A dissertation submitted in fulfilment of the requirements for the degree of Master of Science to the Faculty of Science, University of the Witwatersrand, Johannesburg, 2017 / Transcription factors are proteins that are involved in the regulation of gene expression and are responsible for the tight control of transcription allowing a cell to react to changes in its environment. Transcription factors are thus highly regulated by a variety of mechanisms which include phosphorylation. Forkhead box P2 (FOXP2) is a transcription factor expressed in multiple tissues during embryonic development. FOXP2 like other FOX proteins contains a DNA binding domain known as the forkhead domain (FHD). The effect of phosphorylation of serine 557 in the FHD on the structure and DNA binding was done using a glutamate mutant (to mimic phosphorylation) and an alanine mutant (as a control). Structural characterisation was performed using size exclusion chromatography (SEC), intrinsic fluorescence and far-UV circular dichroism. The effect of phosphorylation on DNA binding was observed using electrophoretic mobility shift assay (EMSA) and isothermal titration calorimetry (ITC). Far-UV circular dichroism and intrinsic fluorescence of the mutants and wild type did not reveal any significant secondary or tertiary structural changes. SEC however revealed a decrease in dimerisation propensity in the Ser557 mutants when compared the wild type (WT). EMSA revealed that DNA binding of S557E is only observed at protein concentrations 40 times in excess of the DNA. DNA binding of the WT and S557A mutants is observed at 5 times and 20 times excess protein respectively. However, using ITC no DNA binding is observed for either S557E or S557A FOXP2 FHD. Thus, it is possible that phosphorylation of serine 557 in the FOXP2 FHD could be a mechanism for inactivation of FOXP2. / XL2017

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Detailed analysis of the site-specific phosphorylation of a glucan phosphate from Saccharomyces cerevesiae has been carried out by 2D NMR techniques. Phosphorylation has been shown to be limited to the C-6 and C-2 positions, with the C-6 resonance showing two slightly different environments. Phosphorylation at C-4 is hindered due to proximity effects with the neighboring glucose ring oxygen. Noncovalently bound, nondialyzable phosphate appears to be coordinated to the nonphosphorylated HO-2 group of the helical polymer.

Small heat shock proteins (hsp) have been implicated in mediation of classic preconditioning in the rabbit. Hsp27 is a terminal substrate of the p38 MAPK cascade. One and 2D gel electrophoresis and immunoblotting of cell fractions was used to determine p38 MAPK and hsp27 phosphorylation levels, respectively, during in vitro ischemia in control, calyculin A (Cal A)-treated (protein phosphatase inhibitor), SB203580-treated (p38MAPK inhibitor) and preconditioned (IPC) isolated adult rabbit cardiomyocytes. The dual phosphorylation of p38 MAPK was increased by early ischemia (30-60 min), after which there was a loss of total cytosolic p38 MAPK. The ischemic increase of p38 MAPK dual phosphorylation was enhanced by IPC. Cal A strongly activated dual phosphorylation of p38 MAPK in oxygenated cells and this was maintained into early ischemia. SB203580 inhibited the dual phosphorylation of p38 MAPK and attenuated the loss of total cytosolic p38 MAPK. In each protocol, ischemia translocated hsp27 from the cytosolic fraction to the cytoskeletal fraction at similar rates and extents. Hsp27 phosphorylation was quantitated as the fraction of diphosphorylated hsp27, based on IEF mobility shifts of hsp27 phosphorylation isoforms. In oxygenated control cells, cytosolic and cytoskeletal hsp27 was highly phosphorylated. After 90 min ischemia, cytoskeletal hsp27 was markedly dephosphorylaled. Cal A slightly increased control cytoskeletal hsp27 phosphorylation. During ischemic incubation, Cal A blocked ischemic dephosphorylation. SB203580 accelerated ischemic hsp27 dephosphorylation and injury. IPC insignificantly decreased the initial rate of ischemic dephosphorylation of hsp27, but not the extent of dephosphorylation in later ischemia. Phosphorylation is regulated by both kinase and phosphatase activities. IPC protection was not correlated with a significant increase in cytosolic or cytoskeletal hsp27 phosphorylation levels during prolonged (> 60-90 min) ischemia.

Indiana University-Purdue University Indianapolis (IUPUI) / The proliferation and differentiation of osteoblasts are influenced by mechanical and geometrical growth environments. A specific aim of my thesis was the elucidation of signaling pathways involved in mechanical stimulation and geometric alterations of the extracellular matrix (ECM). A pair of questions addressed herein was (a) Does mechanical stimulation modulate translational regulation through the phosphorylation of eukaryotic initiation factor 2 (eIF2)? (b) Do geometric alterations affect the phosphorylation patterns of mitogen-activated protein kinase (MAPK) signaling? My hypothesis was mechanical stress enhances the proliferation and survival of osteoblasts through the reduction in phosphorylation of eIF2, while 3-dimensional (3D) ECM stimulates differentiation of osteoblasts through the elevation of phosphorylation of p38 MAPK. First, mechanical stimulation reduced the phosphorylation of eIF2. Furthermore, flow pre-treatment reduced thapsigargin-induced cell mortality through suppression of phosphorylation of protein kinase RNA-like ER kinase (Perk). However, H2O2-driven cell mortality, which is not mediated by Perk, was not suppressed by mechanical stimulation. Second, in the ECM geometry study, the expression of the active (phosphorylated) form of p130Cas, focal adhesion kinase (FAK) and extracellular signal-regulated protein kinase (ERK) was reduced in cells grown in the 3D matrix. Conversely, phosphorylation of p38 MAPK was elevated in the 3D matrix and its up-regulation was linked to an increase in mRNA levels of dentin matrix protein 1 and bone sialoprotein. In summary, our observations suggest the pro-survival role of mechanical stimulation and the modulation of osteoblastic fates by ECM geometry.

Indiana University-Purdue University Indianapolis (IUPUI) / Glycogen is a major energy reserve in most eukaryotes and its rate of synthesis is controlled by glycogen synthase. The activity of eukaryotic glycogen synthase is regulated by the allosteric activator glucose-6-phosphate, which can overcome the inhibitory effects of phosphorylation. The effects of phosphorylation and glucose-6-phosphate on glycogen synthase are mediated by a cluster of six arginines located within a stretch of 12 amino acids near the C-terminus of the enzyme’s polypeptide chain. We studied isoform-2 of yeast glycogen synthase as a model to study the structural and molecular mechanisms that underlie the regulation of the eukaryotic enzymes and our primary tools of investigation were macromolecular X-ray crystallography, site-directed mutagenesis, intein-mediated peptide ligation and enzyme assays. We have solved the tetrameric structure of the yeast enzyme in two different activity states; the resting enzyme and the activated state when complexed with glucose-6-phosphate. Binding of glucose-6-phosphate to glycogen synthase induces large conformational changes that free the active site of the subunits to undergo conformational changes necessary to catalyze the reaction. Further, using site directed mutagenesis and intein-mediated peptide ligation to create specific phosphorylation states of the enzyme we were able to define specific roles for the arginine residues that mediate the regulatory effects of phosphorylation and glucose-6-phosphate activation. Based on these studies, we propose a three state structural model for the regulation of the enzyme, which relate the observed conformational states to specific activity levels. In addition to these regulatory studies, we have also solved the structure of the enzyme complexed with UDP and with substrate analogs, which provide detailed insight into the catalytic mechanism of the enzyme and the ability of glycogen synthase to remain tightly bound to its substrate glycogen.

BACKGROUND/OBJECTIVE: Converging evidence in recent years suggests growth chondrocytes, involved in the integral process of endochondral bone formation and fracture healing, exhibit a dynamic bioenergetic profile despite residing in the nutrient poor cartilaginous environment. Specifically, chondrocytes show an increased dependence on mitochondrial derived oxidative phosphorylation during differentiating, collagen product, but to a differing extent when mineralizing. Therefore, quantitative analysis of mitochondrial dynamics during these varying processes serves to corroborate existing metabolic studies and further elucidate the role of oxidative metabolism during the endochondral process. METHODS: The murine chondroprogenitor cell line ATDC5 was used, and groups were cultured in differentiating, collagen promoted, and mineralizing conditions. Fluorescence confocal 3D image acquisition and bioimaging analysis was used to quantify changes in mitochondrial volume and branch length per mitochondria along with organization and colocalization changes of the actin cytoskeleton to mitochondria in the various conditions over 21 days. RESULTS: We showed that chondrocyte differentiation resulted in significantly increased mitochondrial volume and fusion when compared to non-differentiating groups, and in collagen promoted groups, mitochondrial volume was significantly higher. Additionally, we showed that the process of mineralization resulted in a significant decrease in mitochondrial volume and branch length per mitochondria by day 21 of the experiment. Finally, colocalization analyses of the actin cytoskeleton to mitochondria showed significantly increased overlap in non-differentiating cells when compared to differentiating conditions. CONCLUSIONS: These findings suggest that collagen production is likely an energetically taxing process and mineralization does not heavily rely on oxidative metabolism. Furthermore, the actin cytoskeleton likely plays a role in mitochondrial remodeling that coincides with mitochondrial fission and fusion; increased fission is associated with actin accumulation to mitochondria and fusion is associated with actin disassociation from the outer mitochondrial membrane.

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