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The filamentous cyanobacteria Nostoc punctiforme ATCC 29133 is a model species fordevelopment of sustainable production methods of numerous compounds. One of its uniquefeatures is the anaerobic environment of the strains nitrogen fixing heterocyst cells. To be ableto properly utilize this environment, more knowledge regarding what regulates cell specificexpression is required. In this study, three motifs of the NsiR I promoter of Anabaena sp.PCC 7120 was studied in this system utilizing YFP-fluorescence as a reporter to determinetheir impact on spatial expression pattern. Investigations were performed on immobilizedcells with the use of confocal microscopy and results point towards sigma factor regulation.

Multimeric ligands have the potential to be developed as targeted imaging agents and therapeutics for the diagnosis and treatment of cancer. Multimeric ligands consist of multiple binding residues tethered together by a linker and are capable of simultaneous binding to multiple receptors. This dissertation details the proof-of-principle experiments that establish that multimeric ligands bind with an increased affinity and cooperativity compared to their monomeric counterparts. We have chosen to evaluate combinations of ligands for the human melanocortin 4 receptor (hMC4R), human delta-opioid receptor (hdOR), cholecystokinin-B receptor (CCK-BR), and oxytocin receptor (OTR).Multivalent ligands can be homomeric, meaning that all ligands bind to the same receptor type, or they may be heteromeric, meaning that they bind to different types of receptors. We have evaluated homodimer and homotrimer binding to hMC4Rs, and heterodimer binding to hMC4Rs and hdORs. Ligands for the receptors were tethered together using backbones constructed of polyethylene glycol (PEG) units or different combinations of amino acid repeats. The effects of linker length and rigidity on the binding of multivalent ligands have been evaluated. Additionally, this dissertation details the development of a new lanthanide based binding method used to monitor receptor-ligand interactions. This assay makes use of lanthanide labels attached to a peptide that binds specifically to the receptor of interest. The amount of bound ligand is detected using time-resolved fluorescence (TRF). This assay produces results which are highly reproducible, require less setup time and reagents and do not require special waste disposal, all advantages over the traditional radioligand binding assays. This lanthanide based binding assay has been adapted to evaluate ligand binding to the hMC4R and hdOR.

Marked differences have been found in men’s and women’s sexual response patterns, contingent upon their sexual orientation; opposite- and same-gender attracted men demonstrate greatest genital and self-reported arousal to their preferred stimulus type, whereas other-gender attracted women do not, and findings of same-gender attracted women have been mixed (e.g., Chivers, Seto & Blanchard, 2007; Chivers, Bouchard, Timmers, & Haberl, 2012). Given the complex nature of sexual stimuli that are used in research paradigms involving category-specificity of sexual arousal, however, it is often unclear to what extent contextual cues (cues other than the sexual actor’s sex characteristics; body movement, level of sexual activity, etc.) influence participants’ sexual response patterns. As such, the current study attempted to parse contextual cues from sexual stimuli and examined genital, self-reported, and continuous self-reported responses of same- and other-gender attracted men and women to prepotent sexual features (stimuli believed to elicit automatic sexual arousal: erect penises and vasoengorged vulvas), nonprepotent sexual features (flaccid penises and pubic triangles) and neutral stimuli (clothed men and women). All samples were found to exhibit a category-specific pattern of genital, self-reported, and continuous self-reported sexual arousal. Similarly, genital, self-reported, and continuous self-reported arousal was generally found to be greatest to “prepotent” sexual conditions. Limitations and implications are discussed. / Thesis (Master, Psychology) -- Queen's University, 2013-08-30 11:37:10.216

This thesis is focused on determining the structures of two anti-carbohydrate antibodies to understand how they achieve their specificity toward antigen. First, the structure of the antigen-binding fragment from the monoclonal antibody S64-4 in complex with a pentasaccharide bisphosphate fragment from chlamydial lipopolysaccharide (LPS) has been determined by x-ray diffraction to 2.6 Å resolution. Like the well-characterized antibody S25-2, S64-4 displays a pocket formed by the residues of germline sequence corresponding to the heavy and light chain V gene segments that binds the terminal Kdo (3-deoxy-α-D-manno-oct-2-ulopyranosonic acid) residue of the antigen; however, although S64-4 shares the same heavy chain V gene segment as S25-2, it has a different light chain V gene segment. The new light chain V gene segment codes for a combining site that displays greater avidity, different specificity, and allows a novel antigen conformation that brings a greater number of antigen residues into the combining site than possible in S25-2. Further, while antibodies in the S25-2 family use complementarity determining region (CDR) H3 to discriminate among antigens, S64-4 achieves its specificity via the new light chain V gene segment and resulting change in antigen conformation. These structures reveal an intriguing parallel strategy where two different combinations of germline-coded V gene segments can act as starting points for the generation of germline antibodies against chlamydial antigens and show how anti-carbohydrate antibodies can exploit the conformational flexibility of this class of antigens to achieve high avidity and specificity independently of CDR H3. Second, the structure of a rabbit, single chain variable fragment against terminal mannose-6-phosphate (Man6P) residues, termed scFv M6P-1, has been determined by x-ray diffraction to 2.7 Å resolution with Man6P in the binding site. The Man6P pathway is the predominant pathway that transports acid hydrolases from the trans-Golgi to endosomes. Newly synthesized hydrolases first require the generation of Man6P markers before they can be transported. Maintaining a full complement of hydrolases within lysosomes is essential as failure to do so results in a number of different lysosomal storage diseases. Due to its specificity, scFv M6P-1 is able to diagnose lysosomal storage diseases mucolipidosis II and mucolipidosis III. scFv M6P-1 is also able to purify Man6P containing proteins which may be useful for enzyme replacement therapies. Additionally, scFv M6P-1 is one of the first structures of an antibody fragment that exhibits high specificity for a single carbohydrate residue and is one of the first structures of a rabbit antibody fragment. The specificity of scFv M6P-1, which gives it these unique attributes, is revealed in the structure where multiple hydrogen bonds are seen between the antibody’s heavy chain and the mannose ring while two salt bridges are observed between the antibody’s light chain and the phosphate moiety. Finally, scFv M6P-1 binds in such a way as to allow binding to proteins possessing terminal Man6P residues. Crystallographic challenges that arose during this research included poor crystal growth as well as twinning and these are explored while the structure of scFv M6P-1 complex with Man6P is analysed. / Graduate / 0487 / 0982 / 0307 / dyl.w.evans@gmail.com

Transcription factors (TFs) bind to specific DNA sequences near target genes to precisely coordinate their regulation. Despite the central role of transcription factors in development and homeostasis, the mechanisms by which TFs have evolved to bind and regulate distinct DNA sequences are poorly understood. This dissertation details the highly collaborative work to determine the genetic, biochemical and biophysical mechanisms by which distinct DNA-binding specificities evolved in the steroid receptor (SR) family of transcription factors. Using ancestral protein reconstruction, we resurrected and functionally characterized the historical transition in DNA-binding specificity between ancient SR proteins. We found that DNA-binding specificity evolved by changes in the energetic components of binding; interactions at the protein-DNA interface were weakened while inter-protein cooperativity was greatly improved. We identified a group of fourteen historical substitutions that were sufficient to recapitulate the derived protein's binding function. Three of these substitutions, which we defined as function-switching, were sufficient to change DNA specificity; however, their introduction greatly decreased binding affinity and was deleterious for protein function. A group of eleven permissive substitutions, which had no effect on DNA specificity, allowed for the protein to tolerate the deleterious effects of the function-switching substitutions. They non-specifically increased binding affinity by improving interactions at the protein-DNA interface and increasing inter-protein cooperativity. We then dissected the functional role of individual substitutions in both the function-switching and permissive groups. We first determined the binding affinity of all possible combinations of function-switching substitutions for a library of DNA sequences. This allowed for us to functionally characterize the sequence space that separated the ancestral and derived DNA-binding specificities as well as identify the genetic determinants for DNA specificity. Lastly, we dissected the effects of the permissive substitutions on the energetics of DNA binding to determine the mechanisms by which they exerted their permissive effect. Together, this work provides insight into the molecular determinants of DNA specificity and identifies the molecular mechanisms by which these interactions changed during the evolution of novel specificity in an important transcription factor family. This dissertation includes previously published and unpublished co-authored material. / 2016-01-14

The phenotypic variability in human populations is partly the result of gene polymorphisms and differential gene expression. Studying the variability of gene expression across human populations is essential to understanding the molecular basis for diversity. However, key issues remain unanswered with respect to human expression variability. For example, the role of gene methylation in expression variability is uncertain, nor is it clear what role tissue-specific factors may have. Moreover, the contribution that expression variability has in aging and development is unknown. Here we classified human genes based on their expression variability in normal human breast and brain samples and identified functional aspects associated with high and low expression variability. Interestingly, both high variability and low variability gene sets are enriched for developmentally essential genes. There is limited overlap between the variably expressed genes of different tissues, indicating that tissue-specific rather than individual-specific factors are at work. We also find that methylation likely has a key role in controlling expression variability insofar as genes with low expression variability are likely to be non-methylated. Importantly, we find that genes with high population expression variability are likely to have age-, but not sex-dependent expression. Taken together, our work indicates that gene expression variability is tissue-specific, methylation-dependent, and is an important component of the natural aging process.

Guanine nucleotide exchange factor proteins of the Tiam family are activators of the Rho GTPase Rac1 and critical for cell morphology, adhesion, migration, and polarity. These proteins are modular and contain a variety of interaction domains, including a previously uncharacterized post-synaptic density-95/discs large/zonula occludens-1 (PDZ) domain. Here we report on the structure, specificity, and function of the Tiam1 and Tiam2 PDZ domains. A consensus PDZ-binding motif for Tiam1 was used to predict that two cell adhesion proteins, Syndecan 1 (Sdc1) and Caspr4, are potential Tiam1 PDZ domain binding proteins. Binding interactions were confirmed using fluorescence- and NMR- based binding experiments. The Tiam1 PDZ domain in complex with the C-terminal tails of Sdc1 and phosphorylated Sdc1 were solved using X-ray crystallography. Results showed four residues in two binding pockets in the PDZ domain are important for specificity. Cell biological analysis confirmed the Tiam1/Sdc1 interaction and showed that the PDZ domain has a function in cell-matrix adhesion and cell migration. The four residues deemed important determinants of Tiam1 PDZ domain specificity are not conserved in Tiam2. A combinatorial peptide screen, in combination with biophysical studies, identified a consensus binding sequence for both PDZ domains. Analysis of these consensus sequences and binding assays with peptides derived from native proteins indicated that these two PDZ domains have overlapping but distinct specificities - the Tiam2 PDZ domain was found to bind Caspr4 and neurexin1 but not Sdc1. Additionally, the Tiam2 PDZ domain exhibits significant flexibility in two different regions, a feature not seen in Tiam1. Double-mutant cycle analysis of the four important residues revealed ligand- dependent energetic couplings. Mutating all four residues switched the ligand specificity to that of Tiam2. Analysis of Tiam-family PDZ domain sequences indicated that the PDZ domains segregate into four distinct families based on the residues studied here. A set of "evolved peptides" was used to show the PDZ domain interactions are cooperative throughout the binding pocket in a ligand-specific manner. Collectively, our data suggest that Tiam family proteins have highly evolved PDZ domain/ligand interfaces with distinct specificities and that they have disparate PDZ domain-dependent biological functions.

The goals of gene prediction using computational approaches are to determine gene location and the corresponding functionality of the coding region. A subset of gene prediction is the gene structure prediction problem, which is to define the exon-intron boundaries of a gene. Gene prediction follows two general approaches: statistical patterns identification and sequence similarity comparison. Similarity based approaches have gained increasing popularity with the recent vast increase in genomic data in GenBank. The proposed gene prediction algorithm is a similarity based algorithm which capitalizes on the fact that similar sequences bear similar functions. The proposed algorithm, like most other similarity based algorithms, is based on dynamic programming. Given a genomic DNA, X = x1 xn and a closely related cDNA, Y = y1 yn, these sequences are aligned with matching pairs stored in a data set. These indexes of matching sets contain a large jumble of all matching pairs, with a lot of cross over indexes. Dynamic programming alignment is again used to retrieve the longest common non-crossing subsequence from the collection of matching fragments in the data set. This algorithm was implemented in Java on the Unix platform. Statistical comparisons were made against other software programs in the field. Statistical evaluation at both the DNA and exonic level were made against Est2genome, Sim4, Spidey, and Fgenesh-C. The proposed gene structure prediction algorithm, by far, has the best performance in the specificity category. The resulting specificity was greater than 98%. The proposed algorithm also has on par results in terms of sensitivity and correlation coeffcient. The goal of developing an algorithm to predict exonic regions with a very high level of correctness was achieved.

Methionine is essential for proper functioning of cellular processes such as protein synthesis, transmethylation and polyamine synthesis. Efficient recycling of methionine is important because of its limited bioavailability and metabolically expensive de novo synthesis. Further, cellular accretion of the nucleoside metabolites of the methionine salvage pathway compromises polyamine biosynthesis, transmethylation reactions and quorum sensing pathways, all critical reactions in cellular metabolism. 5’-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) is a key component of the methionine salvage pathway of plants and many bacterial species, including Escherichia coli, Enterococcus faecalis, Salmonella typhimerium, Haemophilus influenza and Streptococcus pneumoniae. In bacteria, this enzyme displays dual-substrate specificity for two methionine metabolites, 5’-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH), and catalyzes the irreversible cleavage of the glycosidic bond to form adenine and the corresponding thioribose products, methylthioribose (MTR) and S-ribosylhomocysteine (SRH), respectively. In plants, MTAN is highly specific towards MTA and shows 0-16 % activity towards SAH. Plants rely on SAH hydrolase to metabolize SAH. Mammals do not have the nucleosidase enzyme and MTA is metabolized by MTA phosphorylase (MTAP). Like plants, mammals utilize SAH hydrolase to degrade SAH. Because MTAN is required for viability in multiple bacterial species and is not found in humans, it has been identified as a target for novel antibiotic development. This thesis describes the structural and functional characterization of bacterial and plant MTANs, with the aim of better understanding the molecular determinants of substrate specificity and the catalytic mechanism of this enzyme. The catalytic activities of representative plant MTANs from Arabidopsis thaliana, AtMTAN1 and AtMTAN2, were kinetically characterized. While AtMTAN2 shows 14 % activity towards SAH relative to MTA, AtMTAN1 is completely inactive towards SAH. As such, AtMTAN1 was selected for further examination and comparison with the bacterial MTAN from Escherichia coli (EcMTAN). The structures, dynamics and thermodynamic properties of these enzymes were analyzed by X-ray crystallography, hydrogen-exchange coupled mass spectrometry and isothermal titration calorimetry, respectively. Our studies reveal that structural differences alone do not sufficiently explain the divergence in substrate specificity, and that conformational flexibility also plays an important role in substrate selection in MTANs. MTANs from the pathogenic bacterial species, Staphylococcus aureus and Streptococcus pneumoniae, were examined kinetically and structurally. Comparison of the structures and catalytic activities of these enzymes with EcMTAN shows that the discrepancies in kinetic activities arefully explained by structural differences, as the overall structure and active sites of these bacterial MTANs are nearly identical. These experiments are in agreement with our proposal that dynamics play a significant role in catalytic activity of MTAN, and suggest that both structure and dynamics must be considered in future antibiotic design. To further our understanding on the catalytic mechanism of MTAN, the putative catalytic residues of AtMTAN1 were identified by structural comparison to EcMTAN and mutated by site-directed mutagenesis. The AtMTAN1 mutants were analyzed by circular dichroism and kinetic studies. Our results suggest that the catalytic mechanism is largely conserved between bacterial and plant MTANs, although the role of the putative catalytic acid remains to be confirmed.