Both the methyl and sulfur groups of the methylthio portion of CQ were shown to arise from methionine. Mass spectral analysis of the CQ isolated from cells grown in the presence of [³⁴S-methyl-²H₃]-L-methionine clearly showed, however, that the methylthio group of CQ is not derived as an intact unit from the methylthio group of methionine. Additional work supported the theory that the methionine sulfur first undergoes transsulfuration to cysteine, which then supplies the sulfur for both the methylthio and the benzo[b]thiophene moieties of CQ. This represents the first example of transsulfuration from methionine to cysteine occurring in archaebacteria.
Biosynthesis of Iron-Sulfur Clusters
Yuvaniyama, Pramvadee (Virginia Tech, 1999-11-17)
It is not known whether biosynthesis of [Fe-S] clusters occurs through a spontaneous self-assembly process or an enzymatic process. However, in the Azotobacter vinelandii nitrogenase system, it has been proposed that NifS and NifU are involved in the mobilization of sulfur and iron necessary for nitrogenase-specific [Fe-S] cluster assembly. The NifS protein has been shown to have cysteine desulfurase activity and can be used to supply sulfur for the in vitro catalytic formation of [Fe-S] clusters. The activity of the NifU protein has not yet been established, but NifU could have functions complementary to NifS by mobilizing iron or serving as an intermediate site necessary for nitrogenase-specific [Fe-S] cluster assembly. A second iron-binding site within NifU was predicted to serve these functions because two identical [2Fe-2S] clusters that had previously been identified within the homodimeric NifU are tightly bound, and the NifU primary sequence is rich in cysteine residues. In this dissertation, I examined the possibility that NifU might mobilize iron or serve as an intermediate site for [Fe-S] cluster assembly, as well as the possibility that NifU could work in concert with NifS. Primary sequence comparisons, amino acid substitution experiments, and biophysical characterization of recombinantly-produced NifU fragments were used to show that NifU has a modular structure. One module is contained in approximately the C-terminal half of NifU and provides the binding site for the [2Fe-2S] cluster previously identified (the permanent [2Fe-2S] cluster). Cysteine residues Cys¹³⁷, Cys¹³⁹, Cys¹⁷⁵, and Cys¹⁷⁵ serve as ligands to the [2Fe-2S] cluster. Another module (referred to as NifU-1) is contained in approximately the N-terminal third of NifU and provides a second iron-binding site (rubredoxin-like Fe(III)-binding site). Cysteine residues Cys³⁵, Cys⁶², Cys¹⁰⁶>, and a putative non-cysteine ligand of unknown origin provide coordination to the iron at this site. The significance of these iron-binding sites was also accessed by showing that cysteine residues involved in providing the rubredoxin-like Fe(III)-binding site and those that provide the [2Fe-2S] cluster binding site are all required for the full physiological function of NifU. The two other cysteine residues contained within NifU, Cys²⁷² and Cys²⁷⁵, are neither necessary for binding iron at either site nor are they required for the full physiological function of NifU. These results provide the basis for a model where iron bound at the rubredoxin-like sites within NifU-1 (one iron per monomer) is proposed to be destined for [Fe-S] cluster formation. It was possible to find in vitro evidence supporting this idea. First, it was demonstrated that NifU and NifS are able to form a transient complex. Second, in the presence of NifS as well as L-cysteine and a reducing agent, the Fe(III) contained at the rubredoxin-like sites within the NifU-1 or NifU homodimer can rearrange to form a transient [2Fe-2S] cluster between the two subunits. Finally, a mutant form of NifU-1 was isolated that appears to be trapped in the [2Fe-2S] cluster-containing form, and this [2Fe-2S] cluster (the transient [2Fe-2S] cluster) can be released from the polypeptide matrix upon reduction with dithionite. Previous work has shown that the permanent [2Fe-2S] clusters of as-isolated NifU are in the oxidized form but can be reduced chemically. The transient [2Fe-2S] cluster formed between rubredoxin-like sites, in contrast, is reductively labile. If the transient cluster serves as an intermediate [Fe-S] cluster to be destined for [Fe-S] cluster assembly, I propose that the permanent [2Fe-2S] clusters could have redox roles participating in either one or all of the following events. The permanent [2Fe-2S] clusters could have a redox function in the acquisition of iron for initial binding at the mononuclear sites. They could also provide reducing equivalents for releasing the transient [2Fe-2S] cluster. In addition, upon releasing the transient [2Fe-2S] cluster, the permanent [2Fe-2S] clusters could provide the appropriate oxidation state of the irons to be destined to nitrogenase metallocluster core formation. Finally, because proteins homologous to NifU and NifS are widely distributed in nature, it is suggested that the mechanism for NifU and NifS in the formation of nitrogenase-specific [Fe-S] clusters could represent a general mechanism for [Fe-S] cluster synthesis in other systems.
Biosynthesis of the Nitrogenase FeMo-cofactor from Azotobacter vinelandii: Involvement of the NifEN complex, NifX and the Fe protein
Goodwin, Paul Joshua (Virginia Tech, 1999-10-25)
The iron-molybdenum cofactor (FeMo-cofactor) of nitrogenase is the subject of one the most intensive biochemical/genetic detective cases of modern science. At the active site of nitrogenase, the FeMo-cofactor not only represents the heart of biological nitrogen fixation, but its synthesis also serves as a model for complex metallocluster biosynthesis. Research in the Dean Lab is focused on furthering the understanding of Fe-S cluster biosynthesis in the nitrogenase enzyme system. Throughout the years, scientists from a broad range of disciplines have focused their intellectual might on deciphering not only the chemistry of the FeMo-cofactor, but also the biosynthesis of this unique metallocluster. Recent advances in the study of FeMo-cofactor biosynthesis have produced considerable insight regarding the complex series of biological reactions necessary for the synthesis of this metallocluster. The work contained within this dissertation represents my efforts to further the understanding of FeMo-cofactor biosynthesis. The concept of a molecular scaffold in FeMo-cofactor biosynthesis is generally accepted in the field of nitrogenase. Previous work has implicated the products of nifE and nifN as providing the assembly site for FeMo-cofactor synthesis. Researchers were able to purify this molecular scaffold, commonly referred to as the NifEN complex, however, detailed characterization was precluded by the inability to obtain sufficient quantities of NifEN. In an effort to fully characterize the NifEN complex, we initiated a gene fusion approach for the high level production NifEN. In addition to gene fusion, a poly-histidine tag was incorporated into NifEN, allowing purification through the application of immobilized metal-affinity chromatography (IMAC). NifEN obtained in this way was characterized using a variety of biophysical techniques and found to contain two [4Fe-4S] clusters in each NifEN tetramer. These clusters were also shown to be completely ligated by cysteine residues. With the information obtained from this study, it is concluded that the [4Fe-4S] clusters of the NifEN complex are likely to play either a structural or a redox role rather than being transferred and becoming incorporated into the FeMo-cofactor. In addition to the biophysical characterization of the NifEN complex, a separate study was started to characterize the apo-MoFe protein. In this study we used IMAC to purify a poly-histidine-tagged apo-MoFe protein produced by a nifB-deletion mutant of A. vinelandii. Using the poly-histidine fusion approach, apo-MoFe protein was obtained in sufficient quantities for detailed catalytic, kinetic and spectroscopic analyses. This multidisciplinary approach confirmed that apo-MoFe protein contained intact P clusters and P cluster environments, as well as the ability to interact with the Fe protein. It was also shown for the first time that this tetrameric form of purified apo-MoFe protein could be activated by the addition of preformed FeMo-cofactor. The NifEN complex was further characterized to investigate the presence of bound FeMo-cofactor intermediates. NifEN purified by IMAC is produced in the absence of the nitrogenase structural genes (nifHDK). In this genetic background, it is believed that the FeMo-cofactor biosynthetic machinery will become obstructed with unprocessed FeMo-cofactor intermediates, such as the Fe-S precursors of FeMo-cofactor, NifB-cofactor. Previous work indicated that NifEN can exist in either a charged or discharged form, based on the presence or absence of the FeMo-cofactor precursor, NifB-cofactor. EPR and VTMCD spectroscopies showed the presence of a new paramagnetic signal associated with NifEN that is believed to be in the charged or precursor bound state. This represents the first spectroscopic evidence for a precursor to the FeMo-cofactor. Furthermore, an interaction of NifEN and NifX was examined by size exclusion chromatography. From this study, NifX exhibited the capacity to bind a chromophore, presumably an FeMo-cofactor precursor, from the NifEN complex. NifX was also capable of binding to isolated FeMo-cofactor and the FeMo-cofactor precursor, NifB-cofactor. Finally, preliminary investigations involving interaction between the Fe protein and NifEN were initiated. Recent findings indicate that NifEN and the Fe protein have the capacity to interact specifically with one another. The interaction of NifEN and Fe protein appears to be dependent on the association of FeMo-cofactor precursor with NifEN. The NifEN complex also has the capacity to accept electrons from the Fe protein in a MgATP dependent manner. The ability of NifEN to accept electrons from the Fe protein may be involved in the role of Fe protein in FeMo-cofactor biosynthesis.
Blood characteristics as predictors of reproductive success in quail species exposed to DDT
Sullivan, Joseph P. (Virginia Tech, 1991)
Present sampling techniques are not capable of assessing both contamination with an organochlorine chemical and reproductive success without the need for removing individuals from that population. Experiments were performed to evaluate vitellogenin, vitamin A, and vitamin E as biomarkers of contamination with DDT, an organochlorine pesticide, and reproductive success in Japanese quail (Coturnix coturnix japonica) or northern bobwhites (Colinus virginianus). The utility of vitellogenin as a biomarker in northern bobwhites was investigated. Female northern bobwhites were dosed with 0, 1, 10, or 100 μg DDT/g body weight via corn oil intubation. The females were induced to lay eggs by providing the proper daylength, and number of eggs laid was monitored. No differences were found for number of eggs laid, egg morphology, or plasma concentration of vitellogenin among dose groups. Dietary supplementation and corn oil intubation were evaluated as alternative dosing techniques because handling involved with intubation may have caused decreased egg production in all treatment groups in the first experiment. Nonlaying female bobwhites were dosed with 0 μg DDT, 25 μg DDT/g food, or 25 μg/g body weight (intubation). Bobwhites receiving DDT via intubation accumulated more DDT in brains and livers than did bobwhites receiving DDT via their diet. The two techniques were found not to be equivalent. Vitamins A and E were investigated as biomarkers of DDT contamination and reproductive success in Japanese quail. Female Japanese quail were given 0, 1, 10, or 25 μg dietary DDT. Significant differences were found among dose groups for reproductive success (number of eggs showing embryonic development), and for plasma concentrations of vitamin A. Concentrations of vitamin E were not measurable. Correlation and regression analyses failed to show a relationship between reproduction and vitamin A concentrations. Vitamins A and E also were investigated as biomarkers in northern bobwhites. Female bobwhites were given 0, 1, 10, or 25 ppm dietary DDT. No significant differences were found among dose groups for reproductive success or for concentrations of either vitamin A or vitamin E. Correlation and regression analyses again failed to show any relationship between reproduction and plasma concentrations of vitamins A or E. During each experiment, concentrations of DDT and its metabolites were measured. DDE/DDT ratios in livers, a means of estimating liver enzyme induction, were calculated. The DDE/DDT ratios in livers of Japanese quail and northern bobwhites were found to be markedly different. More work needs to be done to better evaluate the relationship between differences in enzyme induction and reproductive success among different species.
Boron-Mediated Semireduction of Alkynoic Acid Derivatives
Grams, Robert Justin (Virginia Tech, 2021-04-30)
Organoboron compounds are commonly used precursors for a variety of reactions in organic synthesis as is exemplified by the Suzuki-Miyaura cross-coupling, which is ubiquitous in industry and academia. Additionally, the Chan-Evans-Lam cross-coupling, lithiation-homologation, allylboration, and many other reactions rely on boron to achieve otherwise difficult chemical transformations. Thus, developing novel methods towards the regio- and/or stereoselective installation of boron into organic molecules remain important for designing new drugs. Boron reagents are also useful in chemical transformations that do not ultimately install a boron moiety on the organic molecule. We have developed several methods that achieve the trans-selective borylation or semireduction of internal alkynes, a process dominated by transition metals and often results in incomplete (E)-stereoselectivity. This dissertation describes three novel uses of a diboron reagent or pinacolborane that reduce propiolic acid derivates selectively to (E)-alkenes and one method that installs pinacolatoboron yielding exclusively (E)-β-borylacrylamides. We investigated the trans-selective hydroboration of primary and secondary propiolamides as reports in the literature accomplish trans-hydroboration via transition metal catalysis, which are limited in substrate scope. We discovered that addition of n-butyllithium to propiolamide and pinacolborane exclusively yields (E)-β-borylacrylamides in good to excellent yield. During the reaction, deprotonation of the amide with a strong base generates an alkoxide that coordinates to pinacolborane and forms a boronate complex. Upon warming to room temperature, a hydride transfer is directed to the α-carbon generating a β-carbanion that subsequently captures boron. Workup protonates the amide, furnishing the (E)-β-borylacrylamide product. As a follow-up from the trans-hydroboration of propiolamides described above, we developed a complementary semireduction of primary and secondary propiolamides. In this reaction, addition of catalytic amounts of potassium tert-butoxide to propiolamides generates an alkoxide that coordinates to pinacolborane and rapidly produces (E)-cinnamamides in 35 – 96% yield and >99:1 E:Z stereoselectivity. This reaction effectively reduces an internal alkyne to afford a product with trans geometry. A deuterium labeling study provided mechanistic insight for the transformation suggesting that the β-proton in the products is derived from the amide nitrogen of the propiolamide. Further, we demonstrated the utility of this reaction by augmenting the total synthesis of FK866, a potent nicotinamide mononucleotide adenyltransferase (NMNAT) inhibitor, and isolated the cinnamamide product in good yield with >99:1 E:Z stereoselectivity. Using a similar strategy, we investigated the ability of bis(pinacolato)diboron and base to mediate the α-borylation of propiolic acids. We observed the formation of a semireduced product, i.e., cinnamic acid. In the presence of a crown ether and cesium carbonate, propiolic acid is deprotonated and activates bis(pinacolato)diboron. Subsequent α-borylation and β-carbon protonation affords a highly unstable α-boronic acid derivative that undergoes rapid protodeborylation yielding predominantly (E)-cinnamic acids. The dual role of the carboxylate in activating the diboron reagent and directing α-borylation was unprecedented and is the first transition metal-free method to reduce propiolic acids to (E)-cinnamic acids. In contrast with boron activation from in situ generated alkoxide, an alternative approach is using phosphine catalysts—a major interest in the development of transition metal-free methodology. As such, we investigated the ability of phosphines to mediate the borylation of primary and secondary propiolamides. Surprisingly, we observed an efficient semireduction of primary and secondary propiolamides to their respective (E)-cinnamamides in the presence of catalytic n-tributylphosphine and stoichiometric pinacolborane. We surveyed the scope and reactivity of substrates bearing N-substitutions, electron-rich or deficient aryls, and aliphatics using optimized reaction conditions and produced a library of (E)-cinnamamides in 31 – 98% yield with >99:1 E:Z stereoselectivity. Deuterium labeling studies suggest that hydrogens on the α- and β-carbon come from pinacolborane and the amide hydrogen, respectively. We also trapped and characterized a key intermediate using tris(pentafluorophenyl)borane that supports a mechanism wherein the phosphine catalyst activates the propiolamide by conjugate addition.
Carbon Nanotube Mechanics: Continuum Model Development from Molecular Mechanics Virtual Experiments
Sears, Aaron Thomas (Virginia Tech, 2006-11-07)
Carbon Nanotubes (CNTs) hold great promise as an important engineering material for future applications. To fully exploit CNTs to their full potential, it is important to characterize their material response and ascertain their material properties. We have used molecular mechanics (MM) simulations to conduct virtual experiments on single-wall and multi-wall carbon nanotubes (SWNTs and MWNTs respectively) similar to those performed in the mechanics of materials laboratory on a continuum structure. The output (energy and deformation rather than the load and deflection) is used to understand the material response and formulate macroscopic constitutive relations. From results of MM simulations of axial and torsional deformations on SWNTs, Young's modulus, the shear modulus and the wall thickness of an equivalent continuum tube made of a linear elastic isotropic material were found. These values were used to compare the response of the continuum tube, modeled as an Euler-Bernoulli beam, in bending and buckling with those obtained from the MM simulations. MM simulations have been carried out to find energetically favorable double-walled carbon nanotube (DWNT) configurations, and analyze their responses to extensional, torsional, radial expansion/contraction, bending, and buckling deformations. Loads were applied either to one wall or simultaneously to both walls of an open-ended DWNT. These results were compared against SWNT results. It was found that for simple tension and torsional deformations, results for a DWNT can be derived from those for its constituent SWNTs within 3% error. Radial deformations of a SWNT were achieved by considering a DWNT with the SWNT as one of its walls and moving radially through the same distance all atoms of the other wall of the DWNT thereby causing a pseudo-pressure through changes in the cumulative van der Waals forces which deform the desired wall. Results of radial expansion/contraction of a SWNT were used to deduce an expression for the van der Waals forces, and find through-the-thickness elastic moduli (Young's modulus in the radial direction, Er, and Poisson's ratio ?r?) of the SWNT. We have found four out of the five elastic constants of a SWNT taken to be transversely isotropic about a radial line. MWNTs were studied using the same testing procedures as those used SWNTs. Based on the results from those simulations a continuum model is proposed for a MWNT whose response to mechanical deformations is the same as that of the MWNT. The continuum structure is comprised of concentric cylindrical tubes interconnected by truss elements. Young's modulus, Poisson's ratio, the thickness of each concentric tube, and the stiffness of the truss elements are given. The proposed continuum model is validated by studying its bending and buckling deformations and comparing these results to those from MM simulations. The major contributions to the field on nanotubes and the scientific literature is a simple and robust continuum model for nanotubes. This model can be used to study both SWNTs and MWNTs in either global or local responses by applying different analytic techniques. This model was developed using a consistent engineering methodology that mimicked traditional engineering testing, assumptions and constraints.
Characterization of AgaR and YihW, Members of the DeoR Family of Transcriptional Regulators, and GlpE, a Rhodanese Belonging to the GlpR Regulon, Also a Member of the DeoR Family
Ray, William Keith (Virginia Tech, 1999-08-02)
AgaR, a protein in Escherichia coli thought to control the metabolism of N-acetylgalactosamine, is a member of the DeoR family of transcriptional regulators. Three transcriptional promoters within a cluster of genes containing the gene for AgaR were identified, specific for agaR, agaZ and agaS, and the transcription start sites mapped. Transcription from these promoters was specifically induced by N-acetylgalactosamine or galactosamine, though K-12 strains lacked the ability to utilize these as sole sources of carbon. The activity of these promoters was constitutively elevated in a strain in which agaR had been disrupted confirming that the promoters are subject to negative regulation by AgaR. AgaR-His6, purified using immobilized metal affinity chromatography, was used for DNase I footprint analysis of the promoter regions. Four operator sites bound by AgaR were identified. A putative consensus binding sequence for AgaR was proposed based on these four sites. In vivo and in vitro analysis of the agaZ promoter indicated that this promoter was activated by the cAMP-cAMP receptor protein (CRP). Expression from the aga promoters was less sensitive to catabolite repression in revertants capable of N-acetylgalactosamine utilization, suggesting that these revertants have mutation(s) that result in an elevated level of inducer for AgaR. A cluster of genes at minute 87.7 of the E. coli genome contains a gene that encodes another member of the DeoR family of transcriptional regulators. This protein, YihW, is more similar to GlpR, transcriptional regulator of sn-glycerol 3-phosphate metabolism in E. coli, than other members of the DeoR family. Despite the high degree of similarity, YihW lacked the ability to repress P_glpK, a promoter known to be controlled by GlpR. A variant of YihW containing substitutions in the putative recognition helix to more closely match the recognition helix of GlpR was also unable to repress P_glpK. Transcriptional promoters identified in this cluster of genes were negatively regulated by YihW. Regulation of genes involved in the metabolism of sn-glycerol 3-phosphate in E. coli by GlpR has been well characterized. However, the function of a protein (GlpE) encoded by a gene cotranscribed with that for GlpR was unknown prior to this work. GlpE was identified as a single-domain, 12-kDa rhodanese (thiosulfate:cyanide sulfurtransferase). The enzyme was purified to near homogeneity and characterized. As shown for other characterized rhodaneses, kinetic analysis revealed that catalysis occurs via an enzyme-sulfur intermediate utilizing a double-displacement mechanism requiring an active-site cysteine. K_m (SSO₃²⁻) and K_m (CN⁻) were determined to be 78 mM and 17 mM, respectively. The native molecular mass of GlpE was 22.5 kDa indicating that GlpE functions as a dimer. GlpE exhibited a kcat of 230 s-1. Thioredoxin, a small multifunctional dithiol protein, served as sulfur-acceptor substrate for GlpE with an apparent K_m of 34 mM when thiosulfate was near its K_m, suggesting thioredoxin may be a physiological substrate.
The characterization of Clostridium beijerinckii NRRL B592 cells transformed with plasmids containing the butanol-production genes under the control of constitutive promoters
Tollin, Craig Jeffrey (Virginia Tech, 2012-09-18)
Clostridium beijerinckii is a spore-forming, obligate anaerobe that is capable of producing butanol, acetone and isopropanol. These industrial chemicals are traditionally known as solvents. The regulation of solventogenic fermentation is linked to the onset of sporulation, so that by the time the organism begins to produce solvents, it is also entering into spore formation and metabolic slowdown. The goal of this research project was to study the effect of placing the solvent-production genes from C. beijerinckii under the control of constitutive promoters from other genes, in an attempt to allow an earlier start of butanol production during the growth phase than is the case with the wild-type cells. The aldehyde dehydrogenase from C. beijerinckii NRRL B593 (ald) and alcohol dehydrogenase from C. beijerinckii NRRL B592 (adhA) were placed under the control of the promoter from the acid-producing operon (the BCS operon) in one vector, and under the control of the promoter from the ferredoxin gene in another. In both cases, aldehyde dehydrogenase activity was produced earlier in the growth phase in transformed cells, but alcohol dehydrogenase activity was not. The adhA gene from C. beijerinckii NRRL B592 was paired with the adhB gene from the same organism in a third vector, both under the control of the promoter from the BCS operon. In cells transformed with this vector, alcohol dehydrogenase activity was observed earlier in the growth phase than it was in wild-type NRRL B592 cells.

Browsing by Author "Bevan, David R."

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