Дисертації з теми "ArnB Protein"
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Gowher, Ali. "Characterization of protein factors targeting RNA into human mitochondria." Phd thesis, Université de Strasbourg, 2013. http://tel.archives-ouvertes.fr/tel-01071841.
Повний текст джерелаLi, Yi. "Study of Arnt-interacting proteins on Arnt-dependent signaling pathways." Scholarly Commons, 2006. https://scholarlycommons.pacific.edu/uop_etds/2786.
Повний текст джерелаUchikawa, Emiko. "A structural approach of RNA-protein recognition and kinetics of binding in two examples : tRNA aminoacylation by arginyl-tRNA synthetase and 7SK stabilization by LaRP7." Strasbourg, 2011. http://www.theses.fr/2011STRA6052.
Повний текст джерелаIn the cell, RNA-protein interactions are fundamental to many processes involved in the regulation of gene expression, including pre-mRNA splicing, polyadenylation, editing, transport, cytoplasmic targeting, mRNA turnove and translation. In addition to these post-transcriptional processes, RNA-prote in interactions may also play a key rôle in transcription. Indeed, in addition to its coding capacity, which makes both DNA and RNA recipients of the genetic message, the high variability and conformationnal flexibility of RNA structure creates a number of unique binding sites and the potential for complex regulation by RNA binding proteins. These use a large Iibrary of structural modules in order to recognize RNAs in a combination of sequence- or structure-dependent ways, leading to a wide range of transient to more stable interactions. This manuscript describes our endeavour to reveal the details of RNAprotein interactions at the molecular level in several examples taken in two different fields of cell biology, transcription and translation. Our targets were chosen to better understand the molecular foundation of interactions critical for the cell survival, and represent different binding modes ofproteins to RNA. Aiming to use X-ray crystallography, a well-accepted and reliable mean to analyze recognition details at atomic resolution, we developed for each target a purification protocolleading to homogeneous preparations that were used for crystallization and subjected to various anai}'ses, including functional assays and biophysical characterization
Corsi, Flavia. "Towards the in silico reconstruction of protein interaction networks : identification of DNA- and RNA-protein interfaces, and construction of a database of multiple interactions of proteins." Electronic Thesis or Diss., Sorbonne université, 2019. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2019SORUS452.pdf.
Повний текст джерелаThis thesis focuses on the characterization and prediction of DNA- and RNA-binding sites on protein structures, with some comparisons with protein-protein ones. We compiled and manually curated a non-redundant and representative set of 187 high resolution protein-DNA complexes, with the available 82 protein unbound conformations, that could be used as a reference benchmark. We conducted a comprehensive analysis of sequence- and structure-based properties of protein-DNA/RNA interfaces and compared them with respect to protein-protein interfaces and to non-interacting protein regions. We developed JET2DNA and JET2RNA, new methods for predicting DNA- and RNA-binding sites on protein surfaces. Combining four biologically meaningful descriptors, they outperform other machine-learning methods, in terms of predictive power and robustness to conformational changes. Our tools demonstrated to be instrumental in discovering alternative DNA/RNA-binding sites and in deciphering their properties. This could be very helpful for drug design and repurposing. To give a comprehensive view of plasticity of DNA-binding proteins and structural information on their multiple interactions, we constructed the Protein-(Protein)-DNA database (P(P)DNAdb). It comprises the 187 protein-DNA complexes in our benchmark, protein unbound forms and structures of other complexes where the proteins, or closed homologs, were in contact with other proteins. The user can access properties of the interfaces, visualize conformational changes associated to the binding of different partners and the location of the DNA-binding residues on the unbound structures and on the complexes with the other protein partners
Jarrige, Domitille. "Déchiffrer le "code OPR" pour une meilleure compréhension du rôle physiologique des protéines OPR." Electronic Thesis or Diss., Sorbonne université, 2019. http://www.theses.fr/2019SORUS632.
Повний текст джерелаFollowing endosymbiosis, the chloroplast genome shrunk and became reliant on the host genome for its expression. In Chlamydomonas reinhardtii, Octotricopeptide repeat proteins (OPR), encoded in the nucleus, control the expression of a specific organellar mRNA. The OPR repeat is a degenerate motif of 38 amino-acids, folding into a tandem of antiparallel α-helices which can bind to RNA. An individual OPR repeat is predicted to interact with one given nucleotide thanks to specificity-conferring residues at defined positions within the repeat. OPR proteins contain tracks of successive OPR motifs, thus they can bind to a specific RNA “target” sequence and act on it. I aimed to study this specificity, called the “OPR code”, starting with a draft code based on known OPR protein/mRNA couples. I mutated in vivo the chloroplast targets of some OPR factors to disrupt the OPR/RNA interaction, and then tried to restore it by mutating the specificity-conferring residues in the corresponding repeats. Surprisingly, OPR/RNA interactions seem very resilient, challenging our view of how the specificity is established in vivo. Complementary functional studies that I performed on the OPR factors MDB1 and MTHI1 revealed that chloroplast gene expression might rely on complex networks of nuclear factors. By cooperating those putative systems would be both more specific and more resilient
Mendler, Claudia Theresa [Verfasser], Arne [Akademischer Betreuer] [Gutachter] Skerra, and Markus [Gutachter] Schwaiger. "Protein-Engineering für die In-Vivo-Bildgebung / Claudia Theresa Mendler ; Gutachter: Markus Schwaiger, Arne Skerra ; Betreuer: Arne Skerra." München : Universitätsbibliothek der TU München, 2017. http://d-nb.info/1129874621/34.
Повний текст джерелаPARK, YOUNG CHUL. "Stabilite d'une proteine dimerique complexe : la tyrosyl-arnt synthetase." Paris 7, 1998. http://www.theses.fr/1998PA077266.
Повний текст джерелаTakeuchi, Akiko Krol Alain Allmang-Cura Christine. "RNA-protein interaction in the selenoprotein synthesis machinery." Strasbourg : Université de Strasbourg, 2009. http://eprints-scd-ulp.u-strasbg.fr:8080/1133/01/TAKEUCHI_Akiko_2009.pdf.
Повний текст джерелаThèse soutenue sur un ensemble de travaux. Titre provenant de l'écran-titre. Bibliogr. 11 p.
Holla, Andrea Dorothee [Verfasser], Arne [Akademischer Betreuer] Skerra, and Dirk [Akademischer Betreuer] Haller. "Protein-Engineering eines Anticalins mit Bindungsspezifität für DC-SIGN / Andrea Dorothee Holla. Gutachter: Arne Skerra ; Dirk Haller. Betreuer: Arne Skerra." München : Universitätsbibliothek der TU München, 2012. http://d-nb.info/1031075763/34.
Повний текст джерелаYavrom, Sheena. "Evidence that ARNT plays a role in the regulation of the immunoglobulin heavy chain enhancer and identification of a putative ARNT ligand." Scholarly Commons, 1998. https://scholarlycommons.pacific.edu/uop_etds/516.
Повний текст джерелаTakeuchi, Akiko. "RNA-protein interaction in the selenoprotein synthesis machinery." Strasbourg, 2009. http://www.theses.fr/2009STRA6054.
Повний текст джерелаThe 21st amino acid selenocysteine is encoded by a UGA codon that usually signifies translational termination. Selenoprotein synthesis therefore requires specialized factors. Among these is SBP2 that binds the SECIS, a stem-loop structure in the 3’UTR of selenoprotein mRNAs. In structural analyses of SBP2, we isolated and functionally characterized Drosophila melanogaster SBP2. By comparing it with human SBP2, we identified an additional RNA binding domain that is essential for SECIS and 60S ribosomal subunit binding, and also enables SECIS structure selectivity. In addition, computational and biophysical analyses established that SBP2 is globally unfolded, supporting our hypothesis that SBP2 is an Intrinsically Disordered Protein and becomes folded in the presence of partners yet to be identified. Finally, we searched for potential partners of SBP2 and our results showed that the molecular assembly of selenoprotein mRNPs has many similarities with that of sn/snoRNPs
Mayer, Jan-Peter Andreas [Verfasser], Arne [Akademischer Betreuer] Skerra, Wolfgang [Akademischer Betreuer] Liebl, and Bernhard [Akademischer Betreuer] Küster. "Rationales und kombinatorisches Protein-Engineering mit Lipocalinen / Jan-Peter Andreas Mayer. Gutachter: Wolfgang Liebl ; Arne Skerra ; Bernhard Küster. Betreuer: Arne Skerra." München : Universitätsbibliothek der TU München, 2013. http://d-nb.info/1036262170/34.
Повний текст джерелаLe, Borgne Maïlys. "Étude in vivo de la fonction biologique de la protéine de liaison aux ARN Mex-3B." Thesis, Lyon 1, 2012. http://www.theses.fr/2012LYO10141.
Повний текст джерелаThe RNA binding-protein MEX-3 is a post-transcriptional regulator involved in early embryogenesis of the nematode Caenorhabditis elegans. We have recently reported the characterization of a novel family of four mammalian genes homologous to hMex-3 (called hMex-3A, 3B, 3C and 3D). To gain insight into the biological functions of these proteins in vivo, we disrupted the Mex-3B gene in mice. Using this experimental approach, we found that Mex-3B is as a major regulator of spermatogenesis. We observed that male Mex-3B null mice hypofertile and present an obstruction of seminiferous epithelium. Phagocytic properties of Sertoli cells were impaired, thus impeding the clearance of residual bodies released during spermiogenesis. Exploration of the underlying molecular mechanisms revealed that Mex-3B regulates phagocytosis through the activation and the transport at the peripheral membrane of Rap1GAP, a protein that downregulates the small G protein Rap1. Consistently, the Rap1-dependent recruitment of the junction proteins, connexin 43 and N-Cadherin at the cell surface was compromised in Mex-3B deficient mice. In conclusion, my work highlights a key role gor Mex-3B in the spatial control of Rap1 signaling during spermatogenesis
Kirchner, Christian Oliver [Verfasser], Arne [Akademischer Betreuer] [Gutachter] Skerra, and Wolfgang [Gutachter] Liebl. "Protein-Engineering eines Anticalins mit Bindungsspezifität für das Anthrazyklin-Zytostatikum Doxorubicin / Christian Oliver Kirchner. Betreuer: Arne Skerra. Gutachter: Wolfgang Liebl ; Arne Skerra." München : Universitätsbibliothek der TU München, 2016. http://d-nb.info/1113181958/34.
Повний текст джерелаLindenbaum, Pierre. "Roxan, une nouvelle proteine cellulaire interagissant avec la proteine non-structurale nsp3 du rotavirus : clonelt* : un programme en ligne trouvant des strategies de clonage (doctorat : microbiologie)." Paris 11, 2000. http://www.theses.fr/2000PA114811.
Повний текст джерелаChristians, Arne [Verfasser], and Stefan [Akademischer Betreuer] Wiemann. "Funktionelle Charakterisierung des putativen Tumorsuppressors "Epithelial Membrane Protein 3" / Arne Christians ; Betreuer: Stefan Wiemann." Heidelberg : Universitätsbibliothek Heidelberg, 2014. http://d-nb.info/1180300955/34.
Повний текст джерелаArmaos, Alexandros 1989. "Computational characterization of protein-RNA interactions and implications for phase separation." Doctoral thesis, Universitat Pompeu Fabra, 2020. http://hdl.handle.net/10803/668546.
Повний текст джерелаA pesar de lo que se consideraba anteriormente, el papel del ARN no es solo transportar la información genética del ADN a las proteínas. De hecho, el ARN ha demostrado estar implicado en muchos procesos celulares más complejos. La evidencia reciente sugiere que los transcriptos tienen un papel regulador en la expresión génica y contribuyen a la organización espacial y temporal del entorno intracelular. Lo hacen interactuando con proteínas de unión a ARN (RBP) para formar redes complejas de ribonucleoproteína (RNP), sin embargo, los determinantes clave que rigen la formación de estos complejos aún no se conocen bien. En este trabajo, describiré algoritmos que he desarrollado para estimar la capacidad de los ARN de interactuar con las proteínas. Además, ilustraré aplicaciones de métodos computacionales para proponer una maquinaria alternativa para el Xist lncRNA y su red de interacciones. Finalmente, mostraré cómo las predicciones computacionales pueden integrarse con enfoques de alto rendimiento para dilucidar la relación entre la estructura del ARN y su capacidad para interactuar con las proteínas. Concluyo discutiendo preguntas abiertas y oportunidades futuras para el análisis computacional de la red reguladora de la célula. En general, el objetivo subyacente de mi trabajo es proporcionar a los biólogos nuevas ideas sobre la asociación funcional entre ARN y proteínas, así como herramientas sofisticadas que facilitarán su investigación sobre la formación de complejos RNP.
Pintard, Lionel. "Spb1p est une méthylase de levure impliquée dans la maturation des ARNr." Montpellier 1, 2000. http://www.theses.fr/2000MON1T019.
Повний текст джерелаBarkovskiy, Mikhail [Verfasser], Arne [Akademischer Betreuer] Skerra, Arne [Gutachter] Skerra, and Kay H. [Gutachter] Schneitz. "Protein design of hapten-specific Anticalins as therapeutic antidotes and biochemical reagents / Mikhail Barkovskiy ; Gutachter: Arne Skerra, Kay H. Schneitz ; Betreuer: Arne Skerra." München : Universitätsbibliothek der TU München, 2020. http://d-nb.info/1216626367/34.
Повний текст джерелаKarlikow, Margot. "Drosophila CG4572 protein and the spread of the RNAi antiviral immune signal." Thesis, Paris 6, 2015. http://www.theses.fr/2015PA066713/document.
Повний текст джерелаDuring viral infection, cell survival will depend on adequately giving, receiving and processing information to establish an efficient antiviral immune response. Cellular communication is therefore essential to allow the propagation of immune signals that will confer protection to the entire organism.The major antiviral defense in insects is the RNA interference (RNAi) mechanism that is activated by detection of viral double-stranded RNA (dsRNA). The antiviral RNAi mechanism can be divided in cell- and non-cell- autonomous. In cell-autonomous RNAi, the silencing process is limited to the cell in which the viral dsRNA is produced. In non-cell-autonomous (systemic) RNAi, the interfering effect occurs in cells different from where the viral dsRNA was produced. In insects the systemic RNAi response remains poorly characterized. My PhD explores the role of the Drosophila CG4572/DORA protein in the establishment of systemic antiviral RNAi. It also investigates the nature of immune signals that trigger the antiviral response. I provide evidence for the existence of two different mechanisms of cell-cell communication that allow the spread of the immune signal: extracellular vesicles and tunneling nanotubes. I describe that DORA-positive extracellular vesicles carry fragments of viral RNAs that can spread and confer specific antiviral protection in flies. I also present the characterization of tunneling nanotubes (TNTs) containing components of the RNAi machinery, DORA and dsRNA and I hypothesize on the use of TNTs in the spread of the immune signal.Both mechanisms of cell-to-cell communication are coupled for the first time to the antiviral response in Drosophila melanogaster
Chernov, Konstantin Grigorievich. "Interplay of YB-1 between tubulin and mRNA." Thesis, Evry-Val d'Essonne, 2008. http://www.theses.fr/2008EVRY0040/document.
Повний текст джерелаYB-1 is a major regulator of gene expression in eukaryotic cells. In addition to its role in transcription, YB-1 plays a key role in translation and stabilization of mRNAs. We identify several novels YB-1 protein partners by affinity chromatography of different tissue extracts. We observed that YB-1 interacts with tubulin and microtubules and stimulates microtubule assembly in vitro. Microtubules assembled in the presence of YB-1 exhibited a normal single wall ultrastructure where YB-1 probably coats the outer microtubule wall. Furthermore, we found that YB-1 also promotes the assembly of MAPs-tubulin and subtilisin-treated tubulin. Additionally, we demonstrated that tubulin interferes with mRNA:YB-1 complexes. These results suggest that YB-1 may regulate microtubule assembly in vivo and that its interaction with tubulin may contribute to the control of mRNA translation. The translational status of mRNPs in vivo depends on amount of YB-1 associated with mRNA. We show here that at low YB-1:mRNA ratios mRNP complexes possess an incompact structures, whereas saturated mRNPs are compact. This structural change corresponds to translation inhibition when mRNA moves from polysomal (translatable) to free (untranslatable) mRNPs. Saturated mRNPs bind to microtubules via protein:protein interactions and tend to self-aggregate on microtubule surface. This property could contribute to stress granule formation, mRNPs traffic and localization of translation apparatus within cytoplasm. Finally, the facilitated diffusion model was developed to explain enhancement of microtubule assembly by positively charged natural polyamines in living cells. Altogether our data contribute to the understanding of fundamental biological processes
Falcon, de Longevialle Alexis. "Identification des protéines PPR impliquées dans l'épissage des ARN messagers dans les chloroplastes et les mitochondries chez Arabidopsis Thaliana." Thesis, Evry-Val d'Essonne, 2010. http://www.theses.fr/2010EVRY0015.
Повний текст джерелаThe RNA splicing mechanism in organelles is described to be ancestral to that of the nuclear spliceosome. However, whereas this last complex is well known, only very few splicing factors have been identified and characterized in chloroplasts and mitochondria. Many RNA binding proteins have acquired roles in RNA splicing, and indeed a variety of often unrelated RNA binding proteins have essential functions in splicing of many plastid introns in plants, with varying degrees of specificity. The largest family of RNA binding proteins in plant organelles is the pentatricopeptide repeat (PPR) family. PPR proteins are involved in diverse post-transcriptional processes in organelles. In 2006, among hundreds of higher plant proteins of this family, only one was described as being required for a splicing event - PPR4 was shown to be absolutely and specifically required for the trans-splicing of the rps12 intron 1 in plastids (Schmitz-Linneweber et al., 2006). The main purpose of this PhD thesis was to characterize other PPR proteins involved in this process. By using a reverse genetics approach and by developing tools for the detection of splicing defects, seven new PPR proteins involved in RNA splicing of a subset of chloroplast or mitochondria introns have been characterized. In parallel, in order to characterize proteins involved in PPR-containing complexes, a TAP-TAG approach has been carried out on a few PPR proteins involved in splicing or editing of organellar RNA. The identification of partner proteins of 3 PPR proteins allows us to draw new mechanistic models and new hypotheses. Finally, the final part of the manuscript describes the discovery of splicing isoforms of PPR-encoding mRNAs. Alternative splicing may be involved in regulation of PPR gene expression and/or in increasing the diversity of the PPR protein family
Soicke, Arne [Verfasser]. "Stereoselektive Synthese neuartiger Prolin- und Pseudoprolin-Dipeptidmimetika zur Modulation von Peptid-Protein-Wechselwirkungen / Arne Soicke." München : Verlag Dr. Hut, 2014. http://d-nb.info/1067707913/34.
Повний текст джерелаManival, Xavier. "Etude fonctionnelle et structurale de l'interaction de la protéine antiterminatrice SacY avec son ARN cible chez Bacillus subtilis : mise en évidence d'un nouveau type de domaine protéique de liaison à l'ARN." Montpellier 1, 1997. http://www.theses.fr/1997MON1T010.
Повний текст джерелаRall, Nils Arne [Verfasser], Heinz [Akademischer Betreuer] Neumann, and Henning [Akademischer Betreuer] Urlaub. "A Method for the Quantitative Analysis of Protein-Protein Interactions In Vivo / Nils Arne Rall. Betreuer: Heinz Neumann. Gutachter: Heinz Neumann ; Henning Urlaub." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2016. http://d-nb.info/1096752069/34.
Повний текст джерелаStefani, Arno Gert [Verfasser], and Johannes [Gutachter] Huber. "Nonparametric and Nonasymptotic Confidence Intervals for Estimation of Mutual Information with Applications in Protein-Protein Docking Analysis / Arno Gert Stefani ; Gutachter: Johannes Huber." Erlangen : Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 2018. http://d-nb.info/115500616X/34.
Повний текст джерелаNguyen, Chi Mai. "Post-transcriptional regulation during spermatogenesis : Role of the RNA-binding protein hu." Toulouse 3, 2008. http://thesesups.ups-tlse.fr/365/.
Повний текст джерелаSpermatogenesis, the elaborate process by which sperm are produced, is marked by dramatic proliferation and differentiation. During the late steps of spermatogenesis, transcription suddenly ceases prior the end of differentiation, because of drastic epigenetic modifications that result in chromatin compaction. Thus, haploid germ cells make use of extensive temporal mRNA storage and translation regulation to ensure stage-specific protein synthesis. Factors and cellular compartments involved in these post-transcriptional controls are still poorly understood. During my PhD, I hypothesized that the two RNA binding proteins HuR/ELAVL1 and AUF1/hnRNP D, might play a role in these controls. They bind AU-rich element-containing mRNAs (ARE-mRNAs) in somatic cells and regulate their stability and translation: HuR protects ARE-mRNAs from degradation and favours their translation, whereas AUF1 usually induces their degradation. First, to investigate the contribution of HuR and AUF1 to the post-transcriptional mechanisms occurring in germ cells, I used transgenic mice derived in our laboratory overexpressing HuR (HuRtg) and AUF1 (AUF1tg) in their testes. Strikingly, whereas spermatogenesis proceeded normally in AUF1tg mice, HuR overexpression impaired spermatogenesis, revealing the importance of a regulated expression of HuR to fulfill male germ cell differentiation. The comparative analysis of AU-transcriptome of pre-pubertal wild type testes with that of HuRtg and AUF1tg testes, combined with computational analyses and RNA/Protein immunoprecipitation experiments, revealed that these two proteins regulate different targets mRNAs and thus exhibit different activities. .
Schreiber, Arne [Verfasser]. "Bildungsmechanismus und physiologische Relevanz supramolekularer Proteincluster des Amyloid Precursor Protein APP in der Zellmembran / Arne Schreiber." Bonn : Universitäts- und Landesbibliothek Bonn, 2013. http://d-nb.info/104486785X/34.
Повний текст джерелаBESSE, LAURENT. "Mise au point d'un reactif chimique permettant l'etude des interactions proteine-proteine. Application aux arn polymerases de levure." Paris 11, 1996. http://www.theses.fr/1996PA112232.
Повний текст джерелаRouhana, Jad. "Etude et modulation des interactions protéine-protéine : l’activation de la petite protéine G Arf1 par son facteur d’échange Arno." Thesis, Montpellier 1, 2013. http://www.theses.fr/2013MON13507/document.
Повний текст джерелаArf1 is a small GTPases, essentially involved in the vesicular traffic. Arf1 switch between two conformations, an active form bound to GTP and an inactive form bound to GDP. Arno is one of the exchange factors (GEF) that can activate Arf1, through its catalytic Sec7 domain, promoting the exchange of GDP by GTP. Activated in breast cancer cells, Arf1 plays an important role in the migration and proliferation of cancer cells.The aim of my thesis was the study and the modulation of the interaction between small G proteins and their GEFs, more precisely the Arf1-Arno interaction. My work has been planned around two axes: (1) the study of the interaction between Arf1 and Arno, and its modulation with a known inhibitor Brefeldin A (BFA). (2) The development of a rational strategy for designing inhibitors of protein-protein interaction for the Arf1-Arno complex.In the first part of my PhD work, we set up a Surface Plasmon Resonance (SPR) method allowing to determine the kinetic parameters of the interaction between Arf1 and Arno. We also studied the effects of allosteric partners such as GDP, GTP and Mg2+ as well as the known uncompetitive inhibitor (Brefeldin A). This SPR approach allowed a very informative analysis at qualitative and quantitative levels of the various complexes taking place during the exchange reaction that should help to solve the inhibitory mechanism for the known inhibitors reported in the literature. In the second part of my thesis, we propose a strategy for targeting the interaction between Arf1and Arno. This approach is based on virtual screening of fragments at hotspot regions. Using biophysical techniques such fluorescence techniques, SPR, NMR and X-Ray crystallography, we identified and validated Hits, showing by crystallographic structural data their modes of interaction with the target protein Arno. A fluorescence polarization test was also developed to identify false positive fragments to eliminate promiscuous aggregators. Taken together, our work proposes a method based on SPR allowing the study of known inhibitors of GEFs, understanding at molecular level their mode of action. We also propose a general strategy for finding Hit fragments that designing competitive inhibitor of the interaction small G protein with its GEFs, that can be the scaffold for designing more powerful inhibitors
Sharma, Kamal Kant. "Molecular mechanism of the hepatitis C virus core protein chaperone properties : Physicochemical investigation by fluorescence and surface plasmon resonance." Strasbourg, 2011. https://publication-theses.unistra.fr/public/theses_doctorat/2011/SHARMA_Kamal_Kant_2011.pdf.
Повний текст джерелаOpen reading frame (ORF) of 9. 6kb HCV genomic RNA encodes at least 10 proteins, 4 structural and 6 non-structural, during translation process. The core is one of those 4 structural proteins and considered as a multifunctional chaperone involving in several viral processes like cell proliferation, differentiation, RNA packaging, nucleocapsid formation and recombinant genetic variability. With the virtue of its chaperone properties, Domain D1 dimerises the 3’ untranslated region (3’ UTR) of the genomic RNA. However, the mechanism of the core chaperone activity in the dimerisation of the genomic RNA and in binding with its target nucleic acids are still unknown and were investigated in this present project. To reach this objective, we used fluorescence and surface plasmon resonance (SPR) techniques. By using the native D1 domain and peptides derived from this domain, we first characterized the binding parameters and the conformational changes associated with the binding of these peptides to the native and mutated sequences from HCV 3’ UTR sequences. Next, we investigated the destabilization of model and HCV ODNs secondary structure by the D1 domain and its mutants and found that core peptides only marginally destabilise the secondary structures of ODNs. In a last step, we described the molecular mechanisms of the core chaperone properties based on the hybridization kinetics of various HCV and model oligonucleotides. These chaperone properties of core are thought to intervene in processes like the encapsidation, the synthesis of the complementary strand of the genomic RNA and the recombination mechanisms participating to the genetic variability of the virus
Collet, Axelle. "Caractérisation des enzymes de formation de la coiffe du virus du Nil Occidental et du métapneumovirus humain." Thesis, Aix-Marseille, 2015. http://www.theses.fr/2015AIXM4087.
Повний текст джерелаMy PhD project is focus on the study of the enzymatic activities involved in the RNA capping pathway of two RNA viruses: the West Nile Virus (WNV) and the human metapneumovirus (hMPV). These viruses encode for enzymes allowing the addition of a cap-1 structure (m7GpppN2’Om) to their mRNA 5’ ends. The NS5 N-terminal domain (NS5MTase) of WNV harbours the N7- and 2’O-methyltransferase activities (N7- and 2’O-MTase); and it has been proposed that NS5MTase also bears a guanylyltransferase activity (GTase). I have identified residues involved in the NS5MTase interaction sites with their RNAs substrate. My assays demonstrate the importance of the cap-binding site for the 2’O-methylation but not for the N7-methylation. In parallel, I have tried to identify putative catalytic residues of the GTase activity by reverse genetics. Preliminary results suggest that NS5MTase K29 could be a catalytic residue.Concerning hMPV, I performed a functional analysis of CR-VI+ domain of the protein L. I demonstrated that the CR-VI+ domain harbours the N7- and 2’O-MTase activities and identified the residues involved in the mRNA recruitment. I showed that the methylation order is not canonical with the 2’O-methylation preceding the N7-methylation. Finally, I showed that the domain harbours an additional GTP hydrolysis activity, representing the first step of RNA cap formation for Mononegavirales.This work demonstrates that this MTase domains harbour 2 or 3 of the enzymatic activities required for viral RNA cap synthesis and represent attractive targets for the development of antivirals
Lopes, Anne. "Evolution dirigée de deux aminoacyl-ARNt synthétases : Mise en place et applications d'une méthode de 'protein design'." Phd thesis, Ecole Polytechnique X, 2008. http://pastel.archives-ouvertes.fr/pastel-00003713.
Повний текст джерелаBERAUD, DUFOUR SOPHIE. "Mecanisme d'activation de la protein g, arf1 : role coordonne des membranes lipidiques et du facteur d'echange, arno." Nice, 1999. http://www.theses.fr/1999NICE5305.
Повний текст джерелаDucongé, Frédéric. "Sélection in vitro d'aptamères ARN pouvant interagir avec la structure ARN TAR du VIH-1." Bordeaux 2, 1999. http://www.theses.fr/1999BOR28671.
Повний текст джерелаRibeiro, Diogo. "Discovery of the role of protein-RNA interactions in protein multifunctionality and cellular complexity." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0449/document.
Повний текст джерелаOver time, life has evolved to produce remarkably complex organisms. To cope with this complexity, organisms have evolved a plethora of regulatory mechanisms. For instance, thousands of long non-coding RNAs (lncRNAs) are transcribed by mammalian genomes, presumably expanding their regulatory capacity. An emerging concept is that lncRNAs can serve as protein scaffolds, bringing proteins in proximity, but the prevalence of this mechanism is yet to be demonstrated. In addition, for every messenger RNA encoding a protein, regulatory 3’ untranslated regions (3’UTRs) are also present. Recently, 3’UTRs were shown to form protein complexes during translation, affecting the function of the protein under synthesis. However, the extent and importance of these 3’UTR-protein complexes in cells remains to be assessed.This thesis aims to systematically discover and provide insights into two ill-known regulatory mechanisms involving the non-coding portion of the human transcriptome. Concretely, the assembly of protein complexes promoted by lncRNAs and 3’UTRs is investigated using large-scale datasets of protein-protein and protein-RNA interactions. This enabled to (i) predict hundreds of lncRNAs as possible scaffolding molecules for more than half of the known protein complexes, as well as (ii) infer more than a thousand distinct 3’UTR-protein complexes, including cases likely to post-translationally regulate moonlighting proteins, proteins that perform multiple unrelated functions. These results indicate that a high proportion of lncRNAs and 3’UTRs may be employed in regulating protein function, potentially playing a role both as regulators and as components of complexity
Cid, Samper Fernando 1991. "Computational approaches to characterize RNP granules." Doctoral thesis, Universitat Pompeu Fabra, 2020. http://hdl.handle.net/10803/668449.
Повний текст джерелаLos gránulos ribonucleoproteicos (gránulos RNP, por sus siglas en inglés) son complejos producidos mediante separación líquido-líquido y están constituidos principalmente por proteínas y ARN. Son responsables de numerosos procesos involucrados con la regulación del ARN. Alteraciones en la dinámica de estos complejos de proteínas y ARN están asociadas con la aparición de diversas enfermedades neurodegenerativas como el ELA o FXTAS. Sin embargo, todavía se desconocen muchos aspectos relativos a su organización interna así como las contribuciones específicas del RNA en la formación y funcionamiento de estos complejos. A fin de estudiar la estructura y formación de los gránulos RNP, hemos integrado varias bases de datos de alto rendimiento de reciente aparición. Esto incluye datos sobre la composición proteica y en ARN de los RNP, sobre la interacción de proteínas y ARN extraída de experimentos de eCLIP y sobre la estructura secundaria del transcriptoma (producida mediante PARS). Todos estos datos han sido procesados para comprender las propiedades fundamentales de los ARNs que integran los gránulos, mediante el empleo de métodos computacionales como el análisis de redes o algoritmos de agrupamiento. De esta manera, hemos producido un modelo que integra varias de estas propiedades e identifica candidatos denominados ARNs de andamiaje. Definimos ARNs de andamiaje como moléculas de ARN con una alta propensión a formar gránulos y reclutar un gran número de componentes proteicos a los gránulos RNP. También hemos encontrado que las interacciones proteína-ARN conectan los principales componentes proteicos de consenso de los gránulos de estrés (un tipo específico de gránulos RNP). También hemos estudiado la contribución de las interacciones ARN-ARN y las modificaciones post-transcriptionales del RNA en la organización interna del gránulo. Hemos aplicado estos resultados para la comprensión de la fisiopatología molecular de FXTAS, empleando también algunos datos experimentales originales. En FXTAS, una mutación en el gen FMR1 produce una repetición de microsatélite en 5´ que incrementa su capacidad como ARN de andamiaje. Este mARN mutado es capaz de secuestrar algunas proteínas importantes como TRA2A (un factor de ayuste alternativo) en gránulos RNP nucleares, impidiendo su normal funcionamiento y por consiguiente produciendo algunos síntomas asociados con el progreso de la enfermedad. Una mejor comprensión de los principios que gobiernan la formación y estructura de los gránulos puede permitir desarrollar nuevas terapias (ej: aptámeros) para mitigar el desarrollo de diversas enfermedades neurodegenerativas.
Orelle, Béatrice. "Pancreatitis associated protein (PAP) : clonage, séquençage et expression de l'ARN messager chez le rat et l'homme." Lyon 1, 1991. http://www.theses.fr/1991LYO10069.
Повний текст джерелаCirillo, Davide. "Prediction of protein and nucleic acid interactions." Doctoral thesis, Universitat Pompeu Fabra, 2016. http://hdl.handle.net/10803/403537.
Повний текст джерелаMis estudios de doctorado han tenido como propósito principal el desarrollo de herramientas bioinformáticas para la evaluación de interacciones entre proteínas y ácidos nucleicos (ANs) de forma cuantitativa. Por consiguiente, esta tesis apunta a proporcionar conocimientos sobre características moleculares y mecanismos de asociación proteína-AN aún relativamente desconocidos; concretamente, la asociación de proteínas a ARNs y ARNs no codificantes, a la vez que factores de transcripción y elementos de regulación del ADN. En este proyecto presento dos algoritmos: catRAPIDomics express y PAnDA, cuyas finalidades son las de predecir interacciones proteína-ARN y proteína-ADN respectivamente. Dichos métodos computacionales ofrecen la posibilidad de abordar problemas experimentales, así como de guiar el diseño y procedimiento de nuevas estrategias para su resolución.
Bourdeau-Julien, Isabelle. "ALS-associated RNA-binding protein FUS and mRNA translation regulation." Master's thesis, Université Laval, 2020. http://hdl.handle.net/20.500.11794/68742.
Повний текст джерелаMutations in several genes have been linked to amyotrophic lateral sclerosis (ALS),particularly in the gene coding for the Fused in Sarcoma protein (FUS). Those mutations are found in the part encoding for the nuclear localization signal, making the protein abnormallyabundant in the cytoplasm. Combined with other observations, it suggests that a toxic gainof function of FUS in the cytoplasm would be the cause of the neurodegeneration. ALS is a neurodegenerative disease that affects motor neurons and causes progressive paralysis. The molecular mechanisms causing the disease are still unknown. One of the hypotheses is the disruption of local translation of mRNAs, which allows synapses to respond quickly and independently from the cell body. Insufficient local translation to support long-term synapticactivity would lead to synaptic loss and neurodegeneration. Thereby, the objective of mystudy is to determine the role of FUS in the regulation of mRNA translation by characterizing its interaction with translational components and evaluate its function in an ALS-linked condition. I have shown that FUS is associated with stalled polyribosomes, which suggests that it plays a role in regulating mRNA translation by interacting with the core of translation.There is also an increase in the presence of FUS in the cytoplasm and in its interaction with polyribosomes following inhibition of translation through mTOR, suggesting its role as anegative regulator. In addition, ALS-related mutations amplify FUS inhibitory function bymaking FUS cytoplasmic and reducing protein synthesis. My results show that the FUSprotein would have a role as a translation inhibitor when it is cytoplasmic. There fore, increasing the presence of FUS in the cytoplasm in ALS would result in significant translation inhibition, at a level insufficient to support synaptic activity.
Kapps, Delphine. "Rôle de l'import des ARN de transfert de l'hôte dans le développement Plasmodium." Thesis, Strasbourg, 2016. http://www.theses.fr/2016STRAJ054/document.
Повний текст джерелаThe organism studied in this work is Plasmodium, the malaria parasite. The laboratory identified a membrane protein, called tRip for tRNA import protein, displaying a tRNA binding domain exposed outside of the parasite. In vivo, in P. berghei which is the murine model used, tRip mediates the import of exogenous tRNAs into the parasite cytosol. My PhD work begun with the construction of a tRip-KO strain of P. berghei to investigate the role of tRNA import and the putative involvement of tRip within a proteic complex. The phenotype of the tRip-KO strain is significantly modified compared to the wild-type parasite during the blood stage: its rate of multiplication is much lower. By proteomic analyses, I showed that many proteins are under-regulated in the tRip-KO strain, especially those very rich in asparagines. Moreover, I dentified three protein partners for tRip, being tRNA aminoacylation or modification enzymes. These results suggest that host imported tRNAs could be taken in charge by parasitic enzymes and take part to Plasmodium protein synthesis. This work reveals a new host pathogen interaction and is the first example showing exogenous tRNA import into a cell
Pérez, Cano Laura. "Structural prediction and characterization of protein-RNA interactions / Predicción y caracterización estructural de interacciones proteína-ARN." Doctoral thesis, Universitat de Barcelona, 2013. http://hdl.handle.net/10803/120481.
Повний текст джерелаLa caracterización estructural de complejos proteína-ARN es esencial para lograr una mayor comprensión en el campo de la biología molecular y la regulación celular. Los métodos computacionales de predicción estructural representan una alternativa rápida y poco costosa para la detección y caracterización de complejos biológicos. No obstante, en contraste con la gran variedad de métodos computacionales orientados a la predicción estructural de las interacciones proteína-proteína, existen muy pocos métodos enfocados al estudio de complejos proteína-ARN. En este contexto, el propósito principal de este proyecto de tesis ha sido el desarrollo y aplicación de métodos computacionales para el análisis, caracterización y predicción estructural de complejos proteína-ARN. Con este objetivo, en la primera fase de esta tesis doctoral, se han desarrollado nuevos protocolos para la predicción estructural de este tipo de complejos a partir de métodos de docking entre proteínas previamente descritos, y se han generado potenciales estadísticos por residuo, nucleótido y por pares residuo-nucleótido a partir de estructuras conocidas de complejos proteína-ARN. Dichos potenciales estadísticos por residuo se han aplicado al desarrollo de un método para la predicción de sitios de unión a ARN en proteínas y la identificación de proteínas que unen ARN. Por otro lado, se ha construido un conjunto de pruebas de complejos proteína-ARN para la evaluación de métodos de docking. Usando dicho conjunto de pruebas, se ha estudiado el poder predictivo de los potenciales estadísticos de pares residuo-nucleótido, así como otros términos energéticos, para la evaluación de soluciones de docking de complejos proteína-ARN y se ha desarrollado una nueva función de evaluación de posibles orientaciones de docking en complejos proteína-ARN, integrando aquellos términos energéticos más efectivos a nivel individual. La experiencia acumulada durante las fases iniciales de la tesis permitió la aplicación de técnicas de modelado computacional, en combinación con técnicas experimentales llevadas a cabo por colaboradores, al estudio de translin, una proteína de unión a ácidos nucleicos de gran interés biológico. Así pues, durante la fase final de este proyecto de tesis doctoral se contribuyó a la identificación de los sitios de multimerización y de unión a ácidos nucleicos en translin, y se propuso una primera aproximación estructural y dinámica de las funciones llevadas a cabo por la proteína, contribuyendo a resolver aspectos tan fundamentales como los determinantes estructurales de la unión a ARN.
Fournier, Cécile. "Caractérisation de la fixation de la protéine NEF du virus HIV-1 à l'ARN et mise en évidence de son rôle dans la rétrotranscription." Montpellier 1, 2000. http://www.theses.fr/2000MON1T015.
Повний текст джерелаHazra, Ditipriya. "Insights into the control of mRNA decay by YTH proteins during the transition from meiosis to mitosis in yeasts." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLX041.
Повний текст джерелаInsights into the control of mRNA decay by YTH proteinsduring the transition from meiosis to mitosis in yeasts.Keywords: Epitranscriptomics, mRNA decay, meiosis, multi-protein complexes, YTH domainCell cycle is controlled by multi-layered processes. A gene is transcribed in mRNA which is translated in proteins but innumerable regulation processes are working to control every step of this apparently simple process. Among these regulatory check points, post-transcriptional regulation is an important one, where formation of a protein-RNA complex may direct the cellular fate. Among these RNA binding proteins, YTH domain proteins are most novel, discovered in late 90s. YTH domain proteins are abundant in eukaryotes and absent in prokaryotes. YTH domain proteins constitute the majority of reader proteins that can specifically identify m6A modification. Human beings have five YTH domain proteins YTHDF1-3, YTHDC1-2 (Hazra, D., Chapat, C., & Graille, M. (2019). m6A mRNA Destiny: Chained to the rhYTHm by the YTH-Containing Proteins. Genes, 10(1), 49.). Although it is evident that these proteins are controlling cellular fate, the function of each protein and their network is yet to be elucidated. In yeast, there is only one YTH domain protein present: Pho92 in Saccharomyces cerevisiae and Mmi1 in Schizosaccharomyces pombe. Apart from the YTH domain there is no sequence homology between these two proteins but their cellular function is similar.It is well established that Mmi1 is responsible for degradation of meiosis specific transcripts during vegetative growth of the cell. Mmi1 forms a tight complex with a small protein, Erh1 (Erh1-Mmi1 complex or EMC). EMC can physically interact with Not1 of CCR4-Not complex and recruit it for degradation of DSR (determinant of selective removal) containing RNAs. The action of Mmi1 is in turn regulated by an RRM domain protein, Mei2. During meiosis, Mei2, along with a lncRNA meiRNA sequesters Mmi1 in a nuclear dot, rendering it inactive and ensuring smooth continuance of meiosis. These three proteins, Mmi1-Erh1-Mei2 play a key role in mitosis to meiosis switch.In S. cerevisiae, Pho92 is involved in the degradation of PHO4 transcripts contributing to phosphate metabolism pathway, during phosphate starvation and also participates in the degradation of mRNAs containing the N6-methyladenosine (m6A) epitranscriptomics marks. Similarly, to S. pombe Mmi1, Pho92 recruits CCR4-Not complex by physical interaction with Not1.During my PhD, I have tried to elucidate the role of these two YTH domain proteins from two model organisms, S. cerevisiae and S. pombe, in mRNA degradation and cell cycle regulation using biochemical and structural approaches.Pho92 of S. cerevisiae physically interacts with Not1 of CCR4-Not complex, we were able to determine the boundaries of this interaction. The interaction between these two proteins was studied by Fluorescence anisotropy. The protein complex was successfully purified and crystallization trials are ongoing.From S. pombe, structure of Mei2-RRM3 was solved with and without an RNA. RNA binding properties of Mei2-RRM3 was studied by ITC. The structure of Erh1 was also solved and we tried to elucidate its importance for biological function of Mmi1. A co-crystallization trial was performed with Mmi1-Mei2-RNA but it was unsuccessful and we ended up with Mmi1 crystals
Bisaglia, Marco. "Etude fonctionnelle et structurale de deux protéines impliquées dans le métabolisme des ARN messagers." Palaiseau, Ecole polytechnique, 2002. http://www.theses.fr/2002EPXX0018.
Повний текст джерелаKhoury, Georges. "Étude des mécanismes moléculaires régulant l'expression de la protéine TAT du virus de l'immunodéficience humaine, au niveau de la production de ses ARN messagers et de leur traduction." Thesis, Université de Lorraine, 2012. http://www.theses.fr/2012LORR0251.
Повний текст джерелаHIV-1 Tat protein is essential for viral replication. It allows the transcription of full-length viral RNAs, and due to its apoptotic properties it contributes to the AIDS disease. Hence, it is important to study the mechanisms regulating its production. Alternative splicing of the HIV-1 RNA, in particular, the use of acceptor sites A3 and A7 is required for tat mRNA production. Splicing at site A3 is highly regulated by cis-acting elements contained in a stem-loop structure SLS3A3, located downstream from site A3. By purifying RNP complexes formed in nuclear extract on a segment of the viral RNA containing site A3 followed by mass spectrometry analysis, we were able to highlight the binding of a new inhibitory protein, DAZAP1. Based on a set of ancient laboratory data and new results that I obtained, we have shown that SRSF7 protein, probably in synergy with SRSF1, limits the binding of DAZAP1 and splicing activation at site A3. We also showed that the viral protein Tat exerts a negative feedback control on tat mRNA production by restricting splicing activation of site A3 by SRSF7. The apical part of the stem-loop structure SLS3A3 (B motif) is highly conserved among HIV-1 strains. E Guittet team determined its 3D structure by NMR. The conformation of this apical loop is characteristic of stem-loop structures recognized by dsRBD proteins (double-stranded RNA binding domain). I was able to confirm this hypothesis by purifying RNP complexes formed by the B motif in nuclear extract. Thus, we have shown that the RNA dependent protein kinase (PKR), which plays in humans a major role in response to viral infection, is a partner of the B motif. By using chemical probes specific of the 2D structure of RNAs, I showed that the stem-loop structure SLS3A3 that contains the initiation codon of Tat is present in tat1 mRNA. We then developed a system to study the mechanisms regulating the initiation of translation of Tat protein. By using a bicistronic construct, I was able to confirm the existence of IRES activity in the 5?UTRtat1 region of tat1 mRNA, and define two segments that contain this activity. Preliminary results obtained with a bicistronic construct allowed us to begin testing the effect of different SR and hnRNP proteins on the activity of the IRES
Rushing, Stacy Renée. "Proteins that interact with and mediate the activity of the aryl hydrocarbon receptor and its partner ARNT /." For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2002. http://uclibs.org/PID/11984.
Повний текст джерелаSterz, Kai Raphael [Verfasser], Arnd [Akademischer Betreuer] Kieser, and Bernhard [Akademischer Betreuer] Küster. "A Systematical Analysis of the Signal Transduction Pathways Induced by the Latent Membrane Protein 1 (LMP1) of Epstein-Barr Virus / Kai Raphael Sterz. Gutachter: Bernhard Küster ; Arnd Kieser. Betreuer: Arnd Kieser." München : Universitätsbibliothek der TU München, 2014. http://d-nb.info/1061125955/34.
Повний текст джерелаLaporte, Philippe. "Rôle des ARN non-codants pour des protéines (npcRNAs) dans la régulation de l'architecture de la racine." Paris 11, 2008. http://www.theses.fr/2008PA112135.
Повний текст джерелаPlants are able to modulate their root architecture in order to adapt them to the Abiotic and biotic constraints in soil environment, modifying primary root growth and lateral root organogenesis. Leguminous plants form two types of lateral root organs, lateral roots and nodules. The latter are able to fix nitrogen via the interaction with symbiotic bacteria Rhizobium. In the last years, several non-protein coding RNAs have emerged as new regulators of development, they include small RNAs (mi/tasiRNAs) but also other classes whose mechanisms are unexplored. During this PhD, we explored the role and mechanism of action of npcRNAs in root architecture in Medicago truncatula. First, we identified and characterised the MtMIR166a precursor, containing two tandem copies of MIR166 in a single transcriptional unit. Overexpression of this precursor in M. Truncatula roots affected vascular tissue and both lateral root organogeneses. Secondly, we analysed protein-partners of npcRNA Enod40, a gene involved in M. Truncatula nodule organogenesis. This led to the identification of a novel peptide family, the SNARP genes (for Small Nodulin Acidic RNA-binding Protein). The purified SNARP2 could bind single-stranded RNA and a functional approach based on RNAi revealed a role in the regulation of nodule invasion. The relevance of the Enod40 RNA-SNARP2 interaction was analysed in vitro and in vivo. Finally, I participated in an effort to search for npcRNAs from Arabidopsis thaliana. Several of these novel genes were regulated by abiotic stresses in roots. Altogether, these results contribute to reveal novel roles of npcRNAs and their protein interactors in the control of root architecture
Schelcher, Cédric. "Détermination du mode d'action et des substrats de RNases P protéiques chez Arabidopsis thaliana." Thesis, Strasbourg, 2017. http://www.theses.fr/2017STRAJ044/document.
Повний текст джерелаRNase P is the essential activity that removes 5'-leader sequences from transfer RNA precursors. “PRORP” (PROteinaceous RNase P) defines a novel category of protein only RNase P. Before the characterization of PRORP, RNase P enzymes were thought to occur universally as ribonucleoproteins (RNP). The characterization of PRORP revealed an enzyme with two main domains, an N-terminal domain containing multiple PPR motifs and a C-terminal NYN domain holding catalytic activity. We used a combination of biochemical and biophysical approaches to characterize the PRORP / tRNA complex. The structure of the complex in solution was determined by small angle X-ray scattering and Kd values of the PRORP / tRNA interaction were determined by analytical ultracentrifugation. We also analyzed direct interaction of a collection of PPR mutants with tRNA in order to determine the relative importance of individual PPR motifs for RNA binding. This reveals to what extent PRORP target recognition process conforms to the mode of action of PPR proteins interacting with linear RNA. Altogether, our analysis reveals an interesting case of convergent evolution. It suggests that PRORP has evolved an RNA recognition process similar to that of RNP RNase P. Moreover, we also implemented a PRORP-RNA co-immunoprecipitation approach to determine the full extent of PRORP substrates