Master of Science / Department of Biochemistry / Bruce D. Schultz / John M. Tomich / Peptides based on the second transmembrane segment of the glycine receptor (M2GlyR) were made to provide a potential therapeutic treatment for cystic fibrosis (CF) and a latent absorption enhancer for drug delivery. For similarity of presentation, unique synthetic peptide sequences have been given alpha-numeric designations. Results are presented from studies focusing on four peptides. In the first study, the contributions of synthetic peptides p1171, p1172 and p1173 to net transepithelial ion transport were measured as a first step toward the goal of testing whether pore length or electrostatics of pore lining residues will affect anion transport. Peptide p1130 exhibits many attributes that make it an ideal synthetic peptide for CF treatment, but has low permselectivity for anions. Therefore, it is used as a platform for modification. Peptide p1171 is doubly substituted with diaminopropionic acid at positions T13 and T17. Peptide p1172 and p1173 are separately one and two helical turn(s) inserted into the p1130 backbone. Apical exposure of MDCK monolayers to these peptides caused a rapid increase in short circuit current (Isc), an indicator of net ion transport. The increase in Isc caused by p1172 or p1173 was accompanied by increase in transepithelial electrical conductance (gte). The electrophysiological results suggested that these modified peptides can assemble in the apical membrane of epithelial cells to form functional ion-conducting pores. Peptide NC-1059, which provides for ion transport across epithelial cells derived from many sources, was studied further to assess cellular changes that account for increased gte. NC-1059 increased Isc, gte and enhanced permeation of dextrans in a concentration dependent manner. Results from previous and current studies show that NC-1059 modulated the epithelial paracellular pathway by altering the distribution and abundance of junctional proteins. Immunoblotting and immunolabeling with confocal microscopy showed that NC-1059 induces reorganization of actin and causes a reduction in F-actin abundance in epithelial cells. The distributions were changed and cellular abundances were reduced of tight junction proteins occludin and ZO-1 and adherens junction proteins E-cadherin and β-catenin by NC-1059. These effects were largely reversed in 24 hr and fully recovered in 48 hr. Therefore, NC-1059 has the therapeutic potential to increase the efficiency of drug delivery across barrier membranes.

Master of Science / Department of Chemistry / Duy H. Hua / (+)-myriceric acid A is known as a non-peptide ETA receptor antagonist. It is isolated from the natural plant Myrica cerfera with 0.01% yield which is very low. The total synthesis of (+)-myriceric acid A is being pursued in Hua’s lab. (+)-myriceric acid A specifically blocks the vasoconstriction caused by endothelin-1 (ET-1). Because some derivatives of (+)-myriceric acid A were shown to have ET-1 receptor antagonistic effect, the tetracyclic terpenoid intermediates toward the total synthesis of (+)-myriceric acid A are postulated to have the similar antagonistic activities. The objective of this project is to study the release of vasoconstriction of these synthetic intermediates and compare their antagonistic potency. The ET-1 receptor antagonistic bioactivity of six (+)-myriceric acid A intermediates as well as (+)-myriceric acid A were evaluated by the in vitro spiral modiolar artery (SMA) bioassay. The synthetic intermediates which have not been reported in the literature were previously synthesized in Hua’s laboratory by Dr. Angelo Aguilar and Dr. Aibin Shi. Their synthesis was described in Dr. Aguilar’s PhD thesis. All the antagonistic effect evaluations were based on the SMA’s diameter changes. SMA’s diameter changes were induced by the superfusion of different extracellular solutions. The dose-response curves and straight lines were plotted to compare the antagonistic potency of these compounds. Based on the EC50 value of (+)-myriceric acid A intermediates (0.090 µM ~ 0.582 µM for the curves and 0.095 µM ~ 0.385 µM for the straight lines), all of the compounds have ET-1 receptor antagonistic activity, therefore the synthesis and screening of (+)-myriceric acid A intermediates is probably a promising route to develop new non-peptide ETA receptor antagonists.

Master of Science / Department of Biochemistry / Dolores J. Takemoto / Spinocerebellar ataxia type 14 (SCA14) is a rare, autosomal dominant neurodegenerative disease caused by mutations in the gene encoding for protein kinase Cγ (PKCγ). These mutations affect the translocation and activation of the protein and are particularly damaging to the Purkinje cells of the cerebellum. This translocation and activation leads to the down regulation of gap junction activity by direct phosphorylation on the C-terminal tail of connexin proteins. This process is necessary in terminating the propagation of apoptotic signaling and is disrupted by SCA14-type mutations. Gap junctions allow the passive diffusion of small molecules from one adjoining cell to another. Gap junctions function as electrical synapses in neuronal tissue and are formed from connexin proteins. The connexin family of proteins contains approximately 20 members, each of which is expressed in a tissue dependent manner. One of the dominant connexin proteins expressed in Purkinje cells is connexin 57 (Cx57). Here, I have tested if Cx57 is regulated by PKCγ. This thesis shows that activation of PKC and PKCγ caused internalization of Cx57 gap junction plaques in HT-22 cell culture. PKC and PKCγ activation led to the phosphorylation of Cx57 primarily on serine residues. Furthermore, the expression of SCA14-type PKCγ led to increased sensitivity to oxidative stress, resulting decreased cell viability.

Doctor of Philosophy / Department of Chemistry / Paul E. Smith / The force fields used in computer simulations play an important role in describing a particular system. In order to estimate the accuracy of a force field, physical or thermodynamic properties are usually compared with simulation results. Recently, we have been developing a force field which is called the Kirkwood-Buff Force Field (KBFF). This force field is established by transforming experimental data into Kirkwood-Buff (KB) integrals and then attempting to reproduce those KBIs with molecular dynamic (MD) simulations. Here we investigate a variety of intermolecular interactions in aqueous solutions through KB theory and molecular simulations. First, we describe a force field for the simulation of alkali halide aqueous solutions. These models are developed specifically to reproduce the experimentally determined Kirkwood-Buff integrals and solution activities as a function of molality. Additionally, other experimentally known properties including ion diffusion constants, relative permittivities, the densities and heats of mixing are reproduced by these models. Second, In an effort to understand the interactions which occur between amino acids in solution we have developed new force fields for simple amino acids and their analogs including glycine, betaine, β-alanine, dl-alanine, NH4Cl, NH4Br, N(CH3)4Cl, N(CH3)4Br, CH3NH3Cl, and CH3COONa. The new force fields reproduce the experimental Kirkwood-Buff integrals which describe the relative distribution of all the species in a solution mixture. Furthermore, it is shown that these simple amino acids can be understood in terms of the interactions of their functional groups and that, to a very good approximation, the transferability and additivity usually assumed in the development of biomolecular force fields appear to hold true. Third, an analysis of the effect of a cosolvent on the association of a solute in solution is presented by using the Kirkwood-Buff theory of solutions. The derived expressions provide a foundation for the investigation of cosolvent effects on molecular and biomolecular equilibria, including protein association, aggregation, and cellular crowding. Finally, in an effort to understand peptide aggregation at the atomic level we have performed simulations of polyglycine ((gly)n) using our recently developed force fields. Experimentally, the association of glycine polypeptides increases with n. Our force fields reproduce this behavior, and we investigated the reasons behind this trend. In addition to studying closed ensembles, we also simulate these systems in a semi-open ensemble that was designed to mimic cellular environments typically open to water, using a simple direct approach. The differences between the two ensembles are investigated and compared with our recent theoretical descriptions of aggregating systems using Kirkwood-Buff theory.

Doctor of Philosophy / Department of Biochemistry / Michal Zolkiewski / ClpB is a bacterial heat-shock protein that disaggregates and reactivates strongly aggregated proteins in cooperation with the DnaK chaperone system. ClpB contains two ATP-binding AAA+ modules, a linker coiled-coil domain, and a highly mobile N-terminal domain. It forms ring-shaped hexamers in a nucleotide-dependent manner. The unique aggregation reversing chaperone activity of ClpB involves ATP-dependent translocation of substrates through the central channel in the ClpB ring. The initial events of aggregate recognition and the events preceding the translocation step are poorly understood. In addition to the full-length ClpB95, a truncated isoform ClpB80, that is missing the whole N-terminal domain, is also produced in vivo. Various aspects of the structure and function of ClpB were addressed in this work. The thermodynamic stability of ClpB in its monomeric and oligomeric forms, as well as the nucleotide-induced conformational changes in ClpB were investigated by fluorescence spectroscopy. Equilibrium urea-induced unfolding showed that two structural domains-the small domain of the C-terminal AAA+ module and the coiled-coil domain-were destabilized in the oligomeric form of ClpB, which indicates that only those domains change their conformation or interactions during formation of the ClpB rings. Several locations of Trp-fluorescence probes were also found to respond to nucleotide binding. The biological role of the two naturally-occurring ClpB isoforms was also investigated. We discovered that ClpB achieves optimum chaperone activity by synergistic cooperation of the two isoforms that form hetero-oligomers. We found that ClpB95/ClpB80 hetero-oligomers form preferentially at low protein concentration with higher affinity than homo-oligomers of ClpB95. Moreover, hetero-oligomers bind to aggregated substrates with a similar efficiency as homo-oligomers of ClpB95, do not show enhanced ATPase activity over that of the homo-oligomers, but display a strongly stimulated chaperone activity during the reactivation of aggregated proteins. We propose that extraction of single polypeptides from aggregates and their delivery to the ClpB channel for translocation is the rate-limiting step in aggregate reactivation and that step is supported by the mobility of the N-terminal domain of ClpB. We conclude that the enhancement of the chaperone activity of the hetero-oligomers is linked to an enhancement of mobility of the N-terminal domains.

Doctor of Philosophy / Department of Chemistry / Stefan H. Bossmann / Porin A from Mycobacterial smegmatis (MspA) is an octameric trans-membrane channel protein and is one of the most stable porins known to date. MspA has been successfully isolated and purified to obtain liquid extracts and crystals using a modified extraction procedure. A full analytical assessment has been carried out to authenticate its’ structure, including gel electrophoresis, spectroscopy (fluorescence, UV, FTIR, NMR), HPLC, Bradford protein assay, dynamic light scattering and X-ray crystallography. Nanoscopic vesicle formation of MspA molecules in aqueous media has been thoughroughly investigated. Temperature dependent dynamic light scattering experiments reveal that size of such vesicles is dependent on temperature but is independent of ionic strength of the medium. Zeta potential measurements reveal a steady build up of positive charge on the vesicle surface with increasing temperature. For the first time, wild type (WT) MspA has been utilized as a channel forming agent. This phenomenon has future potential in DNA sequencing and the development of antimycobacterial drugs. Channel activity of WT MspA and mutant A96C MspA has been investigated and has shown to form stable channels across DPhPC lipid bilayers. Blocking of the channel current via external molecules (i.e. channel blocking) is an extremely important process, which helps to evaluate the biosensor ability of the pore. In this regard, two Ruthenium based compounds, Ru(QP-C2)38+ (i.e. RuC2) and Ru(bpy)32+have been successfully employed as channel blocking agents. Both compounds show evidence for channel blocking of WT MspA. However, these results are not reproducible. Three dimensional aggregation behavior of RuC2-MspA vesicles have been thoughroughly investigated. It is evident that addition of RuC2 significantly increases vesicle size and polydispersity of MspA aggregates in solution. The results provide explanations onto the lack of channel blocking ability of MspA by RuC2. Development of a ‘greener’ dye sensitized solar cell with the use of MspA as an electron carrier is investigated for the first time. A series of Ru(II)-phenanthroline-based dyes have been synthesized as non-toxic dyes in this regard. Chemical binding between the dyes and MspA has been achieved successfully. Two types of solar cell prototypes, i.e. TiO2-based (Grätzel type) and FTO-based have been developed and tested. Significant current generation and conversion efficiencies have been achieved for both cell types. This marks the first development of a protein-based photovoltaic device, which has the potential to be developed as a new class of “hybrid soft solar cells”.

Doctor of Philosophy / Department of Biochemistry / Ramaswamy Krishnamoorthi / Insect [beta]-1,3-glucan recognition protein ([beta]GRP), a soluble receptor in the hemolymph, binds to the surfaces of bacteria and fungi and activates serine protease cascades that promote destruction of pathogens by means of melanization or expression of antimicrobial peptides. Delineation of mechanistic details of these processes may help develop strategies to control insect-borne diseases and economic losses. Multi-dimensional nuclear magnetic resonance (NMR) techniques were employed to solve the solution structure of the Indian meal moth (Plodia interpunctella) [beta]GRP N-terminal domain (N-[beta]GRP), which is sufficient to activate the prophenoloxidase (proPO) pathway resulting in melanin formation. This is the first determined three-dimensional structure of N-[beta]GRP, which adopts an immunoglobulin fold. Addition of laminarin, a [beta]-1,3 and [beta]-1,6 link-containing glucose polysaccharide (∼6 kDa) that activates the proPO pathway, to N-[beta]GRP results in the loss of NMR cross-peaks from the backbone [subscript]1[subscript]5N-[subscript]1H groups of the protein, suggesting the formation of a large complex. Analytical ultracentrifugation (AUC) studies of formation of the N-[beta]GRP:laminarin complex show that ligand binding induces self-association of the protein-carbohydrate complex into a macro structure, likely containing six protein and three laminarin molecules (∼102 kDa). The macro complex is quite stable, as it does not undergo dissociation upon dilution to submicromolar concentrations. The structural model thus derived from this study for the N-[beta]GRP:laminarin complex in solution differs from the one in which a single N-[beta]GRP molecule has been proposed to bind to a triple-helical form of laminarin on the basis of a X-ray crystal structure of the N-[beta]GRP:laminarihexaose complex. AUC studies and phenoloxidase activation measurements made with designed mutants of N-[beta]GRP indicate that electrostatic interactions between the ligand-bound protein molecules contribute to the stability of the N-[beta]GRP:laminarin complex and that a decreased stability results in a reduction of proPO activation. These novel findings suggest that ligand-induced self-association of the [beta]GRP:[beta]-1,3-glucan complex may form a platform on a microbial surface for recruitment of downstream proteases, as a means of amplification of the pathogen recognition signal. In the case of the homolog of GNBPA2 from Anopheles gambiae, the malaria-causing Plasmodium carrier, multiligand specificity was characterized, suggesting a functional diversity of the immunoglobulin domain structure.

Doctor of Philosophy / Department of Industrial and Manufacturing Systems Engineering / Zhijian Pei / Donghai Wang / The U.S. economy has been depending on petroleum-based liquid transportation fuels (such as gasoline, diesel, and jet fuels). Currently, about 50% of petroleum used in the U.S. is imported. Petroleum is a finite and non-renewable energy source and its use emits greenhouse gases. Therefore, it is extremely important to develop domestic sustainable alternatives for petroleum-based liquid transportation fuels. Ethanol produced from cellulosic biomass can be such an alternative. However, several technical barriers have hindered large-scale, cost-effective manufacturing of cellulosic ethanol. One such barrier is related to the low density of cellulosic feedstocks, causing high cost in their transportation and storage. Another barrier is low efficiency in conversion of cellulose to fermentable sugar (pretreatment and enzymatic hydrolysis are two major conversion processes), causing high cost in pretreatment and enzymatic hydrolysis of cellulosic biomass. Ultrasonic vibration-assisted (UV-A) pelleting increases both density and sugar yield of cellulosic feedstocks. Incorporating UV-A pelleting into cellulosic ethanol manufacturing may help realize cost-effective manufacturing of cellulosic ethanol. This PhD dissertation consists of 13 chapters. An introduction is given in Chapter 1. Chapter 2 presents a literature review on related topics. Experimental studies regarding effects of input parameters (such as particle size, pressure, and ultrasonic power) on output parameters (density, durability, stability, and sugar yield) are presented in Chapters 3–4. In Chapters 5–6, comparisons are made between UV-A pelleting and ring-die pelleting (a traditional pelleting method) in terms of pellet properties (density and durability), power consumption, and sugar yield under different conditions. Next, effects of input parameters (such as biomass type, particle size, moisture content, pelleting pressure, and ultrasonic power) on power consumption are studied in Chapters 7–9. Chapter 10 presents an investigation on biomass temperature in UV-A pelleting. Chapter 11 presents an investigation on effects of UV-A pelleting on sugar yield and chemical composition of cellulosic biomass. Chapter 12 presents an investigation on influence of UV-A pelleting on biomass characteristics (such as crystallinity index, thermal properties, and morphological structure). Finally, conclusions are presented in Chapter 13.

Master of Science / Division of Biology / Kristin Michel / To date malaria is the most important tropical disease, which is caused by Plasmodium sp. and vectored by anopheline mosquitoes. The mosquito’s immune system is one of the limiting factors of malaria transmission. Immune reactions, such as the prophenoloxidase (PPO) pathway result in the melanization of pathogens, and are effective at limiting parasite numbers. Novel strategies for malaria control aim to exploit the immune system to interrupt parasite transmission by boosting the immune responses in the mosquito vector. Serpins play a crucial role in regulating protease cascades involved in immunity of arthropods. In Anopheles gambiae, the major malaria vector in Sub-Saharan Africa, 18 SRPN genes encoding 23 distinct proteins have been identified. So far, two are identified as active inhibitors, and both affect parasite survival. This research aims to identify additional inhibitory serpins in An. gambiae and elucidate their potential function. Identification of such serpins will enhance our understanding of the immune system of this important vector species and may identify immunoregulators to be used in malaria control. SRPN7, 9, and 18 were tested for their ability to inhibit commercial proteases in vitro. Recombinant SRPN18 had no inhibitory activity, while SRPN7 and 9 inhibited several serine proteases. SRPN7, 9 and 18 were tested against two recombinant An. gambiae clip serine proteases (CLIPBs) that are required for activation of phenoloxidase and thus regulate melanization. Only SRPN9 strongly inhibited CLIPB9 in vitro, suggesting that this serpin is a potential negative regulator of melanization. This hypothesis is further supported by the finding that SRPN9 can inhibit PO activity in insect hemolymph, ex vivo. Taken together, this research identifies SRPN18 as the first non-inhibitory serpin described in mosquitoes. Additionally, this study describes the larval-specific SRPN7 as a functional inhibitor. Future studies on these proteins will elucidate their precise physiological functions. Finally, this thesis provides strong evidence that SRPN9 is a negative regulator of melanization in An. gambiae and may therefore affect pathogen survival within this important vector species.

Doctor of Philosophy / Department of Biological & Agricultural Engineering / Zhijian Pei / Donghai Wang / Renewable fuels derived from lignocellulosic biomass could reduce our dependence on fossil fuel resources and reduce greenhouse gas emissions. Big bluestem is an ecological-dominant warm-season (C4) perennial native grass that comprises as much as 80% of the plant biomass in prairies in the Midwestern grasslands of North America. Its high cellulosic content and low agricultural input recently have made big bluestem a promising feedstock for ethanol production. The overall goals of this study are to evaluate the potential of big bluestem in terms of ethanol production comparing with other native grasses by diluted sulfuric acid pretreatment and simultaneous saccharification and fermentation and to understand the effects of ecotype and planting location on the chemical and elemental compositions and thermal properties as well as fermentable sugar yield of big bluestem along the Great Plains precipitation gradient. A total conversion efficiency of 79.2% and an ethanol concentration of 9.4 g/L were achieved after 72 h fermentation. About 0.262 kg (~0.332 Liters) ethanol could be produced from one kilogram dry mass of big bluestem under the present condition. Planting location had significant effects on chemical and elemental as well as specific heat, thermogravimetric parameters, high heating value and glucan mass yield. Ecotype had significant effects on glucan, xylan, lignin, and ash contents, and C, O, and H elemental fractions as well as specific heat, high heating value and glucan mass yield, whereas planting location significantly affected all measured variables. The ecotype-location interaction had significant effects on glucan, lignin, hydrogen contents and specific heat. Up to 97%, 88% and 80% of the variation in compositions can be explained by annual precipitation, growing degree days and potential evapotranspiration in 2010 respectively. Among all environmental factors, potential evapotranspiration had the most significant effect on thermal properties. Planting location had a stronger influence than ecotype and interaction between location and ecotype. Precipitation in 2010 possibly played a more significant role in divergence of glucan mass yield of the big bluestem.