The methylotrophic yeast Pichia pastoris is widely used for recombinant protein production due to its ability to grow to high cell densities as well as possession of an inducible methanol utilization pathway (MUT). The expression of genes encoding enzymes of the MUT pathway is very tightly regulated. These genes are turned on when methanol but not glucose is used as the sole carbon source. Thus, P. pastoris cells can be grown to high densities in glucose containing medium and expression of genes of MUT pathway can be turned on by changing the carbon source to methanol. This strategy is widely used for recombinant protein production wherein the gene of interest is cloned downstream of the methanol-inducible promoter of the gene encoding the first enzyme of the MUT pathway, alcohol oxidase I (AOXI). Despite production of a large number of recombinant proteins using the AOXI promoter, the mechanism of transcriptional activation of AOXI is not very well understood. It is only recently that a zinc finger protein known as Mxr1p (methanol expression regulator 1) was shown to play a key role in the regulation of AOXI as well as other genes of methanol utilization pathway (1) P. pastoris strains that do not express Mxr1p (mxr1) are unable to grow on peroxisomal substrates such as methanol and oleic acid. Methanol-inducible expression of genes involved in MUT pathway as well as those involved in peroxisome biogenesis (peroxins,) is severely impaired in mxr1 strains. While Mxr1p is constitutively expressed in cells cultured on glucose as well as methanol, it is cytosolic in glucose-grown cells, but nuclear in methanol-grown cells (1). The exact nucleotide sequence to which Mxr1p binds and regulates the expression of genes of MUT pathway is not known. The aim of this thesis is to map the Mxr1p binding sites in the promoters of methanol-inducible genes of P. pastoris. As a first step towards understanding the mechanism of transcriptional regulation of AOXI and other methanol inducible genes of P. pastoris by Mxr1p, the N-terminal region comprising of 150 amino acids, including the zinc finger DNA binding domain of Mxr1p was cloned into an E. coli expression vector and the recombinant protein was purified from E. coli cells. This recombinant protein (referred to as Mxr1p in this study) was used in an electrophoretic mobility shift assay (EMSA) to identify Mxr1p binding sites in the AOXI promoter. EMSA was carried out with sixteen different oligonucleotides spanning AOXI promoter region between -940 and -114 bp. Such studies led to the identification of six Mxr1p binding sites in AOXI promoter. Using a combination of DNase I footprinting as well as EMSA with chimeric double stranded oligonucleotides, the minimal Mxr1p binding site was identified as a 20 bp DNA sequence containing a core 5’CYCC 3’ sequence. Using methylation interference as well as extensive mutagenesis studies, nucleotides critical for Mxr1p binding were identified. Comparative analysis of Mxr1p binding sites identified in our study with the AOXI promoter deletion studies of Hartner et al (2) suggested that the Mxr1p binding sites identified in our study are likely to function as methanol-inducible enhancers in vivo, since deletion of AOXI promoter regions comprising Mxr1p binding sites results in a significant loss of methanol-inducible promoter activity. Thus, Mxr1p binding sites are likely to function as Mxr1p response elements (MXREs) in vivo. Mxr1p is considered to be the P. pastoris homologue of S. cerevisiae Adr1p (alcohol dehydrogenase II [ADH2] synthesis regulator). Adr1p is a key regulator of S. cerevisiae genes involved in the metabolism of glycerol, ethanol and oleic acid. The DNA binding domains of Adr1p and Mxr1p share 82% similarity and 70% identity. We therefore examined whether Mxr1p can bind to the Adr1p binding site of ADH2 promoter(ADH2-UAS1). Our studies indicate that Mxr1p does not bind to ADH2-UAS1. Interestingly, a single point mutation restores Mxr1p binding to ADH2-UAS1. Since Mxr1p is involved in the regulation of a number of genes including AOXI, we examined whether promoters of other Mxr1p-regulated genes also harbour MXREs similar to those identified in AOXI promoter. The promoters of genes encoding dihydroxyacetone synthase (DHAS) and peroxin 8 (PEX8) were chosen for this purpose. A detailed analysis of Mxr1p binding to these promoter sequences led to the conclusion that DHAS and PEX8 promoters also harbour Mxr1p binding sites similar to those of AOXI promoter. Based on these studies, we have derived a consensus sequence for Mxr1p binding. This study is the first report on detailed characterization of Mxr1p binding sites in three methanol-inducible promoters of P. pastoris and thus provides the molecular framework by which this transcription factor functions as a master regulator of genes involved in methanol utilization pathway of P. pastoris. Our study provides the blue print for mapping Mxr1p binding sites in the promoters of other Mxr1p-regulated genes.

The specific recognition of the DNA is crucial for the correct functioning of the cell. Although its mechanisms are extensively studied, the actual process is not yet fully understood, partly due to the variance observed in readout mechanisms so far. In this work, a particular type of specific recognition is examined: the shape readout in the DNA minor groove. Based on a sta- tistical analysis of three-dimensional structures of protein-DNA complexes acquired from the Protein Data Bank, I propose a previously unrecorded readout mechanism of widened minor grooves by hydrophobic amino acids. In addition, the effect of DNA sequence on the topography of the contacted locus, the preferred secondary structures and the interaction between the protein and DNA are explored, as well as the relative information amount of examined features concerning the DNA deformation. 1

No description available.

A preparação, caracterização e estudo de propriedades moleculares e supramoleculares de meso-tetrapiridilporfirinas modificadas com quatro complexos de cloro(bipiridina) platina(II) ligados às posições meta e para de ligantes piridínicos periféricos, foi objetivo desta tese. As supermoléculas isômeras foram isoladas no estado sólido e extensivamente caracterizados por meio de espectroscopia UV/VIS, FT-IR e RMN de Pt-195, assim como através de TGA e espectrometria de massa com ionização por spray de elétrons, ESI-MS, e técnicas de dissociação induzidas por colisão. Medidas de voltametria cíclica e de espectroeletroquímica foram realizadas para caracterizar os estados redox da porfirina central e dos complexos periféricos, mostrando uma semelhança entre as duas formas isômeras. A maior diferença, entretanto, foi observada nas suas propriedades estruturais, diagnosticadas por modelagem molecular, e refletidas na morfologia dos filmes obtida por meio de técnicas de microscopia de varredura por sonda, SPM, e através da associação com filmes de DNA, monitorada com o auxílio de técnicas de espectroscopia eletrônica e ressonância plasmônica de superfície, SPR. No último caso, o DNA foi imobilizado sobre a superfície do sensor de ouro, usando aminotióis adequados, sendo que a interação do isômero meta conduziu a uma resposta contrastante, relevando uma forte ligação com a cadeia do DNA, provavelmente nas proximidades das fendas estruturais menores desse biopolímero. A interação do isômero para com o DNA foi demasiadamente fraca para ser observada por meio de SPR. A associação molecular das porfirinas tetraplatinadas catiônicas com ftalocianinas aniônicas tetrassulfonadas conduziu à formação de pares iônicos em solução. O filme do isômero para imobilizado sobre eletrodo de carbono vítreo apresentou atividade na redução eletrocatalítica de nitrito. Os trabalhos realizados demonstraram que os novos sistemas supramoleculares derivados de porfirinas e complexos de platina proporcionam interessantes materiais híbridos inorgânico-biológicos contendo DNA e metais nobres, com potenciais aplicações em terapia fotodinâmica, sensoriamento e em dispositivos moleculares. / The synthesis, characterization and investigation of the molecular and supramolecular behaviour of meso-tetrapyridylporphyrins containing four chloro(bipyridine) platinum(II) complexes attached at the meta and para positions of the peripheral pyridine ligands is focused on this thesis. The isomeric supermolecules were isolated in the solid state, and extensively characterized by means of UV-visible, FT-IR and 195Pt NMR spectroscopy, as well as, by TGA and electrospray spectrometry associated with collision induced techniques. Cyclic voltammetry and spectroelectrochemical measurements were performed to characterize the redox sites on the porphyrin and peripheral complexes, revealing a close similarity between the two isomeric supermolecules. Major differences were observed on their structural properties, as demonstrated by means of molecular simulations, and by the morphology of the molecular films probed by SPM techniques, and also by their association with DNA films, which was monitored by means of SPR techniques. In the last case, DNA was first immobilized onto the surface of the gold sensor, using suitable aminothiols and the interaction of the meta-isomer led to a contrasting response, exhibiting a strong binding to the DNA chain, presumably at the proximity of the minor grooves. The interaction of the para-isomer with DNA was too weak to be probed by means of the SPR technique. Molecular association of the tetraplatinum porphyrin species, with tetrasulphonated phtalocyanines, leading to ion pairs in solution, was also investigated. The molecular film of the para-isomer immobilized over glass carbon electrode has shown activity in the electrocatalytic reduction of nitrite. This work on the supramolecular porphyrin platinum species provided new interesting approaches for generating hybrid biological-inorganic systems, containing DNA and noble metals, for sensing applications, and molecular devices.

A preparação, caracterização e estudo de propriedades moleculares e supramoleculares de meso-tetrapiridilporfirinas modificadas com quatro complexos de cloro(bipiridina) platina(II) ligados às posições meta e para de ligantes piridínicos periféricos, foi objetivo desta tese. As supermoléculas isômeras foram isoladas no estado sólido e extensivamente caracterizados por meio de espectroscopia UV/VIS, FT-IR e RMN de Pt-195, assim como através de TGA e espectrometria de massa com ionização por spray de elétrons, ESI-MS, e técnicas de dissociação induzidas por colisão. Medidas de voltametria cíclica e de espectroeletroquímica foram realizadas para caracterizar os estados redox da porfirina central e dos complexos periféricos, mostrando uma semelhança entre as duas formas isômeras. A maior diferença, entretanto, foi observada nas suas propriedades estruturais, diagnosticadas por modelagem molecular, e refletidas na morfologia dos filmes obtida por meio de técnicas de microscopia de varredura por sonda, SPM, e através da associação com filmes de DNA, monitorada com o auxílio de técnicas de espectroscopia eletrônica e ressonância plasmônica de superfície, SPR. No último caso, o DNA foi imobilizado sobre a superfície do sensor de ouro, usando aminotióis adequados, sendo que a interação do isômero meta conduziu a uma resposta contrastante, relevando uma forte ligação com a cadeia do DNA, provavelmente nas proximidades das fendas estruturais menores desse biopolímero. A interação do isômero para com o DNA foi demasiadamente fraca para ser observada por meio de SPR. A associação molecular das porfirinas tetraplatinadas catiônicas com ftalocianinas aniônicas tetrassulfonadas conduziu à formação de pares iônicos em solução. O filme do isômero para imobilizado sobre eletrodo de carbono vítreo apresentou atividade na redução eletrocatalítica de nitrito. Os trabalhos realizados demonstraram que os novos sistemas supramoleculares derivados de porfirinas e complexos de platina proporcionam interessantes materiais híbridos inorgânico-biológicos contendo DNA e metais nobres, com potenciais aplicações em terapia fotodinâmica, sensoriamento e em dispositivos moleculares. / The synthesis, characterization and investigation of the molecular and supramolecular behaviour of meso-tetrapyridylporphyrins containing four chloro(bipyridine) platinum(II) complexes attached at the meta and para positions of the peripheral pyridine ligands is focused on this thesis. The isomeric supermolecules were isolated in the solid state, and extensively characterized by means of UV-visible, FT-IR and 195Pt NMR spectroscopy, as well as, by TGA and electrospray spectrometry associated with collision induced techniques. Cyclic voltammetry and spectroelectrochemical measurements were performed to characterize the redox sites on the porphyrin and peripheral complexes, revealing a close similarity between the two isomeric supermolecules. Major differences were observed on their structural properties, as demonstrated by means of molecular simulations, and by the morphology of the molecular films probed by SPM techniques, and also by their association with DNA films, which was monitored by means of SPR techniques. In the last case, DNA was first immobilized onto the surface of the gold sensor, using suitable aminothiols and the interaction of the meta-isomer led to a contrasting response, exhibiting a strong binding to the DNA chain, presumably at the proximity of the minor grooves. The interaction of the para-isomer with DNA was too weak to be probed by means of the SPR technique. Molecular association of the tetraplatinum porphyrin species, with tetrasulphonated phtalocyanines, leading to ion pairs in solution, was also investigated. The molecular film of the para-isomer immobilized over glass carbon electrode has shown activity in the electrocatalytic reduction of nitrite. This work on the supramolecular porphyrin platinum species provided new interesting approaches for generating hybrid biological-inorganic systems, containing DNA and noble metals, for sensing applications, and molecular devices.

Os projetos genoma têm fornecido uma grande quantidade de informação sobre a arquitetura gênica e sobre a configuração física de suas respectivas regiões flanqueadoras (RF). Estas RF contêm informações com o potencial de auxiliar na elucidação de vários processos biológicos, como os mecanismos de expressão gênica e de sua regulação. Estes mecanismos são de extrema importância para a compreensão do correto funcionamento dos organismos e das patologias que os afetam. Uma parte significativa dos mecanismos de controle de expressão gênica atuam na fase transcricional. Na base destes mecanismos está o recrutamento de proteínas que se ligam às regiões promotoras da transcrição, as quais são segmentos específicos de DNA que podem estar localizados tanto próximos à região de início da transcrição (TSS) quanto a centenas ou até a milhares de pares de bases dela. Essas proteínas compõem a maquinaria transcricional e podem ativar ou inibir o processo de transcrição. Experimentalmente, os segmentos regulatórios podem ser identificadas utilizando métodos complexos de biologia molecular, tais como SELEX, ChiP-ChiP, ChIP-Seq, dentre outros. Uma estratégia alternativa aos métodos experimentais é a utilização de metodologias computacionais. Análises computacionais tendem a ser mais rápidas, baratas e flexíveis do que protocolos experimentais, além de poderem ser utilizadas em larga escala. Atualmente, os métodos computacionais disponíveis necessitam de informações experimentais para a definição de padrões globais de preferências de sequências de DNA para a ligação de fatores de transcrição (TFBS, em inglês transcription factor binding sites). Entretanto, esses métodos apresentam uma elevada taxa de falso positivos e, por vezes, apresentam também taxas significativas de falso negativos, além de serem limitados ao estudo de fatores de transcrição de espécies bem conhecidas, o que diminui a área de aplicação dos mesmos. Diante deste cenário, o uso de métodos computacionais que não necessitem da informação referente aos sítios de ligação, bem como os que utilizem parâmetros mais robustos de detecção dos resultados, em detrimento dos escores de pontuação provindos de alinhamentos, podem acrescentar uma sensível melhoria ao processos de predição de regiões regulatórias. Neste projeto, foi desenvolvido um novo modelo computacional (TFBSAnalyzer) para análise e identificação de TFBS em elementos regulatórios, que utiliza técnicas de modelagem molecular para a construção de complexos entre um fator de transcrição ancorado a estruturas de DNA com sequências variáveis de bases e, através de cálculos termodinâmicos de entalpia de ligação, determina uma função de pontuação baseada na energia de ligação e realiza a predição de sítios de ligação ao DNA para o fator de transcrição em análise. Esta abordagem foi testada com três fatores de transcrição como sistemas-modelo, pertencentes à família dos receptores nucleares, a saber: o receptor de estrógeno ER-alfa (Estrogen Receptor Alpha), o receptor de ácido retinoico RAR-beta (Retinoid Acid Receptor Beta) e o receptor X retinóico RXR (Retinoid X Receptor). Os modelos previstos computacionalmente foram comparados aos dados experimentais disponíveis para estes receptores nucleares, os quais apresentaram as seguintes taxas de FP/FN: 10%/0 para RAR-beta e RXR, 21%/6% para ER-alfa. Também simulamos um experimento de ChIP-seq do ER-alfa no genoma humano, cujos genes selecionados foram submetidos a uma análise de enriquecimento de fatores de transcrição curados experimentalmente, que fazem sua regulação, revelando que o receptor de estrógeno está realmente envolvido no processo. Para mostrar a aplicabilidade geral de nosso método, nós modelamos a distribuição de energia de ligação para o receptor NHR-28 isoforma a de Caenorhabditis elegans com DNA . Obtivemos distribuições de energia semelhantes àquelas encontradas para os NRs modelos, portanto seria possível aplicar o método para buscar possíveis TFBSs para este receptor no genoma de C. elegans. Os dados gerados e as metodologias desenvolvidas neste projeto devem acrescentar uma sensível melhoria aos processos de predição de regiões regulatórias e consequentemente auxiliar no entendimento dos mecanismos envolvidos no processo de expressão gênica e de sua regulação. / The genome projects have provided a lot of information about the genetic architecture, as well as on the physical configuration of their flanking regions (FR). These FR have the potential to aid in the elucidation of many biological processes, such as the mechanisms involved in gene expression and its regulation. These mechanisms are extremely important for undeerstanfind the correct functioning of organisms as well as the pathologies that affect them. A significant part of the control mechanisms of gene expression act during transcription. On the basis of this mechanisms is the recruitment of proteins that bind to promoter regions of transcription, which are specific segments of DNA that can be located either near the transcription start site or at hundreds or even thousands of base pairs away. These proteins form the transcription machinery, which can activate or inhibit the transcription process. The regulatory segments can be identified experimentally using complex methods of molecular biology, such as SELEX, ChIP-chip, ChIP-seq, among others. An alternative strategy to these experimental methods is the use of computational methodologies for predicting regulatory regions. Computational analysis tend to be faster, cheaper and more flexible than the experimental protocols, and can be used on a larger scale. Currently, the available computational methods require information previously obtained from experiments in order to define global standards of preference of DNA-Binding sequences for transcription factors (TFBS - Transcription Factor Binding Sites). However, these methods have a high rate of false positives and sometimes also have significant rates of false negatives, besides being limited to the study of transcription factors of well-known species, which decreases their application area. In this scenario, the use of computational methods that do not require previous information concerning the binding sites and use more robust parameters of results detection, instead of alignment scores, may add significant improvement to the processes of predicting regulatory regions. In this project, we developed a new computational model TFBSAnalyzer) for analysis and identification of regulatory elements using molecular modeling techniques for the construction of complexes between a transcription factor bound to specific DNA structures with variable sequences of bases and, by means of thermodynamic calculations of bond enthalpy, provides a scoring function based on the binding energy and predicts the DNA binding sites for the transcription factor in analysis. This approach was tested initially with three transcription factors as models, belonging to the nuclear receptor family, namely estrogen receptor ER-alpha (Estrogen Receptor Alpha), the retinoic acid receptor RAR-beta (Retinoid Acid Receptor Beta) and the retinoic X receptor RXR (Retinoid X Receptor). The computationally predicted models were compared to experimental data available for these nuclear receptors, and presented the following rates of FP/FN: 10%/0 for RAR-beta and RXR, 21%/6% for ER-alpha. We also simulated an experiment of ChIP-seq with ER-alpha with the human genome, where the selected genes were subjected to a transcription factor enrichment analysis, with curated information, revealing that the estrogen receptor is indeed involved in their regulation. To show that our method has a general applicability, we modeled the binding energy distribution for the NHR-28 receptor, isoform a, from Caenorhabditis elegans. The energy distributions obtained were similar to the ones obtained for the model NR, so it would be possible to use the method and search for possible TFBS in the C. elegans genome. The data generated and the methodologies developed in this project should add a significant improvement to the prediction processes of regulatory regions and, consequently, help to understand the mechanisms involved in the gene expression process and its regulation.

Os projetos genoma têm fornecido uma grande quantidade de informação sobre a arquitetura gênica e sobre a configuração física de suas respectivas regiões flanqueadoras (RF). Estas RF contêm informações com o potencial de auxiliar na elucidação de vários processos biológicos, como os mecanismos de expressão gênica e de sua regulação. Estes mecanismos são de extrema importância para a compreensão do correto funcionamento dos organismos e das patologias que os afetam. Uma parte significativa dos mecanismos de controle de expressão gênica atuam na fase transcricional. Na base destes mecanismos está o recrutamento de proteínas que se ligam às regiões promotoras da transcrição, as quais são segmentos específicos de DNA que podem estar localizados tanto próximos à região de início da transcrição (TSS) quanto a centenas ou até a milhares de pares de bases dela. Essas proteínas compõem a maquinaria transcricional e podem ativar ou inibir o processo de transcrição. Experimentalmente, os segmentos regulatórios podem ser identificadas utilizando métodos complexos de biologia molecular, tais como SELEX, ChiP-ChiP, ChIP-Seq, dentre outros. Uma estratégia alternativa aos métodos experimentais é a utilização de metodologias computacionais. Análises computacionais tendem a ser mais rápidas, baratas e flexíveis do que protocolos experimentais, além de poderem ser utilizadas em larga escala. Atualmente, os métodos computacionais disponíveis necessitam de informações experimentais para a definição de padrões globais de preferências de sequências de DNA para a ligação de fatores de transcrição (TFBS, em inglês transcription factor binding sites). Entretanto, esses métodos apresentam uma elevada taxa de falso positivos e, por vezes, apresentam também taxas significativas de falso negativos, além de serem limitados ao estudo de fatores de transcrição de espécies bem conhecidas, o que diminui a área de aplicação dos mesmos. Diante deste cenário, o uso de métodos computacionais que não necessitem da informação referente aos sítios de ligação, bem como os que utilizem parâmetros mais robustos de detecção dos resultados, em detrimento dos escores de pontuação provindos de alinhamentos, podem acrescentar uma sensível melhoria ao processos de predição de regiões regulatórias. Neste projeto, foi desenvolvido um novo modelo computacional (TFBSAnalyzer) para análise e identificação de TFBS em elementos regulatórios, que utiliza técnicas de modelagem molecular para a construção de complexos entre um fator de transcrição ancorado a estruturas de DNA com sequências variáveis de bases e, através de cálculos termodinâmicos de entalpia de ligação, determina uma função de pontuação baseada na energia de ligação e realiza a predição de sítios de ligação ao DNA para o fator de transcrição em análise. Esta abordagem foi testada com três fatores de transcrição como sistemas-modelo, pertencentes à família dos receptores nucleares, a saber: o receptor de estrógeno ER-alfa (Estrogen Receptor Alpha), o receptor de ácido retinoico RAR-beta (Retinoid Acid Receptor Beta) e o receptor X retinóico RXR (Retinoid X Receptor). Os modelos previstos computacionalmente foram comparados aos dados experimentais disponíveis para estes receptores nucleares, os quais apresentaram as seguintes taxas de FP/FN: 10%/0 para RAR-beta e RXR, 21%/6% para ER-alfa. Também simulamos um experimento de ChIP-seq do ER-alfa no genoma humano, cujos genes selecionados foram submetidos a uma análise de enriquecimento de fatores de transcrição curados experimentalmente, que fazem sua regulação, revelando que o receptor de estrógeno está realmente envolvido no processo. Para mostrar a aplicabilidade geral de nosso método, nós modelamos a distribuição de energia de ligação para o receptor NHR-28 isoforma a de Caenorhabditis elegans com DNA . Obtivemos distribuições de energia semelhantes àquelas encontradas para os NRs modelos, portanto seria possível aplicar o método para buscar possíveis TFBSs para este receptor no genoma de C. elegans. Os dados gerados e as metodologias desenvolvidas neste projeto devem acrescentar uma sensível melhoria aos processos de predição de regiões regulatórias e consequentemente auxiliar no entendimento dos mecanismos envolvidos no processo de expressão gênica e de sua regulação. / The genome projects have provided a lot of information about the genetic architecture, as well as on the physical configuration of their flanking regions (FR). These FR have the potential to aid in the elucidation of many biological processes, such as the mechanisms involved in gene expression and its regulation. These mechanisms are extremely important for undeerstanfind the correct functioning of organisms as well as the pathologies that affect them. A significant part of the control mechanisms of gene expression act during transcription. On the basis of this mechanisms is the recruitment of proteins that bind to promoter regions of transcription, which are specific segments of DNA that can be located either near the transcription start site or at hundreds or even thousands of base pairs away. These proteins form the transcription machinery, which can activate or inhibit the transcription process. The regulatory segments can be identified experimentally using complex methods of molecular biology, such as SELEX, ChIP-chip, ChIP-seq, among others. An alternative strategy to these experimental methods is the use of computational methodologies for predicting regulatory regions. Computational analysis tend to be faster, cheaper and more flexible than the experimental protocols, and can be used on a larger scale. Currently, the available computational methods require information previously obtained from experiments in order to define global standards of preference of DNA-Binding sequences for transcription factors (TFBS - Transcription Factor Binding Sites). However, these methods have a high rate of false positives and sometimes also have significant rates of false negatives, besides being limited to the study of transcription factors of well-known species, which decreases their application area. In this scenario, the use of computational methods that do not require previous information concerning the binding sites and use more robust parameters of results detection, instead of alignment scores, may add significant improvement to the processes of predicting regulatory regions. In this project, we developed a new computational model TFBSAnalyzer) for analysis and identification of regulatory elements using molecular modeling techniques for the construction of complexes between a transcription factor bound to specific DNA structures with variable sequences of bases and, by means of thermodynamic calculations of bond enthalpy, provides a scoring function based on the binding energy and predicts the DNA binding sites for the transcription factor in analysis. This approach was tested initially with three transcription factors as models, belonging to the nuclear receptor family, namely estrogen receptor ER-alpha (Estrogen Receptor Alpha), the retinoic acid receptor RAR-beta (Retinoid Acid Receptor Beta) and the retinoic X receptor RXR (Retinoid X Receptor). The computationally predicted models were compared to experimental data available for these nuclear receptors, and presented the following rates of FP/FN: 10%/0 for RAR-beta and RXR, 21%/6% for ER-alpha. We also simulated an experiment of ChIP-seq with ER-alpha with the human genome, where the selected genes were subjected to a transcription factor enrichment analysis, with curated information, revealing that the estrogen receptor is indeed involved in their regulation. To show that our method has a general applicability, we modeled the binding energy distribution for the NHR-28 receptor, isoform a, from Caenorhabditis elegans. The energy distributions obtained were similar to the ones obtained for the model NR, so it would be possible to use the method and search for possible TFBS in the C. elegans genome. The data generated and the methodologies developed in this project should add a significant improvement to the prediction processes of regulatory regions and, consequently, help to understand the mechanisms involved in the gene expression process and its regulation.

STAT5 est une protéine de la signalisation cellulaire normale, qui peut jouer un rôle important dans la transformation, la survie et à la résistance aux inhibiteurs de tyrosine kinase des cellules tumorales. Son activation constitutive par phosphorylation est liée à la présence de protéines oncogéniques comme la protéine de fusion BCR/ABL1 (leucémie myéloïde chronique) ou de formes mutées de KIT (mastocytoses), par exemple. L’inhibition pharmacologique de STAT5 constitue donc un enjeu thérapeutique majeur pour plusieurs pathologies malignes. Nous avons réalisé la première modélisation et les simulations de dynamique moléculaire des principales formes de STAT5 : la forme monomérique cytoplasmique phosphorylée ou non, et la forme dimérique phosphorylée et liée à l’ADN. Nous avons caractérisé les propriétés dynamiques et le réseau allostérique intramoléculaire des monomères de STAT5. Les résultats générés montrent des variations structurales et dynamiques liées à la différence de séquence primaire des isoformes de STAT5 et/ou à la présence du groupement phosphate. Deux poches à la surface des protéines ont également été caractérisées. Leur localisation à proximité de voies de communication allostériques suggère que ces poches pourraient constituer des sites de modulation des fonctions de STAT5. Nous avons également caractérisé les liaisons hydrogènes entre les monomères constituant les dimères de STAT5 et leur reconnaissance de l’ADN. En outre, nous avons identifié des résidus clés aux interfaces entre les entités moléculaires, nous permettant de mieux comprendre les effets de mutations de STAT5 observées en clinique dans certaines pathologies malignes. / STAT5 is a protein involved in normal cell signalling that is crucial for transformation, survival and resistance to tyrosine kinase inhibitors of tumour cells. The constitutive phosphorylation activates STAT5 and is related to oncogenic proteins like the hybrid protein BCR/ABL1 (chronic myeloid leukaemia) or mutated KIT receptor (mastocytosis). The pharmacologic inhibition of STAT5 is thus a major therapeutic concern in several malignant pathologies. We performed the first modelling and molecular dynamics simulations of the main cellular species of STAT5: the cytoplasmic phosphorylated or unphosphorylated monomer, and the phosphorylated dimer bound to DNA. We characterized the dynamical properties and the intramolecular allosteric network of the monomers. The generated results show structural and dynamic variations linked to the primary sequence changes between the two STAT5 isoforms and/or to the phosphate group. Two pockets were characterized at the surface of STAT5. Their location at close proximity of allosteric communication pathways suggests new putative inhibition sites to modulate STAT5 functions. We also described the hydrogen bonds network between the monomers of the dimeric species and the recognition of the DNA. We identified key residues at the interfaces, allowing us to better understand the effects of clinically relevant STAT5 mutations observed in malignancies.

Mycobacterium tuberculosis (M.tb), the causative agent of tuberculosis (TB), has remained the largest killer among infectious diseases for over a century. The increasing emergence of drug resistant varieties such as the multidrug resistant (MDR) and extremely drug resistant (XDR) strains are only increasing the global burden of the disease. Available statistics indicate that nearly one-third of the world’s population is infected, where the bacteria remains in the latent state but can reactivate into an actively growing stage to cause disease when the individual is immunocompromised. It is thus immensely important to rethink newer strategies for containing and combating the spread of this disease. Extraction of iron from the host cell is one of the many factors that enable the bacterium to survive in the harsh environments of the host macrophages and promote tuberculosis. Host–pathogen interactions can be interpreted as the battle of two systems, each aiming to overcome the other. From the host’s perspective, iron is essential for diverse processes such as oxygen transport, repression, detoxification and DNA synthesis. Infact, during infection, both the host and the pathogen are known to fight for the available iron, thereby influencing the outcome of the infection. It is of no surprise therefore, that many studies have investigated several components of the iron regulatory machinery of M.tb and the host. However, very few attempts have been made to study the interactions between these components and how such interactions lead to a better adapted phenotype. Such studies require exploration at multiple levels of structural and functional complexity, thereby necessitating the use of a multiscale approach. Systems biology adopts an integrated approach to study and understand the function of biological systems. It involves building large scale models based on individual biochemical interactions, followed by model validation and predictions of the system’s response to perturbations, such as a gene knock-out or exposure to drug. In multiscale modeling, an approach employed in this thesis, a particular biological phenomenon is studied at different spatiotemporal levels. Studying responses at multiple scales provides a broader picture of the communications that occur between a host and pathogen. Moreover, such an analysis also provides valuable insights into how perturbation at a particular level can elicit responses at another level and help in the identification of crucial inter-level communications that can possibly be hindered or activated for a desired physiological outcome. The broad objectives of this thesis was to obtain a comprehensive in silico understanding of mycobacterial iron homeostasis and metabolism, the influence of iron on host-pathogen interactions, identification of key players that mediate such interactions, determination of the molecular consequences of inhibiting the key players and finally the global response of M.tb to altered iron concentration. Perturbation of iron homeostasis holds a strong therapeutic potential, given its essentiality in both the host and the pathogen. Understanding the workings of iron metabolism and regulation in M.tb has been a main objective, so as to ultimately obtain insights about specific therapeutic strategies that capitalize on the criticality of iron concentration. An in-depth study of iron metabolism and regulation is performed at different levels of temporal and spatial scales using diverse methods, each appropriate to investigate biological events associated with the different scales. The specific investigations carried out in the thesis are as follows, a) Reconstruction of a host-pathogen interaction (HPI) model, with focus on iron homeostasis. This study represented the inter-cellular level analysis and was crucial for the identification of key players that mediate communication between the host and pathogen. Additionally, the model also provided a mathematical framework to study the effect of perturbations and gene knock-outs. b) Understanding the influence of iron on IdeR, an iron-responsive transcription factor, also identified as a key player in the HPI model. The study was carried out at the molecular level to identify atomistic details of how IdeR senses iron and the resulting structural modifications, which finally enables IdeR-DNA interaction. The study enabled identification of residues for the functioning of IdeR. c) Genome scale identification of genes that are regulated by IdeR to obtain an overview of the various biological processes affected by changing iron concentrations and IdeR mutation in M.tb. d) To understand the direct and indirect influences of iron and IdeR on the M.tb proteome using large scale protein-protein interaction network. The study enabled identification of highest differentially regulated genes and altered activity of the different biological processes under differing iron concentrations and regulation. e) Systems level analysis of the M.tb metabolome to investigate the metabolic re-adjustments undertaken by M.tb to adapt to altered iron concentration and regulation. The conceptual details and the background of each of the methods used to study the specific aims are provided in the Methodology chapter (Chapter 2). Construction of the host-pathogen interaction (HPI) model and the insights obtained from this study are presented in Chapter 3. A rule based HPI model was built with a focus on the iron regulatory mechanisms in both the host and pathogen. The model consisted of 194 rules, of which 4 rules represented interactions between the host and pathogen. The model not only represented an overview of iron metabolism but also allowed prediction of critical interaction that had the potential to form bottleneck in the system so as to control bacterial proliferation. Infact, model simulation led to the identification of 5 bottlenecks or chokepoints in the system, which if perturbed, could successfully interfere with the host-pathogen dynamics in favour of the host. The model also provided a framework to test perturbation strategies based on the bottlenecks. The study also established the importance of an iron responsive transcription factor, IdeR for regulating iron concentration in the pathogen and mediating host-pathogen interactions. Additionally, the importance of mycobactin and transferrin as key molecular players, involved in host-pathogen dynamics was also determined. The model provided a mathematical framework to test TB pathogenesis and provided significant insights about key molecular players and perturbation strategies that can be used to enhance therapeutic strategies. Given the importance of IdeR in HPI, its molecular mechanism of activation and dimerization was explored in Chapter 4. The main objective of the study was to explore the structural details of IdeR and its iron sensing capacity at the molecular level. A combination of molecular dynamics and protein structure network (PSN) were used to analyse IdeR monomers and dimers in the presence and absence of iron. PSNs used in this thesis are based on non-covalent interactions between sidechain atoms and are quite efficient in identifying iron induced subtle conformational variations. The study distinctly indicated the role of iron in IdeR stability. Further, it was observed that IdeR monomers can take up two major conformations, the ‘open’ and ‘close’ conformation with the iron bound structure preferring the ‘close’ conformation. Major structural changes, such as the N-terminal folding and increased propensity for dimerization were observed upon iron binding. Interestingly, careful analysis of structure suggests a role of these structural modifications towards DNA binding and has been tested in the next chapter. Overall, the results clearly highlight the influence of iron on IdeR activation and dimerization. The predisposition of IdeR to bind to DNA in the presence of metal is clearly visible even when the simulations are performed solely on protein molecules. However, to confirm the conjectures proposed in this chapter and to obtain the atomistic details of IdeR-DNA interactions, the IdeR-DNA complex was investigated. Chapter 5 focuses on the mechanistic details of IdeR-DNA interactions and the influence of iron on the same. IdeR is known to bind to a specific stretch of DNA, known as the ‘iron-box’ motif to form a dimer-of-dimer complex. Molecular dynamics followed by protein-DNA bipartite network analysis was performed on a set of four IdeR-DNA complexes to obtain a molecular level understanding of IdeR-DNA interactions. A striking observation was the dissociation of IdeR-DNA complex in the absence of iron, undoubtedly establishing the importance of iron for IdeR-DNA binding. At the residue level, hydrogen bond and non-covalent interactions clearly established the importance of N-terminal residues for DNA binding, thereby confirming the conjecture put forth in the previous chapter. An important aspect studied in this chapter is the allosteric nature of IdeR-DNA binding. Recent years have witnessed a paradigm shift in the understanding of allostery. Unlike the classical definition of allostery that was based on static structures, the newer definition is based on the conformational ensemble as represented by the shift in the energy landscape of the protein. The allosteric nature of IdeR-DNA complex was probed using simulated trajectories and indeed they suggest iron to be an allosteric regulator of the protein. Finally, based on the known experimental data and observations presented in Chapters 4 and 5, a multi-step model of IdeR activation and DNA binding has been proposed. In chapter 6, a global perspective of IdeR regulation in M.tb was obtained. This was important to gain insights about the influences of iron and its regulation at the M.tb cellular level. A genome scale identification of all possible IdeR targets based on the presence of ‘iron-box’ motif in the promoter region of the genes was carried out. An interesting aspect of this study was the use of energetic information from previous molecular dynamics study as an input for generation of the motif. A total of 255 such IdeR targets were identified and converted into an IdeR target network (IdeRnet). Along with IdeRnet, an unbiased systems level protein-protein interaction network was also generated. To study the response of the pathogen to external perturbations, iron-specific gene expression data was integrated into the network as node weights and edge weights. Analysis of IdeRnet provides interesting associations between fatty acid metabolism and IdeR regulations. Specific genes such as fadD32, DesA3 or lppW have been found to be affected by IdeR mutation. While IdeRnet discusses the direct associations, the global level responses are monitored by analysing pathways for the flow of information in the protein-protein interaction network (PPInet). Comparisons of the PPInets under conditions such as altering iron concentrations and lack of iron homeostasis led to the identification of the ‘top-most’ active paths under the different conditions. The study clearly suggests a halt in the protein synthesis machinery and decreased energy consumption under iron scarcity and an uninhibited consumption of energy when iron homeostasis is perturbed. In the final chapter (Chapter 7), flux balance analyses has been used to investigate the influence of iron on M.tb metabolism. The importance of iron for metabolic enzymes has already been established in the previous chapter. Additionally, M.tb is known to produce siderophores, an important metabolite that requires amino acids as its precursors, for iron extraction. All this, together highlighted the importance of iron and its regulation of M.tb metabolism. Flux balance analysis has been used previously to study the metabolic alterations that occur in an organism under different conditions. For this study, iron specific gene expression data was also incorporated into the model as reaction bounds and the flux values so obtained were compared in different environmental conditions. The study provided valuable insights into the metabolic adjustments taken up by M.tb under iron stress conditions and correlates well with the responses observed from the interactome as well as experimental observations. Most significantly, changes were observed in the energy preferences of the cell. For instance, it was noted that while the wild type strain of M.tb prefers synthesis of ATP via glycolysis, the IdeR mutant strain preferred oxidative phosphorylation. The picture becomes clearer when one accounts for the uncontrolled utilization of energy and rapid activation of protein synthesis machinery in the IdeR mutant strain. Biological systems are inherently multiscale in nature and therefore for a successful drug target regime, analysis of the genome to the phenome, which captures interactions at multiple levels, is essential. In this thesis, a detailed understanding of iron homeostasis and regulation in M.tb at multiple levels has been attempted. More importantly, insights obtained from one level, formed questions in the next level. The study was initiated at the inter-cellular level, where the influence of iron on HPI was modeled and analysed. From this study, IdeR, an iron-responsive transcription factor was identified as a key player that had the potential to alter host-pathogen interactions in the favour of the host. For a complete understanding of how IdeR regulates iron homeostasis, it was imperative to obtain a molecular level insight of its mechanism of action. Finally, the various aspects of IdeR regulation were investigated at the cellular level by analysing direct and indirect influences of IdeR on M.tb proteome and metabolome. The study suggests certain therapeutic interventions, such as 1) reduction in the concentration of free transferrin various, 2) mutations at the N-terminal sites of IdeR, 3) regulation of proteins involved in production of mycolic acids by iron and 4) perturbation of altering energy sources, which capitalize on iron and should be investigated in detail. In summary, the consequences of iron on TB infection were studied by threading different levels. This is based on the belief that most biological functions involve multiple spatio-temporal levels with frequent cross talks between the different levels, thereby making such multiscale approaches very useful.

During the past decade the effects of macromolecular crowding on reaction pathways is gaining in prominence. The stress is to move out of the realms of ideal solution studies and make conceptual modifications that consider non-ideality as a variable in our calculations. In recent years it has been shown that molecular crowding exerts significant effects on all in vivo processes, from DNA conformational changes, protein folding to DNA-protein interactions, enzyme pathways and signalling pathways. Both thermodynamic as well as kinetic parameters vary by orders of magnitude in uncrowded buffer system as compared to those in the crowded cellular milieu. Ignoring these differences will restrict our knowledge of biology to a “model system” with few practical understandings. The recent expansion of the genome database has stimulated a study on numerous previously unknown proteins. This has whetted our thirst to model the cellular determinants in a more comprehensive manner. Intracellular extract would have been the ideal solution to re-create the cellular environment. However, studies conducted in this solution will be contaminated by interference with other biologically active molecule and relevant statistical data cannot be extracted out from it. Recent advances in methodologies to mimic the cellular crowding include use of inert macromolecules to reduce the volume occupancy of target molecules and the use of immobilization techniques to increase the surface density of molecules in a small volumetric region. The use of crowding agents often results in non-specific interaction and side-reactions like aggregation of the target molecules with the crowding agents themselves. Immobilization of one of the interacting partners reduces the probability of aggregation and precipitation of bio-macromolecules by restricting their degrees of freedom. Covalent linkage of molecules on solid support is used extensively in research for creating a homogeneous surface of bound molecules which can be interrogated for their reactivity. However, when it comes to biomolecules, direct immobilization on solid support or use of organic linkers often results in denaturation. The use of bio-affinity immobilization techniques can help us overcome this problem. Since mild conditions are needed to regenerate such a surface, it finds universal applicability as bio-memory chips. This thesis focuses on our attempts to design a physiologically viable immobilization technique for following rotein-protein/protein-DNA interactions. The work explores the mechanism for biological interactions related to transcription process in E. coli. Chapter 1 deals with the literary survey of the importance and effects of molecular crowding on biological reactions. It gives a brief history of the efforts been made so far by experimentalists, to mimic macromolecular crowding and the methods applied. The chapter tries to project an all-round perspective of the pros and cons of different immobilization techniques as a means to achieve a high surface density of molecules and the advancements so far. Chapter 2 deals with the detailed technicality and applicability of the Langmuir-Blodgett method. It discusses the rationale behind our developing this technique as an alternate means of bio-affinity immobilization, under physiologically compatible conditions. It then goes on to describe our efforts to follow the sequence-specific and sequential assembly process of a functional RNA polymerase enzyme with one immobilized partner and also explore the role of omega subunit of RNAP in the reconstitution pathway. This chapter uses the assembly process of a multi-subunit enzyme to evaluate the efficiency of the LB system as a universal two-dimensional scaffold to follow sequence-specific protein-ligand interaction. Chapter 3 discusses the application of LB technique to quantitatively evaluate the kinetics and thermodynamics of promoter-RNA polymerase interaction under conditions of reduced dimensionality. Here, we follow the interaction of T7A1 phage promoter with Escherichia coli RNA polymerase using our Langmuir-Blodgett technique. The changes in mechanistic pathway and trapping of kinetic intermediates are discussed in detail due to the imposed restriction in the degrees of freedom of the system. The sensitivity of this detection method is compared vis-a-vis conventional immobilization methods like SPR. This chapter firmly establishes the universal application of LB technique as a means to emulate molecular crowding and as a sensitive assay for studying the effects of such crowding on vital biological reaction pathway. Chapter 4 describes the mechanistic pathway for the physical binding of MsDps1 protein with long dsDNA in order to physically protect DNA during oxidative stress. The chapter describes in detail the mechanism of physical sequestering of non-specific DNA strands and compaction of the genome under conditions where a kinetic bottleneck has been applied. The data obtained is compared with results obtained in the previous chapter for the sequence-specific DNA-protein interaction in order to understand the difference in recognition process between regulatory and structural proteins binding to DNA. Chapter 5 deals with the evaluation of the σ-competition model in E. coli for three different sigma factors (all belonging to the σ-70 family). Here again, we have evaluated the kinetic and thermodynamic parameters governing the binding of core RNAP with its different sigma factors (σ70, σ32and σ38) and performed a comparative study for the binding of each sigma factor to its core using two different non-homogeneous immobilization techniques. The data has been analyzed globally to resolve the discrepancies associated with establishing the relative affinity of the different sigma factors for the same core RNA polymerase under physiological conditions. Chapter 6 summarizes the work presented in this thesis. In the Appendix section we have followed the unzipping of promoter DNA sequence using Optical Tweezers in an attempt to follow the temporal fluctuations occurring in biological reactions in real time and at a single molecule level.