Master of Science / Biochemistry / John Tomich / One of the important keys to characterize the biological function of a protein is the study of post-translational modification (PTM). Formation of disulfide bond linkages between cysteine residues within a protein is a common PTM which not only contributes to folding and stabilizing the protein structure, but also to accomplishing its native function. Therefore, the study and discovery of structural-functional relationships of expressed proteins using an isolated proteomics approach has been one of the biggest advances within the field of structural biology in recent years. In this study, rapid disulfide bond mapping of freshly obtained equine serum albumin (ESA) was performed using matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). Highly sensitive MALDI-TOF MS is commonly used for the investigation of disulfide bond linkages in the proteomics field. However, it has also been known that the presence of disulfide bond linkages absorbs the energy which is created by the cysteine-cysteine kinetic vibration, resulting in a decrease of the instrumental sensitivity. To overcome this problem, the disulfide bond mapping method was optimized by applying a combination of chemical labeling, proteolytic enzymes, and matrices. With the optimized method, we were also able to achieve high protein sequence coverage. Obtaining higher sequence coverage of a protein provides more information about a protein which helps to identify the protein by peptide mass fingerprint (PMF) technique. These analyses eventually contribute to the estimation of the possible PTM sites.

Doctor of Philosophy / Department of Biology / Rollie J. Clem / Each year, over 500 million people are infected with mosquito-borne diseases, including malaria, yellow fever and dengue fever, which cause several million deaths, and long-term disability and suffering. This dissertation focused on the mosquito Aedes aegypti, a vector for dengue virus and yellow fever virus. Since Sindbis virus (SINV) is an arthropod-borne virus (arbovirus) that is vectored by A. aegypti and is well characterized at the molecular level, the SINV - A. aegypti model was used to determine whether apoptosis plays a role in the control of vector competency. In Chapter 2, the effects of inducing or inhibiting apoptosis on SINV replication were tested in mosquito cells. It was observed that recombinant SINVs expressing pro-apoptotic genes caused extensive apoptosis in mosquito cells, with decreased virus production after the cells underwent apoptosis. Infection of mosquito cells with SINV expressing the caspase inhibitor P35 inhibited actinomycin D-induced apoptosis, but had no observable effects on virus replication. This study was the first to test directly whether inducing or inhibiting apoptosis affects arbovirus replication in mosquito cells. Chapter 3 examined the effects of silencing apoptosis regulatory genes on SINV replication and dissemination in A. aegypti. Genes which either positively or negatively regulate apoptosis were silenced by RNA interference in mosquitoes, which were then infected with a recombinant SINV expressing green fluorescent protein (GFP). Reciprocal effects were observed on both the occurrence and intensity of expression of GFP in various tissues. These results suggest that systemic apoptosis positively influences SINV replication in A. aegypti. This was the first direct study to explore the role of apoptosis in determining mosquito vector competence for arboviruses. Finally, in Chapter 4, the mechanisms of apoptosis were explored in A. aegypti. Overexpression of IAP antagonists caused extensive cell death in mosquito cells, while silencing the expression of IAP antagonists attenuated apoptosis. The results showed that the IAP binding motif (IBM) of IAP antagonists was critical for their binding to AeIAP1. The IAP antagonists released initiator and effector caspases from AeIAP1 by competing for the binding sites and caused caspase-dependent apoptosis. These findings imply that the mechanisms of IAP antagonists regulating apoptosis are conserved between mosquitoes and the model insect where apoptosis has been mainly studied, Drosophila melanogaster.

Doctor of Philosophy / Department of Biochemistry / John M. Tomich / Channel replacement therapy represents a new treatment modality that could augment existing therapies against cystic fibrosis. It is based on designing synthetic channel-forming peptides (CFPs) with desirable selectivity, high ion transport rates and overall ability to supersede defective endogenous chloride channels. We derived synthetic CFPs from a peptide initially reconstituted from the second transmembrane segment of the α-subunit of Glycine receptor (M2GlyR). Our best candidate peptide NK4-M2GlyR T19R, S22W (p22-T19R, S22W) is soluble in aqueous solutions, has the ability to deliver itself to the epithelial cell membranes without the use of a delivery system, is non-immunogenic, but when assembled into a pore, lacks the structural properties for anion selectivity. Previous findings suggested that threonine residues at positions 13, 17 and 20 line the pore of assembled p22-T19R, S22W and recent studies indicated that an introduction of positively charged 2, 3-diaminopropionic acid (Dap) at either T13 or T17 in the sequence increases transepithelial ion transport rates across the apical membranes of Madin-Darby canine kidney (MDCK) epithelial cells. This study focused on further structural modifications of the pore-lining interface of p22-T19R, S22W assembled pore. It was hypothesized that singly, doubly or triply introduced Dap residues modify the pore geometry and that their positively charged side chains impact discrimination for anions. Dap-substituted p22-T19R, S22W peptides retain the α-helical secondary structure characteristic for their parent p22-T19R, S22W. The sequences containing multiple Dap-substituted residues induce higher short circuit current across the epithelial MDCK cells compared to peptides with single Dap-substitutions or no Dap-substitutions. Whole-cell voltage clamp recordings using Xenopus oocytes indicate that Dap-substituted peptide assemblies induce higher levels of voltage-dependent but non-selective ion current relative to p22-T19R, S22W. Studies using the D-enantiomer of p22-T19R, S22W and shorter truncated sequences of a full length L-p22-T19R, S22W and L-Dap-substituted peptides provided evidence that peptide-induced ion transport rates can be attributed to formation of de novo pathways. Results of preliminary computer modeling studies indicate that Dap residues affect the pore geometry but not ion selectivity. Future studies focusing on modifying the existing electrostatic environment towards anion selectivity will focus on staggering the charged residues of Dap at various locations inside synthetic pores.

Doctor of Philosophy / Department of Biochemistry and Molecular Biophysics / Thu Annelise Nguyen / Gap junctions (GJ) are intercellular channels connecting adjacent cells, allowing small molecules to transport between cells, thereby maintaining all homeostasis. Loss of gap junctional intercellular communication (GJIC) and/or connexins, the gap junction proteins, is a hallmark of cancer. Restoration of GJIC and/or increase of connexin expression have been related to the reduction of tumorigenesis. Connexins have been reported as tumor suppressors due to both GJIC-independent and -dependent mechanisms. Therefore, development of effective agents or methods to enhance GJIC and restore connexin expression in cancer cells is a new strategy in cancer treatment. PQ1, 6-Methoxy-8-[(3-aminopropyl)amino]-4-methyl-5-(3-trifluoromethyl-phenyloxy)quinoline, has been demonstrated to increase GJIC, restore connexin expression, and exert anti-cancer effects on T47D breast cancer cells. Studies of apoptotic pathways showed that PQ1 activated both extrinsic and intrinsic apoptotic pathways, indicating that PQ1 exerts its anti-cancer effects via a GJIC-independent mechanism through the induction of apoptosis. Combinational treatment of PQ1 and cisplatin showed that PQ1 counteracted cisplatin-induced inhibition of GJIC and reduction of connexin expression, thereby increasing the efficacy of cisplatin in T47D cancer cells via a GJIC-dependent mechanism. Further studies of drug distribution and toxicity revealed that administration of PQ1 by oral gavage can be achieved with low toxicity to normal vital organs. All the results suggest that PQ1, a gap junction enhancer, can function as an anti-cancer agent and potentiate the efficacy of antineoplastic drugs via both GJIC-independent and -dependent pathways.

Doctor of Philosophy / Biochemistry and Molecular Biophysics / Phillip E. Klebba / The goal of the research included in this dissertation is to provide a more complete model of the role of TonB, an energy transducing protein that resides in the inner membrane and is an essential component of the iron transport of Escherichia coli under iron-starved conditions. Using fluorescent hybrid proteins, the anisotropy of TonB in the cytoplasmic membrane (CM) of Escherichia coli was determined. With the aim of understanding the bioenergetics of outer membrane (OM) iron transport, the dependence of TonB motion on the electrochemical gradient and the effect of CM proteins ExbB and ExbD on this phenomenon was monitored and analyzed. The native E. coli siderophore, enterobactin chelates Fe⁺³ in the environment and ferric enterobactin (FeEnt) enters the cell by energy- and TonB-dependent uptake through FepA, its OM transporter. The TonB-ExbBD complex in the CM is hypothesized to transfer energy to OM transporters such as FepA. We observed the polarization of GFPTonB hybrid proteins and used metabolic inhibitors (CCCP, azide and dinitrophenol) and chromosomal deletions of exbBD to study these questions. The results showed higher anisotropy (R) values for GFP-TonB in energy-depleted cells, and lower R-values in bacteria lacking ExbBD. Metabolic inhibitors did not change the anisotropy of GFP-TonB in ΔexbBD cells. These findings suggest that TonB undergoes constant, energized motion in the bacterial CM, and that ExbBD mediates its coupling to the electrochemical gradient. By spectroscopic analyses of extrinsic fluorophore labeled site-directed Cys residues in 7 surface loops of Escherichia coli FepA, binding and transport of ferric enterobactin (FeEnt) was characterized. Changes in fluorescence emissions reflected conformational motion of loops that altered the environment of the fluorophore, and we observed these dynamics as quenching phenomena during FeEnt binding and transport in living cells or outer membrane vesicles. Cys residues in each of the 7 surface loops (L2, L3, L4, L5, L7 L8, and L11) behaved individually and characteristically with regard to both fluorophore maleimide reactivity and conformational motion. Fluorescence measurements of FeEnt transport, by either microscopic or spectroscopic methodologies, demonstrated that ligand uptake occurs uniformly throughout the cell envelope, and susceptibility of FeEnt uptake to the proton ionophore m-chlorophenyl hydrazone (CCCP) at concentrations as low as 5 uM. The latter result recapitulates the sensitivity of inner membrane major facilitator transporters to CCCP (Kaback, 1974), providing further evidence of the electrochemical gradient as a driving force for TonB-dependent metal transport.

Doctor of Philosophy / Biochemistry and Molecular Biophysics / Jeroen Roelofs / The proteasome is a large protease in the cell that contributes to the controlled degradation of proteins. This 2.5MDa 26S proteasome complex consists of a 19S regulatory particle (RP) that recognizes substrates and a 20S proteolytic core particle (CP) that hydrolyses substrates. To function optimally all 66 subunits of the proteasome complex need to assemble properly. Efficient and accurate assembly of the proteasome is achieved with the help of proteins that can monitor the quality of the proteasome during pre- and post-assembly processes. The work in this thesis described an investigation into two of such quality control mechanisms. Pba1-Pba2 dimer has been known to facilitate the CP assembly by interacting with the top of the α-ring of CP throughout CP maturation. After CP maturation, RP utilizes same surface to form a CP-RP complex. Our data showed that Pba1-Pba2 binds tightly to the immature CP and prevents RP association. Once matured CP has a reduced affinity for Pba1-Pba2 and shows a higher affinity towards RP, resulting the formation of 26S proteasome complex. Our results imply that during maturation, CP undergoes conformational changes that results in this switch in affinity. Mathematical models indicate that during assembly such an 'affinity switch' quality control mechanism is required to prevent immature CP-RP complex formations. These types of wrong dead end products prevent efficient proteasome complex formation. Proteasomes formed with post-assembly defects are enriched with the proteasome associated protein Ecm29. Here Ecm29 is proposed to function as a quality control factor that inhibits such defective proteasomes to avoid aberrant protein degradation. This would require Ecm29 to preferably bind to mutant proteasomes. While we know Ecm29 interacts with RP as well as CP, we still don’t understand well how it binds to proteasomes holoenzyme. Here, we identify that besides the Rpt5 subunit of RP, Ecm29 binds to alpha7. We showed that conserved acidic residues containing unstructured C-terminal region of the CP subunit alpha7 facilitates the Ecm29-Proteasome interactions. Further mapping revealed the importance of phosphorylation of serine residues at the alpha7 C-terminal tail for Ecm29 interaction. We anticipate that this study leads to identification of specificity of the Ecm29 for the defective proteasomes. Overall this will help us to understand the role of Ecm29 in regulation of defective proteasomes in vivo.

Master of Science / Department of Diagnostic Medicine/Pathobiology / Roman Reddy R. Ganta / Ehrlichia chaffeensis, a Gram-negative organism belonging to the order Rickettsiales, is responsible for an emerging infectious disease in humans, the human monocytic ehrlichiosis. E. chaffeensis also infects several other vertebrate hosts including dogs, goats, coyotes and white tailed deers. This organism is transmitted by an infected tick, Amblyomma americanum. The exact pathogenic mechanisms involved for the persistence of the pathogen in vertebrate hosts are still unclear. E. chaffeensis protein expression varies significantly in vertebrate and tick hosts. Differentially expressed proteins include the immunodominant outer membrane proteins encoded by the p28-Omp multigene locus. The p28-Omp 14 is expressed primarily in tick cells and the p28-Omp 19 is the major expressed protein in macrophages both under in vitro and in vivo conditions. The objective of this study is to prepare recombinant proteins and use them to assess the secondary structures and protein functions. The protein sequences were analyzed with the aid of bioinformatics programs to make structural predictions. The analysis suggested the presence of eight β barrel structures for both the p28-Omp proteins. The coding sequence of the p28-Omp genes were cloned and over expressions of proteins in in E. coli was accomplished by using the plasmid expression construct, pET28. The proteins were purified to near homogeneity and used to refold using detergents to mimic native protein structure in the bacterial outer membrane. Refolding of proteins was analyzed by two methods; SDS-PAGE and Circular Dichroism. The Circular dichroism spectroscopy analysis suggested the formation of β-sheet structures of proteins in micelles formed with the detergents. β-sheet structures may have been formed with the hydrophobic domains of the protein imbedded in the micelles. The hydrophilic segments (predicted by bio informatics analysis) may be exposed to the aqueous phase. The recombinant proteins were also iii used to prepare proteoliposomes and tested for the porin activity. The analysis demonstrated the porin activity for both p28-Omp 14 and 19 recombinant proteins by using mono-, di- and tetra- saccharides as well as for amino acid L-glutamine. This study forms the basis for initiating studies to compare the structural difference between the two differentially expressed proteins of E. chaffeensis.

Doctor of Philosophy / Graduate Biochemistry Group / Dolores J. Takemoto / Eukaryotic cells possess a unique way to communicate with each other by passing metabolites and small molecules through protein pores that connect adjacent cells. Although there are many types and families of protein pores, connexins comprise a unique family. Six connexin monomers assemble into a hemichannel, which is transported to the cell membrane. An opposing cell membrane containing compatible connexin hemichannels is located and connected, forming an intercellular dodecameric protein complex. This results in a protein channel that connects two separate cytoplasmic compartments to each other. This type of channel is known as a gap junction. Connexin expression and function is commonly tissue specific. Of the 21 known human connexins, less than half are currently well characterized. Three connexins are expressed in the lens, connexin 43 (Cx43), 46 (Cx46), and 50 (Cx50). Of these three, Cx46 and Cx50 both have major functions in the mature lens. Cx46 functions as a major gap junction channel, which maintains mature lens homeostasis, while Cx50 possesses growth control properties in the lens. Cx46 expression is modulated in breast and bone tumors, and during ischemia. It is hypothesized that Cx46 provides resistance to hypoxia mediated cell death by prolonging survival. In this study, Cx46 expression was detected in human Y79 retinoblastoma cells. Decreasing the expression of Cx46 in nude mice carrying Y79 xenografts slowed early stage tumor growth. Y79 cells in culture survive for over 72 hours in 1% oxygen in vitro. C46 was upregulated in cultured lens cells when grown under hypoxia. Human lens epithelial cells, rabbit N/N1003A lens cells, and Y79 cells proliferated in 1% oxygen until Cx46 expression was depleted by use of siRNA. Protection from hypoxia-induced cell death was provided by transfection with the C-terminus of Cx46. We further determined that the promoter activity of Cx46 was increased in 1% oxygen. These results indicate that Cx46 would increase in response to hypoxia and suggest a role for Cx46 in protection from hypoxia. The studies demonstrate a novel function for Cx46 in cell survival during hypoxia.

Doctor of Philosophy / Department of Biochemistry and Molecular Biophysics / John M. Tomich / Branched Amphiphilic Peptide Capsules (BAPCs) are peptide nano-spheres comprised of equimolar proportions of two branched peptide sequences bis(FLIVI)-K-KKKK and bis(FLIVIGSII)-K-KKKK that self-assemble in water to form bilayer delimited poly-cationic capsules capable of trapping solutes. We examined the lipid-like properties of this system including assembly, fusion, solute encapsulation, and resizing by membrane extrusion as well as their capability to be maintained at a specific size by storage at 4˚C. These studies along with earlier work from the lab (Gudlur et al. (2012) PLOS ONE 7(9): e45374) demonstrated that the capsules, while sharing many properties with lipid vesicles, were much more robust. We next investigated the stability, size limitations of encapsulation, cellular localization, retention and, bio-distribution of the BAPCs. We demonstrated that the BAPCs are readily taken up by epithelial cells in culture, escape or evade the endocytotic pathway, and accumulate in the peri-nuclear region where they persist without any apparent degradation. The stability and persistence of the capsules suggested they might be useful in delivering radionuclides. The BAPCs encapsulated alpha particle emitting radionuclides without any apparent leakage, were taken up by cells and were retained for extended periods of time. Their potential in this clinical application is being currently pursued. Lastly we studied the temperature dependence of capsule formation by examining the biophysical characteristics of temperature induced conformational changes in BAPCs and examined the structural parameters within the sequences that contribute to their remarkable stability. A region in the nine-residue sequence was identified as the critical element in this process. The ability to prepare stable uniform nano-scale capsules of desired sizes makes BAPCs potentially attractive as delivery vehicles for various solutes/drugs.

Doctor of Philosophy / Department of Chemistry / Paul E. Smith / In the study of biological systems, molecular dynamics (MD) simulations have played an important role in providing atomic details for phenomena of interest. The force field used in MD simulations is a critical factor determining the quality of the simulations. Recently, Kirkwood-Buff (KB) theory has been applied to study preferential interactions and to develop a new force field. KB theory provides a path from quantities determined from simulation data to the corresponding thermodynamic data. Here we combine KB theory and molecular simulations to study a variety of intermolecular interactions in solution. First, recent results concerning the formulation and evaluation of preferential interactions in biological systems in terms of KB integrals are presented. In particular, experimental and simulated preferential interactions of a cosolvent with a biomolecule in the presence of water are described. Second, a force field for the computer simulation of aqueous solutions of amides is presented. The force field is designed to reproduce the experimentally observed density and KB integrals for N-methylacetamide (NMA), allowing for an accurate description of the NMA activity. Other properties such as the translational diffusion constant and heat of mixing are also well reproduced. The force field is then extended to include N,N'-dimethylacetamide and acetamide with good success. The models presented here provide a basis for an accurate force field for peptides and proteins. Comparison between the developed KB force fields (KBFF) and existing force fields is performed for amide and glycine and proves that the KBFF approach is competitive. Also, explicit expressions are developed for the chemical potential derivatives, partial molar volumes, and isothermal compressibility of solution mixtures involving four components at finite concentrations using the KB theory of solutions. A general recursion relationship is also provided which can be used to generate the chemical potential derivatives for higher component solutions. Finally, a pairwise preferential interaction model (PPIM), described by KB integrals is developed to quantify and characterize the interactions between functional groups observed in peptides.