Proteolytic processing of the nonstructural proteins of dengue 2 virus

The genomes of many positive stranded RNA viruses and of all retroviruses are translated as large polyproteins which are proteolytically processed by cellular and viral proteases. Viral proteases are structurally related to two families of cellular proteases, the pepsin-like and trypsin-like proteases. This thesis describes the proteolytic processing of several nonstructural proteins of dengue 2 virus, a representative member of the Flaviviridae, and describes methods for transcribing full-length genomic RNA of dengue 2 virus. Chapter 1 describes the in vitro processing of the nonstructural proteins NS2A, NS2B and NS3. Chapter 2 describes a system that allows identification of residues within the protease that are directly or indirectly involved with substrate recognition. Chapter 3 describes methods to produce genome length dengue 2 RNA from cDNA templates.

The nonstructural protein NS3 is structurally related to viral trypsinlike proteases from the alpha-, picorna-, poty-, and pestiviruses. The hypothesis that the flavivirus nonstructural protein NS3 is a viral proteinase that generates the termini of several nonstructural proteins was tested using an efficient in vitro expression system and antisera specific for the nonstructural proteins NS2B and NS3. A series of cDNA constructs was transcribed using T7 RNA polymerase and the RNA translated in reticulocyte lysates. Proteolytic processing occurred in vitro to generate NS2B and NS3. The amino termini of NS2B and NS3 produced in vitro were found to be the same as the termini of NS2B and NS3 isolated from infected cells. Deletion analysis of cDNA constructs localized the protease domain necessary and sufficient for correct cleavage to the first 184 amino acids of NS3. Kinetic analysis of processing events in vitro and experiments to examine the sensitivity of processing to dilution suggested that an intramolecular cleavage between NS2A and NS2B preceded an intramolecular cleavage between NS2B and NS3. The data from these expression experiments confirm that NS3 is the viral proteinase responsible for cleavage events generating the amino termini of NS2B and NS3 and presumably for cleavages generating the termini of NS4A and NS5 as well.

Biochemical and genetic experiments using viral proteinases have defined the sequence requirements for cleavage site recognition, but have not identified residues within proteinases that interact with substrates. A biochemical assay was developed that could identify residues which were important for substrate recognition. Chimeric proteases between yellow fever and dengue 2 were constructed that allowed mapping of regions involved in substrate recognition, and site directed mutagenesis was used to modulate processing efficiency.

Expression in vitro revealed that the dengue protease domain efficiently processes the yellow fever polyprotein between NS2A and NS2B and between NS2B and NS3, but that the reciprocal construct is inactive. The dengue protease processes yellow fever cleavage sites more efficiently than dengue cleavage sites, suggesting that suboptimal cleavage efficiency may be used to increase levels of processing intermediates in vivo. By mutagenizing the putative substrate binding pocket it was possible to change the substrate specificity of the yellow fever protease; changing a minimum of three amino acids in the yellow fever protease enabled it to recognize dengue cleavage sites. This system allows identification of residues which are directly or indirectly involved with enzyme-substrate interaction, does not require a crystal structure, and can define the substrate preferences of individual members of a viral proteinase family.

Full-length cDNA clones, from which infectious RNA can be transcribed, have been developed for a number of positive strand RNA viruses, including the flavivirus type virus, yellow fever. The technology necessary to transcribe genomic RNA of dengue 2 virus was developed in order to better understand the molecular biology of the dengue subgroup. A 5' structural region clone was engineered to transcribe authentic dengue RNA that contains an additional 1 or 2 residues at the 5' end. A 3' nonstructural region clone was engineered to allow production of run off transcripts, and to allow directional ligation with the 5' structural region clone. In vitro ligation and transcription produces full-length genomic RNA which is noninfectious when transfected into mammalian tissue culture cells. Alternative methods for constructing cDNA clones and recovering live dengue virus are discussed.

Bimetallic olefin polymerization catalysis : mechanisms and applications of proximal effects

This dissertation covers progress with bimetallic polymerization catalysts. The complexes we have designed were aimed at expanding the capabilities of homogeneous polymerization catalysts by taking advantage of multimetallic effects. Such effects were examined in group 4 and group 10 bimetallic complexes; proximity and steric repulsion were determined to be major factors in the effects observed.

Chapters 2 and 3 introduce the rigid p-terphenyl dinucleating framework utilized in most of this thesis. The permethylation of the central arene allows for the separation of syn and anti atropisomers of the terphenyl compounds. Kinetic studies were carried out to examine the isomerization of the dinucleating bis(salicylaldimine) ligand precursors. Metallation of the syn and anti bis(salicylaldimine)s using Ni(Me)2(tmeda) and excess pyridine afforded dinickel bisphenoxyiminato complexes with a methyl and a pyridyl ligand on each nickel. The syn and anti atropisomers of the dinickel complexes were structurally characterized and utilized in ethylene and ethylene/α-olefin polymerizations. Monometallic analogues were also synthesized and tested for polymerization activity. Ethylene polymerizations were performed in the presence of primary, secondary, and tertiary amines – additives that generally deactivate nickel polymerization catalysts. Inhibition of this deactivation was observed with the syn atropisomer of the bimetallic species, but not with the anti or monometallic analogues. A mechanism was proposed wherein steric repulsion of the substituents on proximal nickel centers disfavors simultaneous ligation of base to both of the metal centers. The bimetallic effect has been explored with respect to size and binding ability of the added base.

Chapter 4 presents the optimization of the bisphenoxyimine ligand synthesis and synthesis of syn and anti m-terphenyl analogues. Metallation with NiClMe(PMe₃)₂ yielded phosphine-ligated dinickel complexes, which have been structurally characterized. Ethylene/1-hexene copolymerizations in the presence of amines using Ni(COD)₂ as a phosphine scavenger showed significantly improved activity relative to the pyridine-ligated analogues. Incorporation of amino olefins in copolymerizations with ethylene was accomplished, and a mechanism was proposed based on proximal effects. Copolymerization trials with a variety of amino olefins and ethylene/1-hexene/amino olefin terpolymerizations were completed.

Early transition metal complexes based on the rigid p-terphenyl framework were designed with a variety of donor sets (Chapter 5 and Appendix B). Chapter 5 details the use of syn dizirconium di[amine bis(phenolate)] complexes for isoselective 1-hexene and propylene homopolymerizations. Ligand variation and monometallic complexes were studied to determine the origin of tacticity control. A mechanistic proposal was presented based on the symmetry at zirconium and the steric effects of the proximal metal center. Appendix B covers additional studies of bimetallic early transition metal complexes based on the p-terphenyl. Dititanium, dizirconium, and asymmetric complexes with bisphenoxyiminato ligands and derivatives thereof were targeted. Progress toward the synthesis of these complexes is described along with preliminary polymerization data. 1-hexene/diene copolymerizations and attempted polymerizations in the presence of ethers and esters with the syn dizirconium di[amine bis(phenolate)] complexes demonstrate the potential for further applications of this system in catalysis.

Appendix A includes work toward palladium catalysts for insertion polymerization of polar monomers. These complexes were based on dioxime and diimine frameworks with the intent of binding Lewis acidic metals at the oxime oxygens, at pendant phenolic donors, or at pendant aminediol moieties. The synthesis and structural characterization of a number of palladium and Lewis acid complexes is presented. Due to the instability of the desired species, efforts toward isolation of the desired complexes proved unsuccessful, though preliminary ethylene/methyl acrylate copolymerizations using in situ activation of the palladium species were attempted.

The application of metallointercalators in recognition of and charge transport in nucleic acids

Metal complexes that utilize the 9,10-phenanthrene quinone diimine (phi) moiety bind to DNA through the major groove. These metallointercalators can recognize DNA sites and perform reactions on DNA as a substrate. The site-specific metallointercalator Λ-1-Rh(MGP)_2phi^(5+) competitively disrupts the major groove binding of a transcription factor, yAP-1, from an oligonucleotide that contains a common binding site. The demonstration that metal complexes can prevent transcription factor binding to DNA site-specifically is an important step in using metallointercalators as therapeutics.

The distinctive photochemistry of metallointercalators can also be applied to promote long range charge transport in DNA. Experiments using duplexes with regions 4 to 10 nucleotides long containing strictly adenine and thymine sequences of varying order showed that radical migration is more dependent on the sequence of bases, and less dependent on the distance between the guanine doublets. This result suggests that mechanistic proposals of long range charge transport must involve all the bases.

RNA/DNA hybrids show charge migration to guanines from a remote site, thus demonstrating that nucleic acid stacking other than B-form can serve as a radical bridge. Double crossover DNA assemblies also provide a medium for charge transport at distances up to 100 Å from the site of radical introduction by a tethered metal complex. This radical migration was found to be robust to mismatches, and limited to individual, electronically distinct base stacks. In single DNA crossover assemblies, which have considerably greater flexibility, charge migration proceeds to both base stacks due to conformational isomers not present in the rigid and tightly annealed double crossovers.

Finally, a rapid, efficient, gel-based technique was developed to investigate thymine dimer repair. Two oligonucleotides, one radioactively labeled, are photoligated via the bases of a thymine-thymine interface; reversal of this ligation is easily visualized by gel electrophoresis. This assay was used to show that the repair of thymine dimers from a distance through DNA charge transport can be accomplished with different photooxidants.

Thus, nucleic acids that support long range charge transport have been shown to include A-track DNA, RNA/DNA hybrids, and single and double crossovers, and a method for thymine dimer repair detection using charge transport was developed. These observations underscore and extend the remarkable finding that DNA can serve a medium for charge transport via the heteroaromatic base stack.

In vivo analysis of interactions between trans-acting factors and their target genes

The investigations presented in this thesis use various in vivo techniques to understand how trans-acting factors control gene expression. The first part addresses the transcriptional regulation of muscle creatine kinase (MCK). MCK expression is activated during the course of development and is found only in differentiated muscle. Several in vivo footprints are observed at the enhancer of this gene, but all of these interactions are limited to cell types that express MCK. This is interesting because two of the footprints appear to represent muscle specific use of general transcription factors, while the other two correspond to sites that can bind the myogenic regulator, MyoD1, in vitro. MyoD1 and these general factors are present in myoblasts, but can bind to the enhancer only in myocytes. This suggests that either the factors themselves are post-translationally modified (phosphorylation or protein:protein interactions), or the accessibility of the enhancer to the factors is limited (changes in chromatin structure). The in vivo footprinting study of MCK was performed with a new ligation mediated, single-sided PCR (polymerase chain reaction) technique that I have developed.

The second half of the thesis concerns the regulation of mouse metallothionein (MT). Metallothioneins are a family of highly conserved housekeeping genes whose expression can be induced by heavy metals, steroids, and other stresses. By adapting a primer extension method of genomic sequencing to in vivo footprinting, I've observed both metal inducible and noninducible interactions at the promoter of MT-I. From these results I've been able to limit the possible mechanisms by which metal responsive trans-acting factors induce transcription. These interpretations correlate with a second line of experiments involving the stable titration of positive acting factors necessary for induction of MT. I've amplified the promoter of MT to 10^2-10^3 copies per cell by fusing the 5' and 3' ends of the MT gene to the coding region of DHFR and selecting cells for methotrexate resistance. In these cells, there is a metal-specific titration effect, and although it acts at the level of transcription, it appears to be independent of direct DNA binding factors.