The RAS/RAF/MEK/ERK pathway is the prototypical cellular signal transduction cascade and has been the focus of intense scrutiny over the last two decades. As a mitogenic pathway, its activation is a potent driver of cellular growth and survival, and its deregulation underlies many cancers. While RAS family GTPases have long been recognized as prolific human oncogenes, a landmark study in 2002 also established the RAF family kinase as a bona fide oncogene (Davies et al., 2002). Indeed, aberrant RAS-RAF signaling underlies nearly one-third of all human cancers (Wellbrock et al., 2004). Notably, mutations in RAF are found with astounding frequency in certain cancers (e.g. 70% of malignant melanomas) (Dhomen and Marais, 2007). These findings have identified intercepting aberrant RAF function as an ideal therapeutic target. RAF is a Ser/Thr protein kinase and its activity is strictly regulated by a core complex of at least three proteins, namely, KSR, CNK and HYP (Claperon and Therrien, 2007). The mechanism by which the KSR/CNK/HYP complex regulates RAF function remains enigmatic. In particular, the function of KSR in regulating RAF activity is highly controversial. The work described in this thesis was conducted with the aim of: i) understanding the interactions that underlie formation of the KSR/CNK/HYP complex, and ii) elucidating the mechanism by which the complex regulates RAF function. I have attempted to accomplish these aims using a combination of structural biology, biochemistry and cell biology approaches. I begin by presenting the structure of the SAM domain mediated interaction between CNK and HYP. I describe a model for how the CNK/HYP interaction in turn serves to recruit KSR to form the higher-order KSR/CNK/HYP complex. Subsequently, I describe the allosteric mechanism by which KSR controls RAF activation via the formation of specific side-to-side kinase domain heterodimers of KSR and RAF. Lastly, I describe a potential mechanism by which RAS directly mediates the attainment of the side-to-side dimer configuration of RAF through its own ability to form dimers. The acquisition of the side-to-side dimer configuration is essential for aberrant RAF signaling in cancers, suggesting future RAF inhibition strategies could be aimed at preventing dimer formation.

While protein tyrosine kinases (PTKs) have been extensively characterized in eukaryotes, far less is known about their emerging counterparts in prokaryotes. Studies of close to 20 homologs of bacterial protein tyrosine (BY) kinases have inaugurated a blooming new field of research, all since just the end of the last decade. These kinases are key regulators in the polymerization and exportation of the virulence-determining polysaccharides which shield the bacterial from the non-specific defenses of the host. This research is aimed at furthering our understanding of the BY kinases through the use of X-ray crystallography and various in vitro and in vivo experiments. We reported the first crystal structure of a bacterial PTK, the C-terminal kinase domain of E. coli tyrosine kinase (Etk) at 2.5Å resolution. The fold of the Etk kinase domain differs markedly from that of eukaryotic PTKs. Based on the observed structure and supporting evidences, we proposed a unique activation mechanism for BY kinases in Gram-negative bacteria. The phosphorylation of tyrosine residue Y574 at the active site and the specific interaction of P-Y574 with a previously unidentified key arginine residue, R614, unblock the Etk active site and activate the kinase. Both in vitro kinase activity and in vivo antibiotics resistance studies utilizing structure-guided mutants further support the novel activation mechanism. In addition, the level of phosphorylation of their C-terminal Tyr cluster is known to regulate the translocation of extracellular polysaccharides. Our studies have significantly clarified our understanding of how the phosphorylation status on the C-terminal tyrosine cluster of BY kinases affects the oligomerization state of the protein, which is likely the machinery of polysaccharide export regulation. In summary, this research makes a substantial contribution to the rapidly progressing research of bacterial tyrosine kinases. / Thesis (Ph.D, Biochemistry) -- Queen's University, 2008-09-26 12:45:02.924

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Kinases play a crucial role in regulating cellular signaling cascades, making them therapeutic targets for several human diseases. In human cancers, mis-regulation and mutations of kinases such as EGFR (epidermal growth factor receptor) have been found to drive malignant transformation. Due to the conserved structural elements of protein kinases, the majority of kinase inhibitors available have a tendency to inhibit multiple targets. The biological impact of this promiscuity is insufficiently defined and the prevalence of cellular compensatory mechanisms additionally varies the clinical responses to drug treatment. In order to understand the relationship between selectivity and efficacy, prior to clinical trials, it is essential to characterize how inhibitors interact with the kinome within a cellular context. Monitoring inhibitor-target interactions generally involves in vitro assaying with purified proteins or protein domains, which compromises the native integrity of the kinases. Cellbased assays either gain outcomes from bulk populations that average out cell variance or phenotypic assays that lack molecular resolution. To obtain information on drug interactions on a single cell level, we have developed a method to measure the direct binding of kinase inhibitors to their targets in situ and in vivo. Kinase inhibitors are chemically tagged with fluorophores that serve as acceptors to genetically tagged donor fluorophores on the enzyme and the interaction is measured using FRET-FLIM. With epidermal growth factor receptor (EGFR) and irreversible EGFR inhibitors as the model system, this approach has been applied to image inhibitor-kinase interactions in live and fixed cells. Using this method, a small panel of tyrosine kinase targets, and labeled inhibitors, we were able to investigate the cross-specificity within the panel. Additionally it was found that the specificity of inhibitors for specific kinase conformations enables the distinction between EGFR in the active and inactive conformation by the inhibitor-probes. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2011.

The RAS/RAF/MEK/ERK pathway is the prototypical cellular signal transduction cascade and has been the focus of intense scrutiny over the last two decades. As a mitogenic pathway, its activation is a potent driver of cellular growth and survival, and its deregulation underlies many cancers. While RAS family GTPases have long been recognized as prolific human oncogenes, a landmark study in 2002 also established the RAF family kinase as a bona fide oncogene (Davies et al., 2002). Indeed, aberrant RAS-RAF signaling underlies nearly one-third of all human cancers (Wellbrock et al., 2004). Notably, mutations in RAF are found with astounding frequency in certain cancers (e.g. 70% of malignant melanomas) (Dhomen and Marais, 2007). These findings have identified intercepting aberrant RAF function as an ideal therapeutic target. RAF is a Ser/Thr protein kinase and its activity is strictly regulated by a core complex of at least three proteins, namely, KSR, CNK and HYP (Claperon and Therrien, 2007). The mechanism by which the KSR/CNK/HYP complex regulates RAF function remains enigmatic. In particular, the function of KSR in regulating RAF activity is highly controversial. The work described in this thesis was conducted with the aim of: i) understanding the interactions that underlie formation of the KSR/CNK/HYP complex, and ii) elucidating the mechanism by which the complex regulates RAF function. I have attempted to accomplish these aims using a combination of structural biology, biochemistry and cell biology approaches. I begin by presenting the structure of the SAM domain mediated interaction between CNK and HYP. I describe a model for how the CNK/HYP interaction in turn serves to recruit KSR to form the higher-order KSR/CNK/HYP complex. Subsequently, I describe the allosteric mechanism by which KSR controls RAF activation via the formation of specific side-to-side kinase domain heterodimers of KSR and RAF. Lastly, I describe a potential mechanism by which RAS directly mediates the attainment of the side-to-side dimer configuration of RAF through its own ability to form dimers. The acquisition of the side-to-side dimer configuration is essential for aberrant RAF signaling in cancers, suggesting future RAF inhibition strategies could be aimed at preventing dimer formation.

Protein kinases comprise a fundamental class of cell function regulators that modify proteins by transferring phosphate groups from a nucleoside triphosphate such as ATP to specific amino acid residues on target proteins, altering protein conformation, function, and activity. As such, protein kinases are major regulators of many biological processes, including gene expression, which consists of the transfer of hereditary information in two major processing steps, transcription of DNA into a complementary precursor RNA transcript (pre-mRNA) and its subsequent translated into protein by the ribosome, where it can then go on to perform various processes in the cell. One particular family of protein kinases, otherwise known as serine/arginine protein-specific protein kinases (SRPKs), is conserved throughout eukaryotes and has been shown to be important in regulating gene expression, yet their roles in the gene expression pathway have yet to be elucidated. SRPK are known to phosphorylate serine/arginine (SR) splicing factor proteins, which are involved in mRNA splice site recognition and recruitment of splicing machinery. Members of the LAMMER kinase subfamily of SRPKs have also been shown to be required for efficient pre-mRNA splicing and important for mediating cellular progression through the cell cycle. To determine what other roles SRPKs play in mRNA processing, it is of use to study the homologous SRPK and LAMMER kinases in fission yeast, S. pombe, Dsk1 and Kic1, respectively. S. pombe provides a genetically valuable model for studying kinase function in RNA processing as both RNA processing machinery and SRPKs are conserved through higher eukaryotes. Using a novel green fluorescent protein tagging system based on properties of the MS2 bacteriophage genome, we are able to label specific mRNA transcripts of interest and visualize their locations in the cell using fluorescence microscopy. By visualizing the mRNA trafficking patterns of intron-containing and intronless mRNA transcripts, we show for the first time that deletions of the Dsk1 and Kic1 genes result in the nuclear retention of mRNA, such that Dsk1 and Kic1 are distinctly involved in mRNA export out of the nucleus.

Immunosenescence results in reduced immune response to infections with Streptococcus pneumoniae as well as to pneumococcal polysaccharide vaccines. The antibody response to the capsular polysaccharide (CPS) provides protection against S. pneumoniae infection. CPS immunoresponse is T cell independent and needs the macrophage-derived cytokines such as IL-12, IL-6 and IL-1β to elicit an antibody response. We showed a cytokine dysregulation, i.e. a decrease in IL-12, IL-6 and TNF-α but an increase in IL-10, in the aged (18-24 months old comparable to >65 years in human) compared to young adult mouse (8-12 weeks less than 65 years old) splenic macrophages (SM) or bone marrow derived macrophages (BMDM) activated via TLR4, TLR2 or TLR9 as well as heat killed Streptococcus pneumoniae (HKSP). There is also an age-associated defect in splenic B cells in the production of IgG3 upon stimulation with these ligands. A microarray analysis in SM followed by validation by both qt-RTPCR and western blots indicated that this age-associated defect in aged SM, BMDM and B cells was due to a heightened activity of the PI3K-Akt signaling pathway. We hypothesized that the senescence of immune responses in macrophages and B cells is due to an increase in activity of PI3K/Akt and decrease in the activity of GSK-3, the downstream kinase. Inhibition of the PI3-kinase with either LY294002 or Wortmannin restored the TLR2, 4, 9 and HKSP induced cytokine phenotype of the aged to that of the young adult in both the SM and BMDM and an enhanced IgG3 production in aged mice. We also showed that inhibition of glycogen synthase kinase-3 (GSK-3) the downstream target of the PI3K-Akt signaling pathway with SB216763 in SM, BMDM and B cells resulted in an enhancement in production of IL-10, IL-6 and IL-1β by macrophages and in B cell activation. Treatment of B cells with SB216763 in the presence of ligands for TLR-1/2, 4 or 9 as well as HKSP under in vitro conditions led to enhanced production of IgG3 and IgA, plasma cell formation and a slight increase in the proliferation of the B-cells with no adverse effects on the viability of the cells. Therefore, targeting the PI3K-AKT-GKS-3 signaling pathway could rescue the intrinsic signaling defect in the aged macrophages, increase IL-12 and IL-6, and enhance anti-CPS antibody responses.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 4 uppsatser.

Thesis (Ph. D.)--Case Western Reserve University, 2007. / [School of Medicine] Department of Pharmacology. Includes bibliographical references.

Diss. (sammanfattning) Stockholm : Karol. inst., 2005. / Härtill 4 uppsatser.