Letteratura scientifica selezionata sul tema "Interactions protéine-RNA"
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Tesi sul tema "Interactions protéine-RNA"
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.
Testo completoThis 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
Ribeiro, 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.
Testo completoOver 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
Mahmoudi, Ikram. "Structural and evolutionary analysis of protein-RNA interfaces and prediction perspectives". Electronic Thesis or Diss., université Paris-Saclay, 2024. http://www.theses.fr/2024UPASQ024.
Testo completoProtein-RNA interactions are crucial in numerous cellular pathways and pathologies. Knowledge of their 3D structures is critical for understanding their functions, yet their experimental determination remains challenging. The scarcity of structural data and the inherent flexibility of these complexes have hindered the advancement of protein-RNA interface structural prediction. At the same time, tremendous progress has been made recently for protein-protein interaction prediction thanks to methods leveraging evolutionary information and deep learning.My thesis focused on a detailed evolutionary analysis of protein-RNA interface structures. I first identified 2,022 pairs of structurally homologous interfaces. I explored the conservation of interface contacts among these pairs, discovering a high conservation rate for distance-based and apolar contacts, even in distant homologs. Hydrogen bonds, salt bridges, and π-stacking interactions displayed higher versatility. I investigated mechanisms compensating for non-conserved interactions. I contributed to developing a web interface allowing the community to explore evolutionary structural insights in our datasets. I also participated in a collaborative project with biologists to study a specific protein-RNA interface.Then, I investigated how to incorporate evolutionary signals into protein-RNA structural modeling methods using machine learning models, including logistic regression and CatBoost classifiers. I assessed these models' ability to learn how to transfer contacts from remote interologs and generalize across datasets while mitigating overfitting. Lastly, I explored developing functions based on contact propensities to score protein-RNA docking poses. These efforts constitute a step towards improving protein-RNA structure prediction
Michaux, Charlotte. "Identification et caractérisation fonctionnelle de petits ARN non codants chez Enterococcus faecalis et analyse d'une protéine "RNA-binding"". Caen, 2013. http://www.theses.fr/2013CAEN2094.
Testo completoChevrollier, Nicolas. "Développement et application d’une approche de docking par fragments pour modéliser les interactions entre protéines et ARN simple-brin". Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS106/document.
Testo completoRNA-protein interactions mediate numerous fundamental cellular processes. Atomic scale details of these interactions shed light on their functions but can also allow the rational design of ligands that could modulate them. NMR and X-ray crystallography are the 2 main techniques used to resolve 3D highresolution structures between two interacting molecules. Docking approaches can also be utilized to give models as an alternative. However, the application of these approaches to RNA-protein complexes is hampered by an issue. RNA-protein interactions often relies on the specific recognition of a short singlestranded RNA (ssRNA) sequence by the protein. The inherent flexibility of the ssRNA segment would impose, in a classical docking approach, to explore their resulting large conformation space which is not computationally reliable. The goal of this project is to overcome this barrier by using a fragment-based docking approach. This approach developed from some of the most represented RNA-binding domains showed excellent results in the prediction of the ssRNA-protein binding mode from the RNA sequence and also a great potential to predict preferential RNA binding sequences
Angius, Federica. "Molecular basis of membrane protein production and intracellular membranes proliferation in E. coli". Thesis, Sorbonne Paris Cité, 2017. http://www.theses.fr/2017USPCC217/document.
Testo completoThe most successful expression system used to produce membrane proteins for structural studies is the one based on the T7 RNA polymerase (T7 RNAP) (Hattab et al., 2015). However, the major drawback of this system is the overtranscription of the target gene due to the T7 RNAP transcription activity that is over ten times faster than the E. coli enzyme. Since the isolation of spontaneous mutants, namely C41(DE3) and C43(DE3) (Miroux and Walker, 1996) and the identification of their mutation in the genome, it becomes clear that reducing the amount of the T7 RNAP level removes the toxicity associated with the expression of some membrane proteins (Wagner et al., 2008; Kwon et al., 2015). Also, some membrane proteins require a very low rate of transcription to be correctly folded at the E. coli membrane. The first objective of my PhD was to extend the promoter strength coverage of the T7 based expression system. We used genetic and genomic approaches to isolate and characterize new bacterial strains (Angius et al., 2016) in which the level of T7 RNAP is differently regulated than in existing hosts. A second objective was to understand intracellular membrane proliferation in E. coli. Indeed it has been shown that over-expression of membrane proteins, like overexpression of AtpF of E. coli F1Fo ATP synthase is accompanied by the proliferation of intracellular membranes enriched in cardiolipids (Arechaga et al., 2000). To understand metabolic pathways involved in membrane biogenesis, proliferation and organization, we used a RNA sequencing approach at several time point upon over-expression of the F-ATPase b subunit in C43(DE3) host. On the other hand, in collaboration with Gerardo Carranza and Ignacio Arechaga (University of Cantabria, Spain) we studied C43(DE3) cls mutants, in which the cardiolipids genes A, B and C are deleted, to test how they participate to intracellular membranes structuration
Capozi, Serena. "Dynamique d'interaction entre la protéine SRSF1 et l'ARN et cinétique de formation du spliceosome". Thesis, Montpellier, 2016. http://www.theses.fr/2016MONTT067.
Testo completoSRSF1, formerly known as ASF/SF2, belongs to the SR protein family, which is a conserved family of RNA-binding protein that plays essential roles as regulators of both constitutive and alternative splicing. Hundreds of RNA targets have been described for SRSF1 but how SRSF1 selects its targets from the entire pool of cellular pre-mRNAs remains an open question. In vitro and in vivo studies have shown that SR proteins recognize short degenerated motifs often present in multiple copies at ESEs. Similar cryptic motifs are however frequently present in pre-mRNAs, and this low specificity of binding contrasts with the great fidelity of exon definition. To better understand the mechanism of action of SRSF1, I performed a kinetic study of SRSF1-RNA interactions in live cells using advanced microscopic techniques. Taking advantage by the CRISPR system, I tagged endogenous SRSF1 with Halo protein, and I combined photobleaching (FRAP) and single particle tracking (SPT) techniques to estimate diffusion and binding rates of SRSF1. I measured the duration of individual binding events, both on the cellular pool of pre-mRNAs and on specific targets. Our results indicate that binding of SRSF1 does not exceed few seconds, even on high-affinity targets. This rapid kinetics allows SRSF1 to rapidly sample the entire pool of nascent RNAs continuously produced in cells. Moreover, we provided a kinetic analysis of snRNP dynamics at a single-molecule resolution in the nucleoplasm of living cells. Our results enabled us to determine diffusion coefficients of snRNPs and their RNA binding duration in vivo
Robert-Paganin, Julien. "Étude structurale et fonctionnelle de la régulation de l’hélicase Prp43". Thesis, Paris 5, 2014. http://www.theses.fr/2014PA05P633/document.
Testo completoRNA helicases from the DEAH/RHA family are involved in most of essential processes of life such as pre-mRNA splicing, ribosome biogenesis, replication, transcription or viral RNA sensing. These enzymes are able to catalyze RNA unwinding, secondary structures reorganization or RNA-protein complexes remodeling. The DEAH/RHA helicase Prp43 is remarkable because it is bifunctional, as it is involved both in pre-mRNA splicing, where it is responsible of spliceosome and lariat recycling and in the biogenesis of the two ribosomal subunits. Prp43 is activated by five protein partners: Ntr1, Gno1, Pfa1, RBM5 and GPATCH2. These protein partners all possess a G-patch domain and are able to stimulate helicase and ATPase activity of Prp43. The structure of Prp43 in complex with ADP has been solved by X-ray crystallography. The structure reveals that the nucleotide is bound to the enzyme in a novel mode that has never been observed in other known helicase structures. The specific feature of this binding mode is the base, stacked between phenylalanine (F357) from RecA2 domain and an arginine (R159) from RecA1 domain. Features of the activation of Prp43 by G-patch proteins are unclear. In this work, we investigated the role of base stacking in the activation of Prp43. We present several structures of Prp43 bound to all the nucleotide diphosphates (NDP) and deoxynucleotide diphosphates (dNTP). These results indicate that there are differences in stacking according to the (d)NDP bound to the enzyme. NTPase activity assays revealed that when stacking is weakened, Prp43 activity cannot be properly regulated by its protein partner Pfa1. Moreover, point mutations F357A and R159A show that stacking of F357 permits to modulate Prp43 activity. All these results allow us to propose a model of NTPase activity activation of Prp43 by G-patch proteins and to highlight the importance of base stacking in this regulation
Paternina, Osorio J. Antonio. "Biocomputational tools for transcriptome-wide analyses of RNA-binding proteins". Electronic Thesis or Diss., Université Paris sciences et lettres, 2020. http://www.theses.fr/2020UPSLE058.
Testo completoPost-transcriptional Gene Expression Regulation is a complex network that involves RNA-binding proteins and non-coding RNAs to orchestrate the complex life of mRNAs. In metazoans, the Exon Junction Complex (EJC) is a multi-protein complex deposited onto mRNAs exon junctions during splicing. The EJC interacts with numerous factors and is important for coupling pre-mRNA splicing with mRNA nuclear export, localization, translation, and decay. Despite its central role in gene expression and in organism development, the comprehensive map of EJC binding sites is lacking. Crosslinking and immunoprecipitation coupled with high-throughput sequencing (CLIP-seq) aims to identify transcriptome-wide RNAprotein interactions in vivo. Yet, current trends in CLIP-seq data analysis gravitate towards painting a global landscape rather than characterizing individual binding sites. However, we observed that current peak callers applied to EJC CLIP data yield results with limited reproducibility and sensibility. During my PhD, we developed a dedicated strategy to detect EJC signal enrichment at the exon level. By aggregating data from several replicates, we built a list of robust genes with reproducible EJC loading rate. Within robust genes, we assigned a robustness score to each exon according to frequency of detection across replicates. We found that the exon robustness score was correlated to the thymidine (T) content of EJC binding sites. Assuming this was due to cross-linking chemistry, we corrected the score for the T content and found exons with either high or low detection rates. The last suggests that EJC loading is not homogeneous along a transcript, but rather differential. Thus, we established an unprecedented binding site map of the EJC in living cells validated by statistical tools. Crossing this map with other information showed that EJC loading is independent of transcript expression levels or known gene functional annotations. Although the scope of this work does not include possible explanations for this differential loading, it presents a first reproducible and specific data analysis pipeline to detect EJC-loaded exons. Altogether, our contribution is twofold. First, we proposed a robust way to detect EJC signal enrichment at the exon level and demonstrated quantitatively that our approach is more reproducible and more sensitive compared to conventional tools. Second, we proved that the EJC can be present on some, and absent on other exons of the same transcript suggesting that EJC loading is a regulated process following a code that remains to be discovered
Ben, ouirane Kaouther. "Apport des approches in silico aux études structure-fonction de la polymérase du virus de l'hépatite C". Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS323.
Testo completoThe hepatitis C virus is an RNA virus that synthesises its new genomes in the infected host cells thanks to an RNA-dependent RNA polymerase (RdRp) termed NS5B. This polymerase has been a prime target for antiviral therapy. Numerous direct antiviral drugs are now approved in the HCV treatment and allow very high rates of treatment success. These drugs target among others the HCV NS5B RdRp with the sofosbuvir being one of the most successful drugs.Tremendous efforts have been made in the past decades to characterize NS5B, in particular structurally and biochemically. However, there is little information about the molecular mechanisms of NS5B ribonucleotides entry and selection and in general on the atomistic details of the RNA replication mechanism, although the involvement of two magnesium dications in catalysis is well established in this family of polymerases. Since 2015, structures of ternary complexes of NS5B have been resolved by crystallography offering very valuable details about the binding of nucleotides at the NS5B active site.In this work, we took advantage of these structural data to address the ribonucleotides entry and to further explore the nucleotide addition cycle in NS5B using molecular modelling and molecular dynamics simulations. We used both conventional molecular dynamics techniques and biased simulations that enhance sampling such as Steered Molecular Dynamics (SMD), Targeted Molecular Dynamics (TMD) or accelerated Molecular dynamics (aMD).Based on our modelling results, we found that the access to the active site through the nucleotides tunnel is checked by successive NS5B elements. First, the entering ribonucleotide together with an associated magnesium Mg(B) binds next to a loop that overhangs the nucleotide tunnel and interactions with its triphosphate moiety orient it base-first towards the active site. Second, the ribonucleotide encounters a checkpoint constituted by the residues of motif F3(R158) and motif F1(E143) where it is blocked until the arrival of a second magnesium ion, the Mg(A). This allowed the motif F3 to undergo small structural rearrangements leading to the advancement of the nucleotide towards the active site to interrogate the RNA template base prior to the complete nucleotide insertion into the active site.Our simulations pointed out that these dynamics are finely regulated by the second magnesium dication, thus coordinating the entry of the correct magnesium-bound nucleotide with shuttling of the second magnesium necessary for the two-metal ion catalysis. This entry mechanism is specific to viral RdRps and may explain why modified ribonucleotides can be so successful as drugs against RNA viruses