FKBP-65 is a member of the immunophilin class of proteins consisting primarily of the cyclophilins and the FKBP's which bind the immunosuppressant drugs cyclosporin A and FK506, respectively. Immunophilins possess peptidylprolyl cis-trans isomerase (PPiase) activity which is inhibited upon binding of their respective macrolides. Specific cellular targets of most immunophilins and the role of PPiase activity in vivo remain largely unknown. FKBP-65 has been proposed as a molecular chaperone of tropoelastin (TE), the soluble precursor of elastin (Davis et al. 1998). TE contains 12% proline residues, many of which are found in VPGVG repeats. When P2 is in the trans conformation, these motifs form repeated type-II ~-turns and ~-spirals resulting in selfassociation of TE via an inverse temperature-dependent transition known as coacervation. Coacervation can be monitored by turbidity increases at 300 nm. We have used purified recombinant FKBP-65 in coacervation assays with chick aorta TE to show that FKBP65 specifically affects the coacervation characteristics of TE in a concentration-dependant manner. The overall extent of coacervation of TE could be increased by more than 2-fold over controls by inclusion of nM amounts of FKBP-65 in the assay. Also, FKBP-65 decreases the coacervation onset temperature of TE by 5-l 0°C. Structural evidence suggests that the influence of FKBP65 on tropoelastin coacervation may be due to its ability to increase the ~ structural content of tropoelastin. These results suggest that FKBP-65 may be a physiologically relevant, TE-specific molecular chaperone. / Thesis / Master of Science (MSc)

The principal aim of this study was to discover, through virtual screening, new nonimmunosuppressive inhibitors for the human immunophilin FKBP12, a target of the immunosuppressant drugs rapamycin and FK506. The enzyme acts as peptidyl-prolyl isomerase catalysing protein folding in the cell. Structurally similar isomerase domains are important for molecular recognition in multi-domain chaperone proteins. FKBP inhibitors have been shown to have protective effects against nerve damage and are therefore interesting targets for the treatment of neurodegenerative diseases. Virtual screening has been used to discover novel inhibitors for protein drug targets. Recent advances in computational power and the availability of large virtual libraries, such as the EDULISS database at Edinburgh University, have enhanced the appeal of this approach. X-ray structures of known protein-ligand complexes were examined to obtain an understanding of the key non-covalent interactions in the FKBP12 binding pocket. Virtual screening hits were selected using macromolecular docking and programs that employed a ligand-based approach. The bulk of the virtual screening in this study used Edinburgh University’s in-house program LIDAEUS. In the course of this study nearly three hundred compounds were screened in the laboratory using biophysical and biochemical binding assays. Thirty four compounds were found to have an affinity for FKBP12 of less than one hundred micromolar. To test virtual hits, it was necessary to select the most appropriate medium-throughput biophysical assay. The aim was to employ methods with sufficient sensitivity to detect compounds with affinity in the order of one hundred micromolar, coupled with the capacity to screen hundreds of compounds in a week. This study used a wide variety of biophysical techniques, these including: electrospray ionisation mass spectrometry, surface plasmon resonance and isothermal titration calorimetry. There was a particular emphasis on the quality of data from electrospray ionisation mass spectrometry. A correlation was found between the cone voltages that gave 50 % dissociation of the complex with the enthalpic contribution to the free energy of binding. From the careful examination of the differences in charge-state distributions between a pure protein and a protein-ligand mixture, it was possible to determine if a protein-ligand complex had been present in solution prior to dissociation during the electrospray process. This observation provides the basis for an assay that could be of general utility in detecting very weak inhibitors.

The Sun is the ultimate energy source on Earth. Photosynthetic organisms are able to catalyze the conversion of solar energy to chemical energy by a reaction called photosynthesis. In plants, this process occurs inside a green organelle called the chloroplast. The protein complexes involved in the photosynthetic light reactions are situated in the thylakoid membrane, which encloses a tiny space called lumen. The Peptidyl-Prolyl cis-trans Isomerase (PPIase) family is the most abundant protein family in the thylakoid lumen. The three PPIase subfamilies, cyclophilins, FKBPs (FK506 binding proteins) and parvulins form a group by their enzymatic activity despite lack of sequence similarity between the subfamilies. Cyclophilins and FKBPs, collectively called immunophilins, were originally discovered as the targets of the immunosuppressive drugs cyclosporine A and FK506, respectively. By suppressing the immune response in humans, these immunophilin-drug complexes revolutionized the field of organ transplantation by preventing graft rejection. Cis-trans isomerization of peptide bonds preceding the amino acid proline is the rate-limiting step of protein folding and several immunophilins have been shown to be important for catalysis of protein folding in vivo. PPIases have been found to be part of large protein complexes as well as in functions such as signalling, protein secretion, RNA processing and cell cycle control. A picture is therefore emerging in which the actual interaction between the PPIase and its target is perhaps more important than the PPIase activity. In the present work, PPIases have been characterized in the chloroplast thylakoid lumen of Spinacia oleracea (spinach) and Arabidopsis thaliana (Arabidopsis). The most active PPIase in the spinach lumen was identified as the cyclophilin TLP20. AtCYP20-2, the Arabidopsis homologue of TLP20, was found to be upregulated at high light and attached to the thylakoid membrane, more precisely to the outer regions of photosystem II supercomplexes. In Arabidopsis, up to 5 cyclophilins and 11 FKBPs were predicted to reside in the lumen. Of these 16 immunophilins, only 2 were identified as active PPIases and significant differences were observed between the two plant species. AtCYP20-2, like TLP20, is an active isomerase although AtFKBP13 is the most active PPIase in the lumen of Arabidopsis. Mutant Arabidopsis plants deficient in AtCYP20-2 displayed no phenothypical changes or decrease in total lumenal PPIase activity. Being the only active PPIase in the mutants, the redox sensitive AtFKBP13 is proposed to compensate for the lack of AtCYP20-2 by oxidative activation. In agreement with the experimental data, the sequence analyses of catalytic domains of lumenal immunophilins demonstrate that only AtCYP20-2 and AtFKBP13 possess the amino acids found essential for PPIase activity in earlier studies of human cyclophilin A and FKBP12. It is concluded that with the exception of AtCYP20-2 and AtFKBP13 most immunophilins in the lumen of Arabidopsis lost their PPIase activity on peptide substrates and developed other specialized functions.

The involvement of mitochondrial signaling in mammalian PCD regulation has been examined extensively via biochemical analyses and cellular studies in vitro. However there still exist considerable gaps in our knowledge regarding its contribution in specific tissues and cell types during mammalian development in vivo. In addition, given the numerous pathologic conditions associated with aberrant PCD, modulation of this signaling process represents an attractive target for therapeutic intervention. In this thesis I have therefore examined the regulation of mitochondrion-mediated PCD signaling as it pertains to several forms of developmental and injury-induced cell death. In the first component of the thesis I have examined the differential sensitivity of Bcl2 on the survival of motor neuron populations from two distinct developmental origins (alpha and gamma motor neurons), demonstrating that gamma motor neurons are preferentially affected in Bcl2 null mice. Thus, Bcl-2 plays a critical in vivo in regulating subtype-specific motor neuron survival during development. In the second study I have demonstrated that a major portion of the neuroprotective effect exerted by the immunophilins cyclosporin A and FK-506 are mediated through calcineurin signaling; rather than MOMP-mediated events as previously held. Additional findings of this study demonstrated the first neuroprotective effects of the pyrethroid insecticide cypermethrin and calcineurin-mediated control of Bad phosphorylation. Such findings establish a link between calcineurin signaling and mitochondrion-mediated cell survival. The above studies established critical features of mitochondrion-mediated PCD in regulating survival of several neuronal subpopulations. I therefore followed these studies with an examination of how post-mitochondrial PCD signaling is regulated following MOMP permeabilization. Specifically I examined regulation of the Smac-IAP-caspase axis, investigating how combinatorial deletion of Casp3 and Diablo alter PCD progression in mouse embryonic fibroblasts. Using a series of injury stimuli in the context of biochemical and cellular analyses I have developed a model of how endogenous Smac/DIABLO regulates executioner caspase activity. Collectively these studies elucidate key aspects of mitochondrial signaling during both developmental and injury-induced PCD in vivo.

The involvement of mitochondrial signaling in mammalian PCD regulation has been examined extensively via biochemical analyses and cellular studies in vitro. However there still exist considerable gaps in our knowledge regarding its contribution in specific tissues and cell types during mammalian development in vivo. In addition, given the numerous pathologic conditions associated with aberrant PCD, modulation of this signaling process represents an attractive target for therapeutic intervention. In this thesis I have therefore examined the regulation of mitochondrion-mediated PCD signaling as it pertains to several forms of developmental and injury-induced cell death. In the first component of the thesis I have examined the differential sensitivity of Bcl2 on the survival of motor neuron populations from two distinct developmental origins (alpha and gamma motor neurons), demonstrating that gamma motor neurons are preferentially affected in Bcl2 null mice. Thus, Bcl-2 plays a critical in vivo in regulating subtype-specific motor neuron survival during development. In the second study I have demonstrated that a major portion of the neuroprotective effect exerted by the immunophilins cyclosporin A and FK-506 are mediated through calcineurin signaling; rather than MOMP-mediated events as previously held. Additional findings of this study demonstrated the first neuroprotective effects of the pyrethroid insecticide cypermethrin and calcineurin-mediated control of Bad phosphorylation. Such findings establish a link between calcineurin signaling and mitochondrion-mediated cell survival. The above studies established critical features of mitochondrion-mediated PCD in regulating survival of several neuronal subpopulations. I therefore followed these studies with an examination of how post-mitochondrial PCD signaling is regulated following MOMP permeabilization. Specifically I examined regulation of the Smac-IAP-caspase axis, investigating how combinatorial deletion of Casp3 and Diablo alter PCD progression in mouse embryonic fibroblasts. Using a series of injury stimuli in the context of biochemical and cellular analyses I have developed a model of how endogenous Smac/DIABLO regulates executioner caspase activity. Collectively these studies elucidate key aspects of mitochondrial signaling during both developmental and injury-induced PCD in vivo.

La réplication et l’assemblage du virus de l’hépatite C (VHC) sont régulés finement dans le temps et l’espace par les interactions protéiques entre le virus avec l’hôte. La compréhension de la biologie du virus ainsi que sa pathogénicité passe par les connaissances relatives aux interactions virus/hôte. Afin d’identifier ces interactions, nous avons exploité une approche d’immunoprécipitation (IP) couplée à une détection par spectrométrie de masse (MS), pour ensuite évaluer le rôle des protéines identifiées dans le cycle viral par une technique de silençage génique. Les protéines virales Core, NS2, NS3/4A, NS4B, NS5A et NS5B ont été exprimées individuellement dans les cellules humaines 293T et immunoprécipitées afin d’isoler des complexes protéiques qui ont été soumis à l’analyse MS. Ainsi, 98 protéines de l’hôte ont été identifiées avec un enrichissement significatif et illustrant une spécificité d’interaction. L’enrichissement de protéines connues dans la littérature a démontré la force de l’approche, ainsi que la validation de 6 nouvelles interactions virus/hôte. Enfin, le rôle de ces interactants sur la réplication virale a été évalué dans un criblage génomique par ARN interférant (ARNi). Deux systèmes rapporteurs de la réplication virale ont été utilisés : le système de réplicon sous-génomique (Huh7-Con1-Fluc) et le système infectieux (J6/JFH-1/p7Rluc2a), ainsi qu’un essai de toxicité cellulaire (Alamar Blue). Parmi les protéines de l’hôte interagissant avec le VHC, 28 protéines ont démontré un effet significatif sans effet de toxicité cellulaire, suggérant fortement un rôle dans la réplication du VHC. Globalement, l’étude a mené à l’identification de nouvelles interactions virus/hôte et l’identification de nouvelles cibles thérapeutiques potentielles. / Hepatitis C virus (HCV) replication and assembly are tightly regulated in time and space within the cell, most likely due to protein interactions between virus and host. In order to better understand HCV biology and its pathogenesis, there is a need to unravel virus/host interaction network. We extended our knowledge of virus/host interactions by the identification of cellular proteins associated to HCV proteins using an immunoprecipitation (IP) technique coupled to mass spectrometry (MS), and further evaluate the role of retrieved interactors using gene knockdown. FLAG-tagged viral proteins Core, NS2, NS3/4A, NS4B, NS5A and NS5B have been expressed individually in 293T human cells, and immunoprecipitated protein complexes have been submitted to MS analysis for identification of host proteins. In this study, 98 proteins were significantly enriched and showed specific interaction to a viral protein. Retrieval of previously characterized interacting proteins proved the strength of the method. Six newly identified interactors by MS were individually confirmed using IP of viral proteins. We evaluated the role of identified interactors in HCV replication by performing a functional lentivirus-based RNA interference (RNAi) screen. Two reporter systems were used: the sub- genomic replicon (Huh7-Con1-Fluc) and a full length infectious clone (J6/JFH-1/p7Rluc2a), as well as the cellular toxicity assay Alamar blue. Of the identified host interactors, 28 proteins showed a significant effect on HCV replication upon gene knockdown and without cellular toxicity. Overall, the study led to the identification of novel virus/host interactions essential in HCV life cycle and provides novel potential drug targets.

La réplication et l’assemblage du virus de l’hépatite C (VHC) sont régulés finement dans le temps et l’espace par les interactions protéiques entre le virus avec l’hôte. La compréhension de la biologie du virus ainsi que sa pathogénicité passe par les connaissances relatives aux interactions virus/hôte. Afin d’identifier ces interactions, nous avons exploité une approche d’immunoprécipitation (IP) couplée à une détection par spectrométrie de masse (MS), pour ensuite évaluer le rôle des protéines identifiées dans le cycle viral par une technique de silençage génique. Les protéines virales Core, NS2, NS3/4A, NS4B, NS5A et NS5B ont été exprimées individuellement dans les cellules humaines 293T et immunoprécipitées afin d’isoler des complexes protéiques qui ont été soumis à l’analyse MS. Ainsi, 98 protéines de l’hôte ont été identifiées avec un enrichissement significatif et illustrant une spécificité d’interaction. L’enrichissement de protéines connues dans la littérature a démontré la force de l’approche, ainsi que la validation de 6 nouvelles interactions virus/hôte. Enfin, le rôle de ces interactants sur la réplication virale a été évalué dans un criblage génomique par ARN interférant (ARNi). Deux systèmes rapporteurs de la réplication virale ont été utilisés : le système de réplicon sous-génomique (Huh7-Con1-Fluc) et le système infectieux (J6/JFH-1/p7Rluc2a), ainsi qu’un essai de toxicité cellulaire (Alamar Blue). Parmi les protéines de l’hôte interagissant avec le VHC, 28 protéines ont démontré un effet significatif sans effet de toxicité cellulaire, suggérant fortement un rôle dans la réplication du VHC. Globalement, l’étude a mené à l’identification de nouvelles interactions virus/hôte et l’identification de nouvelles cibles thérapeutiques potentielles. / Hepatitis C virus (HCV) replication and assembly are tightly regulated in time and space within the cell, most likely due to protein interactions between virus and host. In order to better understand HCV biology and its pathogenesis, there is a need to unravel virus/host interaction network. We extended our knowledge of virus/host interactions by the identification of cellular proteins associated to HCV proteins using an immunoprecipitation (IP) technique coupled to mass spectrometry (MS), and further evaluate the role of retrieved interactors using gene knockdown. FLAG-tagged viral proteins Core, NS2, NS3/4A, NS4B, NS5A and NS5B have been expressed individually in 293T human cells, and immunoprecipitated protein complexes have been submitted to MS analysis for identification of host proteins. In this study, 98 proteins were significantly enriched and showed specific interaction to a viral protein. Retrieval of previously characterized interacting proteins proved the strength of the method. Six newly identified interactors by MS were individually confirmed using IP of viral proteins. We evaluated the role of identified interactors in HCV replication by performing a functional lentivirus-based RNA interference (RNAi) screen. Two reporter systems were used: the sub- genomic replicon (Huh7-Con1-Fluc) and a full length infectious clone (J6/JFH-1/p7Rluc2a), as well as the cellular toxicity assay Alamar blue. Of the identified host interactors, 28 proteins showed a significant effect on HCV replication upon gene knockdown and without cellular toxicity. Overall, the study led to the identification of novel virus/host interactions essential in HCV life cycle and provides novel potential drug targets.