PTP69D is a receptor protein tyrosine phosphatase (RPTP) with two intracellular catalytic domains (Cat1 and Cat2), which has been shown to play a role in axon outgrowth and guidance of embryonic motorneurons, as well as targeting of photoreceptor neurons in the visual system of Drosophila melanogaster. Here, we characterized the developmental role of PTP69D in the giant fiber (GF) neurons; two interneurons in the central nervous system (CNS) that control the escape response of the fly. In addition to guidance and targeting functions, our studies reveal an additional role for PTP69D in synaptic terminal growth in the CNS. We found that inhibition of phosphatase activity in catalytic domain (Cat1) proximal to the transmembrane domain did not affect axon guidance or targeting but resulted in stunted terminal growth of the GFs. Cell autonomous rescue and knockdown experiments demonstrated a function for PTP69D in the GFs, but not its postsynaptic target neurons. In addition,complementation studies and structure-function analyses revealed that for GF terminal growth, Cat1 function of PTP69D requires the immunoglobulin and the Cat2 domain but not the fibronectin type III repeats nor the membrane proximal region. In contrast, the fibronectin type III repeats, but not the immunoglobulin domains, were previously shown to be essential for axon targeting of photoreceptor neurons. Thus, our studies uncover a novel role for PTP69D in synaptic terminal growth in the CNS that is mechanistically distinct from its function during earlier developmental processes. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2014. / FAU Electronic Theses and Dissertations Collection

Thesis (Ph. D.)--University of Alabama at Birmingham, 2008. / Title from first page of PDF file (viewed June 6, 2008). Includes bibliographical references.

Thesis (Ph. D.)--University of Oklahoma. / Bibliography: leaves 135-155.

A proteína tirosina fosfatase eta de rato (rPTPeta), é uma RPTP transmembranar do tipo classe I. A rPTP eta e seu homólogo DEP-1 provenientes, respectivamente, de ratos e de humanos, estão inibidas em células neoplásicas. Este fenótipo maligno é revertido após reconstituição exógena, o que sugere que a capacidade restauradora da rPTP eta pode ser uma ferramenta importante na terapia de alguns tipos de câncer. Portanto, o objetivo deste projeto incluiu o estudo molecular, biofísico e estrutural do domínio catalítico da rPTPeta (rPTPetaDC). Para isso, sub-clonamos no vetor pET-28a(+) o inserto que codifica para a região C-terminal da rPTPeta . Em seguida, bactérias E. coli da linhagem BL21 (DE3) foram transformadas com o plasmídeo e a proteína recombinante expressada e purificada. A His6-rPTPetaDC purificada teve a cauda de histidina subseqüentemente removida por digestão com trombina. O ponto isoelétrico de 7,3 da proteína de 41kDa foi medido experimentalmente e a sua funcionalidade acessada pelo ensaio de hidrólise do pNPP. A enzima apresentou uma atividade específica de 9nmol/min/microg a qual é compatível com as atividades específicas descritas para as RPTPu, RPTPalfa, PTPB1 e SHP2. A estrutura secundária e a estabilidade da rPTPetaDC recombinante foi analisada por dicroísmo circular e espectroscopia de fluorescência. A rPTPetaDC mostrou-se estável a 18 graus Celsius e propriamente enovelada (Santos, et al., Prot. Expr. Purif., 2005. Anexo A). A proteína foi, em seguida, submetida a diferentes condições de cristalização e a estudos estruturais em solução. Nas condições de 0,1M de MES, pH 6,5 e 20% PEG 10000 cresceram cristais que difrataram na resolução de 1,87Å. Os cristais pertencem ao grupo espacial P2(1)2(1)2(1) com parâmetros de célula unitária: a=46,46; b=63,07; c=111,64 Å, e com uma única molécula por unidade assimétrica (Matozo, et al., Acta crystallogr. F, 2006. Anexo B). A estrutura da rPTPetaDC, em solução, foi analisada usando-se a técnica de SAXS e medidas de anisotropia de fluorescência. Os dados de SAXS mostraram que a proteína, forma dímeros alongados, com Rg de 2,65nm e Dmax de 8,5nm. A conformação da rPTPetaDC analisada por modelos de homologia sugere que seu dímero está mais próxima da estrutura cristalográfica dimérica da RPTPalfa-D1. Alem disso, a caracterização da rPTPetaDC por anisotropia de fluorescência demonstrou que o Kd do dímero da rPTPetaDC é de 21,6 + 2,0uM e a variação da energia livre de Gibbs dímero-monômero é de 7,2kcal/mol (Mtozo, et al., Biophys. J., 2007. Anexo C ). / The rat protein tyrosine phosphatase eta, rPTPeta, is a transmembrane RPTP, with an intracellular portion composed of a unique catalytic region. The rPTPeta and the human homolog DEP-1 are down-regulated in rat and human neoplastic cells, respectively. However, the malignant phenotype is reverted after exogenous reconstitution of rPTPeta, suggesting that its function restoration could be an important tool for gene therapy of several types of cancer. Therefore, the objective of our project aimed on the molecular, biophysical and structural study of the catalytic domain of rPTPeta, rPTPetaDC. We began our study cloning the rPTPetaDC into PET28a(+) vector, followed by its expression in Escherichia coli, and purification. The His6-tag from the rPTPetaDC purified was subsequently removed by thrombin digestion. PhastGel IEF electrophoresis demonstrated that the isoelectric point of the 41kDa was 7.3. To assess the functionality of the rPTPetaDC we used the pNPP hydrolysis assay and observed that the enzyme has a specific activity of 9nmol/min/ug. The experimentally determined rPTPetaDC specific activity showed to be in the same range as the previously reported activities for RPTPu, RPTPalfa, PTPB1 and SHP2. The secondary structure and stability of the recombinant protein was analyzed by circular dichroism and fluorescence spectroscopy. The results demonstrated that rPTPetaDC was stable at 18 Celsius and properly folded (Santos, et al., Prot. Expr. Purif., 2005. In attachment A). Then, the purified protein was submitted to different crystallization conditions and structural studies in solution. Crystals appeared at 0.1M MES, pH 6.5 and 20% PEG 10,000 and diffracted with resolution of 1.87Å. The crystals belong to spatial group P2(1)2(1)2(1) with unit cell parameters of a=46.46, b=63.07, c=111.64Å and contained one molecule for asymmetric unit (Matozo, et al., Acta crystallog. F, 2006. In attachment B). Also, the structural of rPTPetaDC, in solution, was analyzed by SAXS and fluorescence anisotropy. SAXS data showed that the protein forms elongated dimers in solution with an Rg of 2.65nm and a Dmax of 8.5nm. The rPTPetaDC conformation in solution, studied by homology models, suggested that the rPTPetaDC dimer architecture is more closely related to the crystal structure of RPTPalfa-D1. The characterization of rPTPetaDC by fluorescence anisotropy measurements demonstrated that the Kd of the dimer is 21.6 + 2.0uM and the energy Gibbs dimer-monomer is equal to 7.2kcal/mol (Matozo, et al., Bioph. J., 2007. In attachment C).

Orientador: Kleber Gomes Franchini / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências Medicas / Made available in DSpace on 2018-08-17T05:12:29Z (GMT). No. of bitstreams: 1 Marin_TalitaMiguel_D.pdf: 34867811 bytes, checksum: 839d8dbb3d76170bebebbc5e8619b847 (MD5) Previous issue date: 2010 / Resumo: Estudos do nosso laboratório demonstraram que a quinase de adesão focal (FAK) é ativada e contribui para a regulação dos mecanismos de sinalização que determinam as alterações fenotípicas de cardiomiócitos submetidos a estímulos mecânicos. Em estudo anterior demonstramos através da inibição farmacológica da Shp2, que a mesma contribui para a regulação do nível de fosforilação em resíduos de tirosina (atividade) da FAK e regulação da expressão de genes associados ao fenótipo hipertrófico em células em cultura. O presente estudo foi realizado para examinar o impacto da depleção da Shp2,induzida por silenciamento gênico, na atividade da FAK e nas alterações fenotípicas de Miócitos Ventriculares de Ratos Neonatos (MVRNs) em condições basais e de estímulo mecânico e os efeitos da introdução de mutações no gene da Shp2, que resultem em perda, ganho ou deleção da proteína, sobre a atividade da FAK e sobre as alterações fenotípicas nos corações de camundongos. A depleção dos níveis protéicos da Shp2 por siRNA específico induziu ao aumento da fosforilação da Tyr397, Src Tyr418, AKT Ser473, TSC2 Thr1462, e S6 quinase Thr389, à re-expressão do gene fetal marcador molecular de hipertrofia cardíaca (?-MHC) e à um fenótipo hipertrófico dos MVRNS não estirados. A inibição da atividade do complexo FAK/Src através do tratamento dos MVRNs com PP2 {4-amino-5-(4-chlorophenyl)-7-(t-butyl)pyrazolo[3,4-d]pyrimidine}aboliu o aumento na fosforilação da AKT, TSC2, e S6 quinase, bem como a hipertrofia dos MVRNs induzida pela depleção da Shp2. A inibição da mTOR (mammalian target of rapamycin) com rapamicina bloqueou o surgimentos da hipertrofia nos MNRNs tratados com siShp2. Os MVRNs tratados com PP2 ou com RNA de interferência, específico para a FAK, apresentaram-se deficientes na ativação e aumento da fosforilação da FAK, Src, ERK (extracellular signal-regulated kinase), AKT, TSC2, e S6 quiinase, e na indução de aumento da área celular em resposta ao estimulo mecânico de estiramento cíclico prolongado in vitro. A Hipertrofia em resposta ao estiramento prolongado também foi prevenida pelo tratamento dos MVRNs com rapamicina. Os resultados são consistentes em apontar que a perda ou diminuição da função da Shp2 (por depleção, mutação ou deleção gênica cardíaco-específica) induz ao aumento da ativação da FAK, AKT e via da mTOR/S6K , que são vias de sinalização sabidamente envolvidas nos processos hipertróficos do miocárdio. Interessantemente os animais portadores de mutação LS-Shp2 apresentaram redução de 50% da atividade fosfatase relacionada ao imunoprecipitado de Shp2 no miocárdio, recapitularam a desordem humana apresentando baixa estatura, dismorfia craniofacial, evidências morfológica, histopatológica, ecocardiográficas e molelculares de presença de cardiomiopatia hipertrófica. Notavelmente o tratamento desses animais com o inibidor específico da mTOR, rapamicina, foi capaz de reverter completamente o fenótipo hipertrófico dos animais LS-Shp2. Consistentemente, o ganho de função da Shp2 (no miocárdio), induzido por mutação NS (Noonan Syndrome), foi acompanhado de diminuição da atividade basal da FAK, bem como da AKT e de proteínas envolvidas na via da mTOR e de redução da área total e largura dos cardiomiócitos adultos quando comparados aos extraídos de animais selvagens. Em conjunto, os dados, aqui apresentados, indicam que a tirosino-fosfatase Shp2 contribui para regular o nível de fosforilação da FAK em cardiomiócitos e para a regulação da expressão de gêneses do programa hipertrófico e do tamanho celular através da modulação da atividade da FAK e mTOR. Sugere também, que a inibição prolongada de Shp2 pode, por si só, induzir ao aparecimento de hipertrofia cardíaca através da FAK pela modulação da via mTOR/S6K / Abstract: Focal Adhesion Kinase (FAK) has been implicated in the sensing and transduction of mechanical forces, which drive changes in cardiac myocyte function and structure, in response to hemodynamic overload, into biochemical events in cardiac myocytes. This study was performed to examine whether Shp2 (Src homology region 2, phosphatase 2) controls Focal Adhesion Kinase (FAK) activity and its trophic actions in cardiomyocytes. Our study was performed in neonatal rat ventricular myocytes subjected to depletion of Shp2 by RNA interference and genetically modified mice carrying mutations that induce gain and loss of function and Shp2 cardiac-specific conditional gene deletion.Depletion of Shp2 by specific small interfering RNA increased the phosphorylation of FAK Tyr397, Src Tyr418, AKT Ser473, TSC2 Thr1462, and S6 kinase Thr389 and induced hypertrophic gene expression pattern (?- MHC) and phenotype of nonstretched NRVMs. Inhibition of FAK/Src activity by PP2 {4-amino-5-(4-chlorophenyl)-7- (t-butyl)pyrazolo[3,4-d]pyrimidine} abolished the phosphorylation of AKT, TSC2, and S6 kinase, as well as the hypertrophy of NRVMs induced by Shp2 depletion. Inhibition of mTOR (mammalian target of rapamycin) with rapamycin blunted the hypertrophy in NRVMs depleted of Shp2. NRVMs treated with PP2 or depleted of FAK by specific small interfering RNA were defective in FAK, Src, extracellular signal-regulated kinase, AKT, TSC2, and S6 kinase phosphorylation, as well as in the hypertrophic response to prolonged stretch. The stretch-induced hypertrophy of NRVMs was also prevented by rapamycin. Subsequently we tested the hypothesis that the introduction of mutations in the Shp2 gene, causing protein deletion or loss of protein function, would contribute to increase the levels of tyrosine phosphorylation of FAK resulting in a hypertrophic phenotype in mice hearts. Likewise, we investigated the possibility that the introduction of a mutation in the Shp2 gene, which leads to gain of function, would result in decrease phosphorylation of FAK. The results were consistent in pointing out that the loss of protein or impairment of the function of Shp2 (gene deletion, depletion or mutation) induces increased activation of FAK, AKT and a the mTOR/S6K pathways, which are signaling pathways known to be involved in controlling cardiac growth and hypertrophy. Ls-Shp2 mice recapitulated the human disorder, with short stature, craniofacial dysmorphia, and morphological, histological, echocardiographic and molecular evidence of hypertrophic cardiomyopathy (HCM). Heart and/or cardiomyocyte lysates from LS-Shp2 mice showed decreased Shp2 catalytic activity, consistent with previous reports that LS mutants have dominant negative effects. Remarkably, the cardiac hypertropic phenotype in LS-Shp2 mice were completely reversed by treatment with the mTOR inhibitor, rapamycin. Consistently, the gain of function of Shp2 (induced by mutation) was accompanied by decreased basal activity of FAK and AKT and proteins involved in the mTOR signaling pathway. These findings demonstrate that basal Shp2 tyrosine phosphatase activity controls the size of cardiomyocytes by downregulating a pathway that involves FAK/Src and mTOR signaling pathways. Our results also establish the tight regulation of FAK phosphorylation by Shp-2 as a potential counter-regulatory signaling in the control of the hyperthophic genetic program in cardiac myocytes / Doutorado / Biologia Estrutural, Celular, Molecular e do Desenvolvimento / Doutor em Fisiopatologia Medica

Orientador: Kleber Gomes Franchini / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas / Made available in DSpace on 2018-08-07T07:19:32Z (GMT). No. of bitstreams: 1 Marin_TalitaMiguel_M.pdf: 14587191 bytes, checksum: b8bac41b29ca5081a5bcb225f83e4773 (MD5) Previous issue date: 2006 / Resumo: Arrazoado. A Quinase de Adesão Focal (FAK) é ativada e contribui para a regulação da sinalização que determina as alterações fenotípicas de cardiomiócitos estimulados mecanicamente. A regulação da atividade da FAK é complexa e depende de mecanismos intramoleculares e da cooperação com a tirosino-quinase Src. Há evidências de que a tirosino-fosfatase SHP-2 contribui para a regulação do nível de fosforilação em resíduos de tirosina e, portanto da atividade da FAK em miócitos ventriculares de ratos neonatos em cultura (MVRNs). Este estudo objetivou examinar se a SHP-2 modula o nível de fosforilação da FAK em MVRNs. Examinamos se em MVRNs controle (i.e. não submetido a estímulo mecânico), a atividade da SHP-2 contribui para o baixo nível de fosforilação em tirosina da FAK e se em MVRNs submetidos a estímulos mecânicos a inibição da atividade da SHP-2 paralela a dissociação FAK/SHP-2 exerce papel permissivo na elevação da fosforilação da FAK. Material e Métodos. Utilizou-se modelo de sobrecarga pressora por coarctação da aorta em ratos (miocárdio-VE) e estiramento in vitro em MVRNs. As abordagens experimentais incluíram técnicas de imunoprecipitação, western blot, imunohistoquímica, atividade de tirosino fosfatase in vitro, expressão de SHP-2 recombinante e avaliação da expressão do gene da cadeia pesada de beta-miosina (ß- miosina). Resultados. A coarctação da aorta (miocárdio-VE) e o estiramento (MVRNs) aumentaram a fosforilação da FAK no resíduo tirosina 397, em miocárdio-VE (200%) e em MVRNs estirados (75%). A FAK imunoprecipitada de amostras controles, encontrou-se associada a SHP-2 e o estímulo mecânico acompanhou-se de redução dessa associação, no miocárdio (60%) e em MVRNs (84%). Experimentos com imunohistoquímica e microscopia confocal demonstraram co-localização da FAK e da SHP-2 em MVRNs controle. Ocorreu redução da atividade de tirosino-fosfatase em imunoprecipitados de anticorpo anti-FAK (25%) e anticorpo anti-SHP-2 (25%) de miocárdio-VE de animais submetidos à coarctação da aorta, e anti-FAK (20%) e anti-SHP-2 (40%) de MVRNs estirados. A SHP-2 recombinante foi capaz de reduzir (70%) in vitro a fosforilação da FAK ativada por estímulo mecânico. Ocorreu aumento (125%) da quantidade de FAK fosforilada em MVRNs controles tratados com TFMS (inibidor seletivo da atividade da SHP-2); naqueles submetidos ao estiramento, o aumento em relação aos MVRNs estirados, mas não tratados com TFMS, foi menor (40%). Ocorreu paralelamente, diminuição (40%) da associação FAK/SHP-2 e aumento da expressão do gene fetal da cadeia pesada da ß - miosina (110%) em MVRNs tratados com TFMS; Os MVRNs tratados concomitantemente com TFMS e PP2 (inibidor farmacológico da FAK), apresentaram atenuação desse aumento (25%). Conclusão. Os dados sugerem que a SHP-2 modula o nível de fosforilação da FAK em MVRNs, exercendo papel inibitório na ativação da FAK, contribuindo para o seu baixo nível de fosforilação em MVRNs e miocárdio na ausência de estímulo mecânico. A diminuição da associação FAK/SHP-2, da atividade específica da SHP-2 em MVRNs ou miocárdio submetidos a estímulos mecânicos e o aumento da fosforilação da FAK mediante tratamento dos MVRNs com TFMS, indicam que a redução da atividade da SHP-2 e da associação a FAK, é um importante mecanismo que colabora para o aumento de fosforilação da FAK em MVRNs submetidos a estímulos mecânicos sustentados. O aumento da expressão da cadeia pesada da ß ¿ miosina conseqüente à inibição da atividade da SHP-2 e a atenuação desse aumento, perante a concomitante inibição da atividade da FAK, corrobora nossa hipótese de que a SHP-2 modula a ativação da FAK em cardiomiócitos, influenciando a reprogramação gênica característica da ativação da sinalização hipertrófica, por estímulo mecânico / Abstract: Mechanical forces drive changes in cardiac myocyte function and structure that occur in response to hemodynamic overload. Focal Adhesion Kinase (FAK) has been implicated in the sensing and transduction of mechanical forces into biochemical events in cardiac myocytes. This study was performed to examine whether the protein tyrosine-phosphatase SHP-2 plays a role in baseline and stretch induced FAK activation and signaling in cultured neonatal rat ventricular myocytes (NRVMs).NRVMs were subjected to cyclic stretch up to 60 min, studied by coimmunoprecipitation, immunoblotting, tyrosine-phosphatase activity assay, RT-PCR, and used in assays utilizing recombinant SHP-2 catalytic domain. Analysis was extended to NRVMs treated with Shp2 inhibitor TFMS and with FAK/Src Inhibitor PP2. FAK had a relatively low basal level of phosphorylation at Tyr397 in non-stretched NRVMs. Cyclic stretch (1HZ, 10%) induced rapid and sustained (up to 60 min) increases in phosphorylation of FAK at Tyr397. The results of coimmunoprecipitation assays indicated that FAK and SHP-2 are associated in non-stretched NRVMs, but cyclic stretch markedly reduced (to 25% and 60% after 10 and 60 min, respectively) the amount of SHP-2 recovered from the anti-FAK antibody precipitates. The tyrosine phosphatase activity of the anti-SHP-2 immunocomplex taken from non-stretched cardiac myocytes was relatively high, but it was markedly reduced (to 60% after 10 and 60 min) in samples of stretched cells. The recombinant PTP domain of SHP-2 was demonstrated to be able to dephosphorylate the native FAK immunoprecipitated from NRVMs. The inhibition of SHP-2 activity by the pharmacological inhibitor TFMS markedly increased FAK phosphorylation at Tyr397 in non-stretched NRVMs to levels comparable to those seen in stretched cells. Treatment with TFMS lasting for 4h was accompanied by a marked increase (to 200) the expression of beta-myosin heavy chain mRNA in non-stretched NRVMs. This effect was attenuated by 25% in NRVMs simultaneous treated with the FAK/Src inhibitor PP2.In conclusion, the present data demonstrated that the basal FAK phosphorylation at Tyr397 is modulated by SHP-2 and that inhibition of SHP-2 during cyclic stretch has a permissive role on FAK activation by mechanical stress. Our results also establish the tight regulation of FAK phosphorylation by SHP-2 as a potential counter-regulatory signaling in the control of the hyperthophic genetic program in cardiac myocytes / Mestrado / Medicina Experimental / Mestre em Fisiopatologia Médica

Protein Tyrosine Phosphatases (PTPs) initiate, modulate and terminate key cellular processes by dephosphorylating phosphotyrosine (pY) residues on signaling proteins. The coordinated action of PTPs with their cognate tyrosine kinases is crucial for the maintenance of cellular homeostasis. Five Receptor Tyrosine Phosphatases (RPTPs) DLAR, PTP99A, PTP69D,PTP10D and PTP52F are involved in the axon guidance process of the fruit-fly Drosophila melanogaster. The receptors in these RPTPs comprise of Cell Adhesion Molecules (CAMs) whilethe cytosolic region contains the catalytic PTP domains. Extensive studies on the genetic interactions between these RPTPs reveal that these five RPTPs collaborate, compete or are partially redundant in some developmental contexts. While the genetic interactions between these RPTPs are well characterized, the role of domain-domain interactions and the mechanism(s) of substrate recognition are poorly understood. The aim of this study was to understand the molecular basis for these interactions using a combination of biophysical, biochemical and structural biology tools. This thesis is organized as follows: Chapter 1: The introductory chapter of this thesis highlights the mechanistic issues in signal transduction with an emphasis on the role of the RPTPs in the neuro-development of Drosophila melanogaster. The first part of this chapter describes the structural features and the catalytic mechanism of the PTP domain. This is followed by a description of the mechanisms that modulate the activity of a PTP domain. The latter part of the chapter summarizes the role ofthese RPTPs in axon guidance of Drosophila melanogaster. The interactions between the RPTPsbased on genetic data provide a mechanistic hypothesis that could be examined in vitro. The studies described in the subsequent chapters of this thesis were performed to evaluate this hypothesis. Chapter 2: This chapter reports our observations on the so-called construct dependence on the expression of recombinant PTP domains in Escherichia coli. This chapter details the strategies used to obtain recombinant PTP domains in a soluble form suitable for biochemical and structural studies. This study involved substantial optimization in the size of the protein and overexpression strategies to avoid inclusion-body formation. Five strains of E. coli as well as three variations in purification tags viz., poly-histidine peptide attachments at the N-and C-termini and a construct with Glutathione-S-transferase at the N-terminus were examined. In this study, we observed that inclusion of a 45 residue stretch at the N-terminus was crucial for the over-expression of the PTP domains, influencing both the solubility and the stability of these recombinant proteins. While the addition of negatively charged residues in the N-terminal extension could partially rationalize the improvement in the solubility of these constructs, conventional parameters like the proportion of order-promoting residues or the aliphatic index did not correlate with the improved biochemical characteristics. The findings in this chapter suggest that the inclusion of additional parameters like secondary structure propensities apart from rigid domain predictions could play a crucial role in obtaining a soluble recombinant protein upon expression in E. coli. Chapter 3: This chapter reports the crystal structure of the PTP domain of PTP10D and PTP10Dsubstrate/inhibitor complexes. These structural studies revealed aromatic ring stacking interactions that mediate substrate recruitment into the PTP active site. In particular, these studies revealed the role of conserved aromatic residue in Motif 1 (Phenylalaline 76 in case ofPTP10D). Mutation of Phenylalanine 76 residue to a Leucine (similar to the mutation found in the inactive distal PTP domains in other bi-domain PTPs) resulted in a sixty-fold decrease in the catalytic efficiency of the enzyme. Fluorescence kinetic measurements to monitor ligand binding showed a three fold increase in the half time of enzyme-ligand complex formation. These studies highlight the role of the KNRY loop in substrate recruitment at the active of the PTP domain and the role of this segment in modulating the kinetics of the enzyme-substrate complex formation. Chapter 4: This chapter describes a strategy to utilize protein-protein interaction data to identify putative peptide substrates for a given protein. This study was performed in collaboration with Shameer Khader and Prof. R. Sowdhamini at the National Center for Biological Sciences (NCBS).This integrated search approach, called ‘PeptideMine’ was developed into a web-server for experimental and computational biologists. The Peptide Mine strategy combines sequence searches in the 'interacting sequence space' of a protein using sequence patterns or functional motifs. A compilation of indices that describe the chemical and solubility properties of potential peptide substrates to facilitate investigation by in vitro or in silico studies is also obtained from this server. The biological significance of such a design-strategy was examined in the context of protein-peptide interactions in the case of RPTPs of Drosophila melanogaster. Chapter 5: In this chapter, we report an analysis of the influence of the membrane distal (D2) domain on the catalytic activity and substrate specificity of the membrane proximal (D1) domain using two bi-domain RPTPs as a model system. Biochemical studies reveal contrasting roles for the D2 domain of the Drosophila Leukocyte antigen Related (DLAR) and Protein Tyrosine Phosphatase on Drosophila chromosome band 99A (PTP99A). While D2 lowers the catalytic activity of the D1 domain in DLAR, the D2 domain of PTP99A leads to an increase in the catalytic activity of its D1 domain. Substrate specificity, on the other hand, is cumulative, whereby the individual specificities of the D1 and D2 domains contribute to the substrate specificity of these two-domain enzymes. Molecular dynamics simulations on structural models of DLAR and PTP99A revealed a conformational rationale for the experimental observations. These studies suggested that concerted structural changes mediate inter-domain communication resulting in either inhibitory or activating effects of the membrane distal PTP domain on the catalytic activity of the membrane proximal PTP domain. Chapter 6: This chapter describes biochemical studies to understand the role of the D2 domain of PTP99A. While the catalytic activity of PTP99A is localized to its membrane proximal (D1)domain, the inactive membrane distal (D2) domain influences the catalytic activity of the D1domain. Phosphatase activity, monitored using small molecule as well as peptide substrates, suggested that the D2 domain activates D1. Thermodynamic measurements on the bi-domain(D1-D2 protein) as well as single domain PTP99A protein constructs suggest that the presence of the inactive D2 domain influences the stability of the bi-domain protein. The mechanism by which the D2 domain activates and stabilizes the bi-domain protein is governed by a few interactions at the inter-domain interface. In particular, we note that mutating Lys990 at the interface attenuates inter-domain communication. This residue is located at a structurally equivalent position to the so-called allosteric site of a canonical PTP, PTP1B. These observations suggest functional optimization in bi-domain RPTPs wherein the inactive PTP domain modulates the catalytic activity of the bi-domain enzyme. Chapter 7: This chapter summarizes the experimental and computational studies on the Drosophila melanogaster PTP domains. The salient features of the experimental data that revealed hitherto uncharacterized sequence-structure relationships in the conserved PTP domain are highlighted. The latter part of this chapter briefly suggests the scope of future research in this area based on some of the findings reported in this thesis. Appendix : This thesis has an appendix section with four parts. These comprise of technical details and auxiliary work that was not included in the main text of the thesis. Appendix I describes cloning strategies, purification protocols and a list of all recombinant proteins used in this study. Appendix II describes the standardization of the ‘Three Phase partitioning’ protocol for refolding and solubilization of protein from inclusion bodies. Appendix III includes theimmunochemical work performed to elucidate the localization of PTP10D in Drosophila embryos. Appendix IV describes the work on a Quercetin 2,3 Dioxygenase from Bacillus subtilis with an emphasis on the role of metal ions in modulating catalytic activity in this class of proteins.

Indiana University-Purdue University Indianapolis (IUPUI) / The addition and removal of phosphate groups is a key regulatory mechanism for many cellular processes. The balance between phosphorylation and dephosphorylation is delicate and must be maintained in order for proper cell functions to be carried out. Protein kinases and phosphatases are the keepers of this balance with kinases adding phosphate groups and phosphatases removing them. As such, mutation and/or altered regulation of these proteins can be the driving factor in disease. Phosphatase of Regenerating Liver (PRL) is a family novel of three dual specificity phosphatases (DSPs) first discovered in the regenerating liver tissue of rats. PRLs have also been shown to act as oncogenes in cell culture and in animal models. However, the physiological substrate and mechanisms of the PRLs are not yet known. Recently, our lab has developed a PRL 2 knockout mouse and found several striking phenotypes all of which correspond to a significant increase in PTEN. We also found that PRL 2 is targetable by small molecular inhibitors that can potentially be used to disrupt tumor growth and spermatogenesis. Furthermore, a PTEN heterozygous mouse model crossed into our PRL 2 knockout line was generated to investigate the relevance of PRL interaction with PTEN in cancer.

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Résumé : Bien que l’hypoxie soit un puissant inducteur de l’angiogenèse, l’activation des facteurs de croissance est perturbée en hyperglycémie au niveau du pied et du cœur. Cette perturbation entraîne la perte de prolifération et de migration chez les cellules endothéliales, musculaires lisses vasculaires et péricytes empêchant la formation de nouveaux vaisseaux qui mènera à l’amputation des membres inférieurs chez les patients diabétiques. Une étude a démontré qu’une augmentation de la protéine tyrosine phosphatase Src homology-2 domain-containing phosphatase-1 (SHP-1) en condition hyperglycémique chez les péricytes entraînait l’inhibition de la signalisation du PDGF-BB, ce qui résultait en le développement d’une rétinopathie diabétique. Nous avons alors soulevé l’hypothèse que l’expression de SHP-1 dans les cellules musculaires lisses vasculaires affecte la prolifération et la migration cellulaire par l’inhibition de la signalisation de l’insuline et du PDGF-BB en condition diabétique. Nos expérimentations ont été effectuées principalement à l’aide d’une culture primaire de cellules musculaires lisses primaires provenant d’aortes bovines. Comparativement aux concentrations normales de glucose (NG : 5,6 mM), l’exposition à des concentrations élevées de glucose (HG : 25 mM) pendant 48 h a résulté en l’inhibition de la prolifération cellulaire par l’insuline et le PDGF-BB autant en normoxie (20% O2) qu’en hypoxie (24 dernières heures à 1% O2). Lors des essais de migration cellulaire, aucun effet de l’insuline n’a été observé alors que la migration par le PDGF-BB fut inhibée en HG autant en normoxie qu’en hypoxie. L’exposition en HG à mener à l’inhibition de la signalisation de la voie PI3K/Akt de l’insuline et du PDGF-BB en hypoxie. Aucune variation de l’expression de SHP-1 n’a été observée mais son activité phosphatase en hypoxie était fortement inhibée en NG contrairement en HG où on observait une augmentation de cette activité. Finalement, une association a été constatée entre SHP-1 et la sous-unité bêta du récepteur au PDGF. En conclusion, nous avons démontré que l’augmentation de l’activité phosphatase de SHP-1 en hypoxie cause l’inhibition des voies de l’insuline et du PDGF-BB réduisant les processus angiogéniques des cellules musculaires lisses vasculaires dans la maladie des artères périphériques. / Abstract : Even though hypoxia is a strong angiogenic inducer, pro-angiogenic factor signaling pathways in peripheral limb and heart are altered by hyperglycemia. This disruption leads to loss of endothelial cells, vascular smooth muscle cells and pericytes proliferation and migration preventing new blood vessel formation which results in amputation of lower extremities in diabetic patients. A study has shown that increase expression of the protein tyrosine phosphatase Src homology-2 domain-containing phosphatase-1 (SHP-1) in hyperglycemic condition in pericytes caused PDGF-BB signaling inhibition resulting in the development of diabetic retinopathy. Our hypothesis is that SHP-1 expression in vascular smooth muscle cells inhibits cell proliferation and migration induced by insulin and PDGF-BB in diabetic condition. Our experiments were performed using primary culture of vascular smooth muscle cells (SMC) from bovine aortas. As compared to normal glucose concentrations (NG:5,6 mM), high glucose level (HG: 25 mM) exposure for 48h inhibited SMC proliferation induced by insulin and PDGF-BB in both normoxia (20% O2) or hypoxia (1% O2 for the last 24h). During cell migration assays, no effect of insulin was observed while PDGF-BB action of SMC migration was reduced in HG in both normal and low oxygen concentrations. HG exposure lead to inhibition of insulin- and PDGF-BB-stimulated PI3K/Akt signaling pathway in hypoxia. No variation of SHP-1 expression was observed in HG condition. However, SHP-1 phosphatase activity was elevated in HG condition during hypoxia as compared to NG concentrations. Finally, our data showed an association between SHP-1 and the PDGF receptor beta subunit. In conclusion, our results demonstrated that the increase of SHP-1 phosphatase activity in hyperglycemia and hypoxia environment caused inhibition of insulin and PDGF-BB signaling pathways reducing angiogenic processes in vascular smooth muscle cells contributing to peripheral arterial disease in diabetes.