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Najmabadi, Sepideh. "Drosophila model of myosin myopathy rescued by overexpression of a TRIM-protein family member." Thesis, Högskolan i Skövde, Institutionen för hälsa och lärande, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-17919.
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Laing distal myopathy is inherited in an autosomal dominant manner usually before the age of five that initially involves the dorsiflexion in the ankles’ and in big toes to the finger extensors. Weakness of the flexor muscles in the neck is seen in most affected individuals and mild facial weakness is also often present. Hypertrophic or dilated cardiomyopathy, starting at birth to respectively second or third decade of life, is the symptom in the affected humans.This study performed on Drosophila melanogaster, has evaluated whether feeding MuRF1 enzyme (which has a similar role as ABBA enzyme) to Drosophila larvae, in different concentrations, will have a positive effect on the larvae’s muscular abilities through an analysis of their manifestation, the distance they manage to crawl and the time it takes for them to turn from a ventral up to dorsal up position.The result show no significant impact on larvae ability to turn or crawl between different groups fed with MuRF1 enzyme, nor between the two control groups, wild larvae and mutated larvae. Other studies have proven that there is a significant difference in muscular ability between wild and mutated larvae, so explanations to why this study did not manage to replicate these results were evaluated. The study found that how many days has passed since hatching has a significant impact on performance of turning and crawling for wild larvae that are not treated with enzyme.There are a number of improvement suggestions to the experimental design and the methodology to enable a proper evaluation of the research aim of this thesis. Future research on the topic should implement these and redo the experiments and measurements of this study. In addition, the quantity of larvae that reaches pupa stage should be captured to evaluate whether the MuRF1 enzyme has a positive impact on mutated larvae reaching pupation stage. The most important parts of the improvement proposals to measure the ability of larvae when they are about the same age, as this was proven with statistical significance to have an impact on crawling and turning.
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Zhang, Xuzhe. "Eutherian-specific gene TRIML2 attenuates inflammation in the evolution of placentation." University of Cincinnati / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1573576401238203.
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MASCARO, MARTINA. "Ruolo di TRIM18, gene che causa la sindrome di Opitz, nel controllo della ciliogenesi attraverso l'autofagia." Doctoral thesis, Università degli Studi di Trieste, 2021. http://hdl.handle.net/11368/2996095.
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TRIM18/MID1 è una E3-Ubiquitina ligasi appartenente alla famiglia di proteine TRIM che si localizza sui microtubuli. Le mutazioni con perdita di funzione nel gene MID1 sono state associate alla forma legata all'X della sindrome di Opitz, una malattia genetica caratterizzata da difetti nello sviluppo della linea mediana ventrale. All'interno della cellula, MID1 esiste come un complesso macromolecolare microtubulare, costituito da diversi interattori non tutti ancora identificati. Tra questi, α4 è una delle subunità regolatorie della proteina fosfatasi 2A (PP2A). È stato riportato che MID1 riduce il pool microtubulare dei livelli proteici della subunità catalitica di PP2A (PP2Ac), portando così all'ipofosforilazione dei suoi substrati. Le cellule prive di MID1 mostrano livelli aumentati di PP2Ac e una ridotta associazione tra mTOR e Raptor, portando a una downregulazione della via di segnalazione di mTORC1. Ciò suggerisce che MID1 può agire a monte della segnalazione di mTORC1. Tuttavia, i meccanismi patogenetici della sindrome di Opitz non sono ancora stati del tutto compresi, ma alcune caratteristiche cliniche sono condivise con un'altra classe di patologie in cui i geni che controllano le dinamiche del ciglio primario sono mutati, ovvero le ciliopatie. Detto questo, abbiamo ipotizzato che MID1 possa essere coinvolto nella regolazione dei processi in cui il ciglio primario è direttamente o indirettamente coinvolto.
Il ruolo di MID1 nel ciglio primario è stato studiato in una linea di cellule epiteliali umane e in fibroblasti di embrioni di topo (MEF) wild-type e Mid1-/Y. I dati mostrano che la overespressione di MID1 e la delezione di Mid1 nelle cellule di topo causano entrambe difetti della ciliogenesi e/o della lunghezza del ciglio primario, suggerendo un ruolo nella regolazione dell'assemblaggio di questo organello. Essendo le dinamiche del ciglio primario regolate dall'autofagia, controllata a sua volta anche attraverso la segnalazione di mTORC1, ci siamo chiesti se i difetti del ciglio primario causati da MID1 potessero essere dovute ad alterazioni nella via dell'autofagia. Analizzando gli stessi modelli cellulari, abbiamo osservato alterazioni nell'autofagia basale e nel flusso autofagico indotto dalla mancanza di nutrienti nelle cellule che overesprimono MID1 e nei MEF deleti per Mid1.
I miei risultati indicano che MID1 è un regolatore negativo sia della ciliogenesi che dell'allungamento del ciglio, a seconda del tipo di cellula e delle condizioni di coltura, nonché un regolatore dell'autofagia, come riportato per altri membri della famiglia TRIM. Presi insieme i nostri risultati possono far comprendere i meccanismi patogenetici della sindrome di Opitz e suggeriamo di considerare questa malattia come una nuova ciliopatia.<br>TRIM18/MID1 is an E3 Ubiquitin ligase belonging to the TRIM family of proteins that localises on microtubules. Loss-of-function mutations in the MID1 gene have been associated with the X-linked form of Opitz G/BBB syndrome, a genetic disorder characterised by defects in ventral midline development. Within the cell, MID1 exists as a microtubular macromolecular complex, consisting of several MID1 interactors not all identified yet. Among them, α4 is one of the regulatory subunits of Protein Phosphatase 2A (PP2A). MID1 has been reported to decrease the microtubular pool of PP2A catalytic subunit (PP2Ac) protein levels, thus leading to hypo-phosphorylation of its target proteins. MID1-lacking cells show increased levels of PP2Ac and a reduced association between mTOR and Raptor, leading to a downregulation of the mTORC1 signalling complex. This suggest that MID1 may act upstream of the mTORC1 signalling. Nevertheless, Opitz syndrome pathogenetic mechanisms have not been understood yet, but some clinical features are shared with another class of pathologies where genes controlling primary cilium dynamics are mutated, i.e. ciliopathies. Given this, we hypothesised that MID1 might be involved in the regulation of processes in which the primary cilium is directly or indirectly involved.
The role of MID1 in primary cilium was investigate in a human epithelial cell line and in wild-type and Mid1-/Y Mouse Embryo Fibroblasts (MEFs). The data show that MID1 overexpression and Mid1 depletion both cause impairment in primary ciliogenesis and/or primary cilia length, suggesting a role in the regulation of ciliary assembly. Being primary cilium dynamics regulated by autophagy, also controlled through mTORC1 signalling, we asked whether primary cilia impairments caused by MID1 could be due to misregulations in the autophagy pathway. By analysing the same cellular models, we observed alterations in basal autophagy and in the starvation-induced autophagy flux in MID1-overexpressing cells and in Mid1-/Y MEFs.
My results indicate that MID1 is a negative regulator of both ciliogenesis and ciliary elongation – depending on cell type and culture condition – as well as a regulator of autophagy pathway, as reported for other members of the TRIM family. Taken together our results can give new insights on the Opitz syndrome pathogenetic mechanisms and we can suggest to consider this disease as a new ciliopathy.
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Demange, Antonin. "Protéines à motif tripartite (TRIM) chez le porc (Sus scrofa) et réplication du rétrovirus endogène porcin." Phd thesis, Université Rennes 1, 2013. http://tel.archives-ouvertes.fr/tel-00992386.
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Les études des interactions entre cellules hôtes et rétrovirus ont conduit à définir le concept de restriction virale dont les facteurs constituent une part de l'immunité innée des cellules hôtes. Ces facteurs contribuent au contrôle des rétrovirus endogènes (ERV) dont l'émergence peut être associée à certaines pathologies telles que des leucémies ou des immunodéficiences. Chez le porc, certains ERV (PERV) sont réplicatifs, pourtant aucune pathologie ne leur a, à ce jour, été associée. Les mécanismes de restriction virale impliqués dans ce phénomène ont fait l'objet de nombreuses études. Elles n'ont cependant concerné que certains facteurs. Les protéines porcines à motif tripartite (poTRIM) n'ont ainsi fait l'objet que de peu d'études. Pourtant, de nombreux membres de cette famille participent à la restriction virale chez d'autres organismes que le porc. La présente étude s'intéresse par conséquent aux orthologues porcins de ces protéines et à leur relation avec les PERV. L'élaboration d'une stratégie d'expression de ces protéines dans un modèle humain, sensible à l'infection par le PERV nous a permis d'évaluer et de caractériser les effets des TRIM sur le cycle infectieux du PERV. Cette stratégie a mis en évidence une activité de restriction par TRIM8 tandis que TRIM44 semble au contraire agir en faveur de la réplication virale. En ce qui concerne poTRIM11, elle favorise l'entrée du PERV tout en inhibant son expression. L'étude a également confirmé l'insensibilité du PERV vis-à-vis de poTRIM5α. L'ensemble de ces résultats contribuent à la compréhension de la relation entre la réplication des PERV et le contrôle mené par son hôte.
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Fraser, S. J. "Characterising retroviral restriction by TRIM proteins." Thesis, University College London (University of London), 2016. http://discovery.ucl.ac.uk/1532045/.
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Tripartite motif (TRIM) proteins are numerous in the human proteome, and a number of these molecules are known to restrict retroviral replication. TRIM5α (T5α) is one such factor. It targets the viral capsid and imposes a block to infection between entry and reverse transcription. Capsid recognition is mediated by the C-terminal B30.2 domain, which contains surface-exposed loops of high amino acid variability. Restriction is then effected via proteasome recruitment and the induction of innate immune cascades. Although T5α is well-characterised in this respect, other factors – such as the highly divergent TRIM1 (T1) – remain poorly understood. To further characterise the T1 restriction phenotype, chimeras of this protein and its non-restricting paralogue, T18, were generated by overlapping PCR. The restriction activities of the resulting molecules were then measured using an established flow cytometry assay. These experiments revealed that T1 also binds capsid via the B30.2 domain, although the majority of this region can be functionally replaced. Other aspects of T1 biology addressed in this work include the contribution of N-terminal components to restriction potency, and the relationship between protein expression level and restriction activity. Following a number of attempts to generate a functional chimera of T1 and 5α, the latter half of this thesis explores how the spacing between capsid-binding and effector domains can influence restriction activity. To this end, a panel of mutations were made in the linker 2 (L2) region of T5α, and their effects on restriction measured. These experiments revealed that even small changes in interdomain spacing can have profound phenotypic consequences. Collectively, this work reinforces the notion that TRIM family members share a common overall design, allowing individual components to be shuffled between them. At the same time, each molecule has been shaped by unique evolutionary pressures, which can render them sensitive even to relatively minor modifications.
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Fekete, Richard Alfred. "Characterizing the protein and DNA interactions of the F plasmid DNA binding protein, TraM." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/NQ60291.pdf.
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Marafie, Sulaiman. "TRIM7, a novel binding protein of the mTORC2 component Sin1." Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/trim7-a-novel-binding-protein-of-the-mtorc2-component-sin1(c344b542-0706-4ec0-be06-ce6683cee52e).html.
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TRIM7 is a member of the TRIM (tripartite motif-containing) protein superfamily. This family has been implicated in many disorders such as genetic diseases, neurological diseases, and cancers. Little is known about the function of TRIM7 except that it interacts with glycogenin and may regulate glycogen biosynthesis. Recently, a yeast two-hybrid protein-protein interaction screen revealed the binding of TRIM7 to Sin1, a protein found in a complex with the mammalian target of rapamycin (mTOR) protein kinase. mTOR can form two complexes, mTORC1 and mTORC2, which are important for cell growth, differentiation, and survival. Sin1 is a core component of mTORC2 and is critical for mTORC2 stability and activity. It was confirmed by co-immunoprecipitation that TRIM7 associates with Sin1 and mTOR in cultured mammalian cells. Furthermore, it was demonstrated that TRIM7 is a phosphoprotein, although it was not directly targeted by mTOR in vitro. Similar to some other TRIM family proteins, it was demonstrated that TRIM7 has a ubiquitin E3 ligase function allowing it to autoubiquitinate both in vitro and in cells. The autoubiquitination of TRIM7 was dependent on its RING domain. Further characterization of TRIM7 indicated that it can both homo-oligomerise as well as hetero-oligomerise with other members of its sub-class of TRIM proteins and that it co-localises with them into discrete cytoplasmic loci. To determine the cellular function of TRIM7, a stable cell line expressing an shRNA directed against TRIM7 was generated. Successful knock down of TRIM7 was achieved and this led to an increase in the protein levels of components of the mTORC2 complex, including Sin1. This coincided with an increase in cell proliferation. In conclusion, this research identifies a novel role for TRIM7 as a ubiquitin ligase involved in regulating cell proliferation and provides a potential link between TRIM7 and the mTOR pathway, a major transducer of proliferative and cell survival signals.
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Simpson, Shmona. "Genetic, structural, and functional exploration of the restrictive capacity of TRIM proteins against immunodeficiency viruses." Thesis, University of Oxford, 2017. https://ora.ox.ac.uk/objects/uuid:1af588ba-603a-4f39-9443-bb1a95d983f5.
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HIV-2 differs from HIV-1 in that many infected people experience normal survival, whilst only 20% progress rapidly to AIDS. Understanding mechanisms of delayed HIV-2 disease progression could provide new insights into HIV control. The Caio Community Cohort was established in Guinea-Bissau in the setting of high HIV-2 prevalence. This thesis investigates the role of polymorphic host restriction factors of the TRIM family in HIV-2 outcome. TRIM proteins are a family of E3 ubiquitin-ligases, where closely-related TRIM5α and TRIM22 are thought to inhibit HIV-1 transcription, uncoating and budding. There was an association between TRIM5α amino acid substitution R136Q and reduced HIV-2 viral load/prolonged survival. Conversely, P479L was enriched among HIV-2 infected participants and progressors with CD4+ T cell decline. TRIM22 was highly polymorphic in this cohort, revealing three novel coding variants. Although most substitutions were located in the putative virus-interacting PRYSPRY domain, two in the coiled-coil, D155N and R242T, showed significant and divergent associations with survival. R242T was enriched in HIV-2 infected participants, who progressed to death at twice the rate of wild-type controls. In silico studies predicted D282, D360, and R321 of TRIM22 to be highly conserved, exposed residues, for which polymorphisms would be deleterious. When aligned with sequences from the potent HIV-1 restriction factor, rhesus macaque TRIM5α, TRIM22 substitutions R321K, T415I, and D360Y were spatially relevant to residues involved in HIV-1 restriction. The role of TRIM22 in HIV restriction was supported by in vitro pilot studies showing that TRIM22 was upregulated by HIV-1 infection in a lymphoid cell line and co-localised with the HIV-1 capsid protein p24. Overexpression of TRIM22 resulted in the restriction of VSV-G pseudotyped HIV-1 and SIVmac. The R242T substitution diminished TRIM22's restriction of HIV-1 and SIVmac: protein analysis suggested that this may be due to the inability of the R242T mutant to fully dimerise.
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Liu, Sunbin. "Investigation of protein-protein interactions within the human spliceosomal U4/U6.U5 tri-snRNP particle." Doctoral thesis, [S.l.] : [s.n.], 2005. http://webdoc.sub.gwdg.de/diss/2005/liu/liu.pdf.
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Xin, Gang. "The role of TREM proteins in lung homeostasis and inflammation." Thesis, Imperial College London, 2011. http://hdl.handle.net/10044/1/9058.
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The family of Triggering Receptors Expressed on Myeloid Cells (TREM) contain novel activating receptors of the Ig super-family that are expressed on myeloid cells. TREM-1 is a transmembrane glycoprotein expressed on blood neutrophils and a subset of monocytes, but not on lymphocytes or other cell types and is upregulated by bacterial and fungal products. TREM-1 signaling potentiates the outcome of Toll-like Receptor (TLR) signaling. Blockade of TREM-1 prevents experimentally induced septic shock. In addition to the membrane-bound form, a soluble TREM-1 molecule (sTREM-1) exists that regulates membrane bound TREM-1 by competing against the, as yet, unknown natural TREM-1 ligand. sTREM-1 is detected at high levels during bacterial infection and asthma and is used as a predictive biomarker for severe inflammation. TREM-2 on, the other hand is not known to be secreted and the membrane bound form is reported to prevent TLR signaling and promote osteoclastogenesis. The expression and function of TREM proteins during respiratory viral infection is not currently known. In this thesis we investigate the hypothesis that TREM-1 signaling contributes to excessive cytokine production during pulmonary viral infection in a murine model and that soluble TREM-1 and membrane bound TREM-2 proteins are anti-inflammatory. We show, for the first time, the following novel mechanisms that significantly increase our understanding of this important receptor family: 1) TREM-1 is highly up-regulated during influenza and the subsequent release of sTREM-1 likely contributes to secondary bacterial super-infection, 2) Blockade of TREM-1 at the onset of viral infection significantly reduces the risk of secondary bacterial pneumonia and 3) TREM-2 expressing macrophages that appear during the resolution of influenza-induced inflammation display a regulatory phenotype that can reduce TLR responsiveness of inflammatory macrophages. Taken together, our data suggests that TREM-1 proteins represent a novel therapeutic target for the alleviation of influenza-induced pathology and that TREM-2 expression identifies a novel population of regulatory macrophages.
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Ruiz, Echartea Maria Elisa. "Pairwise and Multi-Component Protein-Protein Docking Using Exhaustive Branch-and-Bound Tri-Dimensional Rotational Searches." Electronic Thesis or Diss., Université de Lorraine, 2019. http://www.theses.fr/2019LORR0306.
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La détermination des structures tri-dimensionnelles (3D) des complexes protéiques est cruciale pour l’avancement des recherches sur les processus biologiques qui permettent, par exemple, de comprendre le développement de certaines maladies et, si possible, de les prévenir ou de les traiter. Face à l’intérêt des complexes protéiques pour la recherche, les difficultés et le coût élevé des méthodes expérimentales de détermination des structures 3D des protéines ont encouragé l’utilisation de l’informatique pour développer des outils capables de combler le fossé, comme par exemple les algorithmes d’amarrage protéiques. Le problème de l’amarrage protéique a été étudié depuis plus de 40 ans. Cependant, le développement d’algorithmes d’amarrages précis et efficaces demeure un défi à cause de la taille de l’espace de recherche, de la nature approximée des fonctions de score utilisées, et souvent de la flexibilité inhérente aux structures de protéines à amarrer. Cette thèse présente un algorithme pour l’amarrage rigide des protéines, qui utilise une série de recherches exhaustives rotationnelles au cours desquelles seules les orientations sans clash sont quantifiées par ATTRACT. L’espace rotationnel est représenté par une hyper-sphère à quaternion, qui est systématiquement subdivisée par séparation et évaluation, ce qui permet un élagage efficace des rotations qui donneraient des clashs stériques entre les deux protéines. Les contributions de cette thèse peuvent être décrites en trois parties principales comme suit. 1) L’algorithme appelé EROS-DOCK, qui permet d’amarrer deux protéines. Il a été testé sur 173 complexes du jeu de données “Docking Benchmark”. Selon les critères de qualité CAPRI, EROS-DOCK renvoie typiquement plus de solutions de qualité acceptable ou moyenne que ATTRACT et ZDOCK. 2) L’extension de l’algorithme EROS-DOCK pour permettre d’utiliser les contraintes de distance entre atomes ou entre résidus. Les résultats montrent que le fait d’utiliser une seule contrainte inter-résidus dans chaque interface d’interaction est suffisant pour faire passer de 51 à 121 le nombre de cas présentant une solution dans le top-10, sur 173 cas d’amarrages protéine-protéine. 3) L’extension de EROSDOCK à l’amarrage de complexes trimériques. Ici, la méthode proposée s’appuie sur l’hypothèse selon laquelle chacune des trois interfaces de la solution finale doit être similaire à au moins l’une des interfaces trouvées dans les solutions des amarrages pris deux-à-deux. L’algorithme a été testé sur un benchmark de 11 complexes à 3 protéines. Sept complexes ont obtenu au moins une solution de qualité acceptable dans le top-50 des solutions. À l’avenir, l’algorithme EROS-DOCK pourra encore évoluer en intégrant des fonctions de score améliorées et d’autres types de contraintes. De plus il pourra être utilisé en tant que composant dans des workflows élaborés pour résoudre des problèmes complexes d’assemblage multi-protéiques<br>Determination of tri-dimensional (3D) structures of protein complexes is crucial to increase research advances on biological processes that help, for instance, to understand the development of diseases and their possible prevention or treatment. The difficulties and high costs of experimental methods to determine protein 3D structures and the importance of protein complexes for research have encouraged the use of computer science for developing tools to help filling this gap, such as protein docking algorithms. The protein docking problem has been studied for over 40 years. However, developing accurate and efficient protein docking algorithms remains a challenging problem due to the size of the search space, the approximate nature of the scoring functions used, and often the inherent flexibility of the protein structures to be docked. This thesis presents an algorithm to rigidly dock proteins using a series of exhaustive 3D branch-and-bound rotational searches in which non-clashing orientations are scored using ATTRACT. The rotational space is represented as a quaternion “π-ball”, which is systematically sub-divided in a “branch-and-bound” manner, allowing efficient pruning of rotations that will give steric clashes. The contribution of this thesis can be described in three main parts as follows. 1) The algorithm called EROS-DOCK to assemble two proteins. It was tested on 173 Docking Benchmark complexes. According to the CAPRI quality criteria, EROS-DOCK typically gives more acceptable or medium quality solutions than ATTRACT and ZDOCK. 2)The extension of the EROS-DOCK algorithm to allow the use of atom-atom or residue-residue distance restraints. The results show that using even just one residue-residue restraint in each interaction interface is sufficient to increase the number of cases with acceptable solutions within the top-10 from 51 to 121 out of 173 pairwise docking cases. Hence, EROS-DOCK offers a new improved search strategy to incorporate experimental data, of which a proof-of-principle using data-driven computational restraints is demonstrated in this thesis, and this might be especially important for multi-body complexes. 3)The extension of the algorithm to dock trimeric complexes. Here, the proposed method is based on the premise that all of the interfaces in a multi-body docking solution should be similar to at least one interface in each of the lists of pairwise docking solutions. The algorithm was tested on a home-made benchmark of 11 three-body cases. Seven complexes obtained at least one acceptable quality solution in the top-50. In future, the EROS-DOCK algorithm can evolve by integrating improved scoring functions and other types of restraints. Moreover, it can be used as a component in elaborate workflows to efficiently solve complex problems of multi-protein assemblies
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Ahmadi, Farhana. "Interaction of toll-like receptor 4 with the adaptor proteins MAL and TRAM." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610209.
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Rüßmann, Florian. "The eukaryotic chaperonin TRiC domain-wise folding of multi-domain proteins." Diss., Ludwig-Maximilians-Universität München, 2013. http://nbn-resolving.de/urn:nbn:de:bvb:19-157246.
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Villebeck, Laila. "Structural rearrangements of actins interacting with the Chaperonin systems TRiC/Prefoldin and GroEL/ES." Doctoral thesis, Linköping : Univ, 2007. http://www.bibl.liu.se/liupubl/disp/disp2007/tek1099s.pdf.
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McCarthy, Kevin Raymond. "Viral and Host Determinants of Primate Lentivirus Restriction by Old World Primate TRIM5alpha Proteins." Thesis, Harvard University, 2014. http://nrs.harvard.edu/urn-3:HUL.InstRepos:13065027.
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The host restriction factor TRIM5α mediates a post-entry, pre-integration block to retroviral infection that depends upon recognition of the viral capsid by the TRIM5α PRYSPRY domain. The two predominant alleles of rhesus macaque TRIM5α (rhTRIM5αQ and rhTRIM5αTFP) restrict HIV 1, but cannot restrict the macaque-adapted virus SIVmac239. To investigate how TRIM5α recognizes retroviral capsids, we exploited the differential sensitivities of these two viruses to identify gain-of-sensitivity mutations in SIVmac239, and we solved the structure of the SIVmac239 capsid N-terminal domain. When mapped onto this structure, single amino acid substitutions affecting both alleles were in the β-hairpin. In contrast, mutations specifically affecting rhTRIM5αTFP surround a highly conserved patch of amino acids that is unique to capsids of primate lentiviruses. This "patch" sits at the junction between the binding sites of multiple cellular cofactors (cyclophilin A, Nup-358 cyclophilin A-like domain, Nup-153 and CPSF6). Differential restriction of these alleles is due to a Q/TFP polymorphism in the first variable loop (V1) within the PRYSPRY domain. Q reflects the ancestral state (present in the last common ancestor of Old World primates) and has remained unmodified in all but one lineage of African monkeys, the Cercopithecinae. While Q-alleles can be found among some Cercopithecinae primates, in others Q has been replaced by a G or overwritten by a two amino acid insertion (giving rise to TFP in macaques). In one lineage, the Q to G substitution was later followed by an adjacent 20 amino acid duplication. We found that these modifications in TRIM5α specifically impart the ability to restrict Cercopithecinae SIVs without altering β-hairpin recognition. At least twice Cercopithecinae TRIM5αs independently evolved to target the same conserved patch of amino acids in capsid. Based on these findings, we propose that the β-hairpin is a retrovirus associated molecular pattern widely exploited by TRIM5α proteins, while recognition of the cofactor binding region was driven by the emergence of the ancestors of modern Cercopithecinae SIVs. Distribution on the Cercopithecinae phylogenetic tree indicates that selection for these changes in TRIM5α V1 began 11-16 million years ago, suggesting that primate lentiviruses are at least as ancient.
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Gumpper, Kristyn Nicole. "Maintaining Cardiac and Gastric Physiology: TRIM Proteins as Central Factors in Regulation of Organ Homeostasis at the Cellular Level." The Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu1563287863754715.
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Ghoorah, Anisah W. "Extraction de connaissances pour la modélisation tri-dimensionnelle de l'interactome structural." Thesis, Université de Lorraine, 2012. http://www.theses.fr/2012LORR0204/document.
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L'étude structurale de l'interactome cellulaire peut conduire à des découvertes intéressantes sur les bases moléculaires de certaines pathologies. La modélisation par homologie et l'amarrage de protéines ("protein docking") sont deux approches informatiques pour modéliser la structure tri-dimensionnelle (3D) d'une interaction protéine-protéine (PPI). Des études précédentes ont montré que ces deux approches donnent de meilleurs résultats quand des données expérimentales sur les PPIs sont prises en compte. Cependant, les données PPI ne sont souvent pas disponibles sous une forme facilement accessible, et donc ne peuvent pas être re-utilisées par les algorithmes de prédiction. Cette thèse présente une approche systématique fondée sur l'extraction de connaissances pour représenter et manipuler les données PPI disponibles afin de faciliter l'analyse structurale de l'interactome et d'améliorer les algorithmes de prédiction par la prise en compte des données PPI. Les contributions majeures de cette thèse sont de : (1) décrire la conception et la mise en oeuvre d'une base de données intégrée KBDOCK qui regroupe toutes les interactions structurales domaine-domaine (DDI); (2) présenter une nouvelle méthode de classification des DDIs par rapport à leur site de liaison dans l'espace 3D et introduit la notion de site de liaison de famille de domaines protéiques ("domain family binding sites" ou DFBS); (3) proposer une classification structurale (inspirée du système CATH) des DFBSs et présenter une étude étendue sur les régularités d'appariement entre DFBSs en terme de structure secondaire; (4) introduire une approche systématique basée sur le raisonnement à partir de cas pour modéliser les structures 3D des complexes protéiques à partir des DDIs connus. Une interface web (http://kbdock.loria.fr) a été développée pour rendre accessible le système KBDOCK<br>Understanding how the protein interactome works at a structural level could provide useful insights into the mechanisms of diseases. Comparative homology modelling and ab initio protein docking are two computational methods for modelling the three-dimensional (3D) structures of protein-protein interactions (PPIs). Previous studies have shown that both methods give significantly better predictions when they incorporate experimental PPI information. However, in general, PPI information is often not available in an easily accessible way, and cannot be re-used by 3D PPI modelling algorithms. Hence, there is currently a need to develop a reliable framework to facilitate the reuse of PPI data. This thesis presents a systematic knowledge-based approach for representing, describing and manipulating 3D interactions to study PPIs on a large scale and to facilitate knowledge-based modelling of protein-protein complexes. The main contributions of this thesis are: (1) it describes an integrated database of non-redundant 3D hetero domain interactions; (2) it presents a novel method of describing and clustering DDIs according to the spatial orientations of the binding partners, thus introducing the notion of "domain family-level binding sites" (DFBS); (3) it proposes a structural classification of DFBSs similar to the CATH classification of protein folds, and it presents a study of secondary structure propensities of DFBSs and interaction preferences; (4) it introduces a systematic case-base reasoning approach to model on a large scale the 3D structures of protein complexes from existing structural DDIs. All these contributions have been made publicly available through a web server (http://kbdock.loria.fr)
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Volkmann, Bianca [Verfasser], Thomas [Akademischer Betreuer] Gramberg, Andreas [Gutachter] Burkovski, and Andreas [Gutachter] Burkovski. "The role of TRIM proteins in retrovirus and retroelement restriction / Bianca Volkmann ; Gutachter: Andreas Burkovski, Andreas Burkovski ; Betreuer: Thomas Gramberg." Erlangen : Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 2020. http://d-nb.info/1216332967/34.
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Zhang, Yanhui, and 张雁惠. "Modulation of transient outward potassium channels by protein tyrosinekinases and demonstration of TRPC and TRPM channels in human atrialmyocytes." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B47161644.
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My PhD project investigated the regulation of human cardiac transient outward potassium current (Ito) by protein tyrosine kinases (PTKs) and the functional expression of transient receptor potential (TRP) channels in human atrial myocytes to make an advanced understanding of human cardiac electrophysiology and pathophysiology.
The modulation of human cardiac Itoby PTKs was studied in human atrial myocytes and HEK 293 cells expressing hKv4.3 (coding human cardiac Ito). We found that the broad-spectrum PTK inhibitor genistein, the selective EGFR kinase inhibitor AG556, and the Src-family kinases inhibitor PP2 inhibited human atrial Itoand the inhibitory effect was countered by the protein tyrosine phosphatase (PTP) inhibitor orthovanadate. Similar results were observed in hKv4.3-HEK cells. Interestingly, tyrosine phosphorylation of hKv4.3channels was reduced by genistein, AG556, and PP2,and the reduction was antagonized by orthovanadate. The mutant Y136F of hKv4.3 lost the inhibitory response to AG556, whileY108F lost the response to PP2.The double mutant Y108F-Y136F hKv4.3 failed to respond to both AG556 and PP2, and exhibited a dramatic reduction of tyrosine phosphorylation. These results indicate that native cardiac Itois regulated by both EGFR and Src family kinases.
In the second part, we studied whether TRPC channels would mediate the nonselective cation current described previously in human atrial myocytes. It was found that TRPC1 channel activator thapsigargin activated the current, and the effect was suppressed by La3+or prevented by intracellular anti-TRPC1 antibody. Endothelin-1 and angiotensin II stimulated the current, andthe effect was inhibited by La3+and/or 2-APB. RT-PCR and Western blot analysis revealed that in addition to the TRPC1 channels mediating the nonselective cation current, the components of store-operated Ca2+channels (SOCs), STIM1 and Orai1 were abundantly expressed in human atria. The interaction of TRPC1, STIM1, and Orai1 was confirmed by co-immunoprecipitation. Interestingly, we found that protein expression of TRPC1 and STIM1, but not Orai1, was up-regulated in human atria with atrial fibrillation.
The third part of the project determined whether TRPM7 channels were expressed in human atrial myocytes, since this channel was reported in human atrial fibroblasts, conferring atrial fibrosis in human atria with atrial fibrillation. We found a TRPM7 -like current which was potentiated by acidic pH, and inhibited by La3+and 2-APB, and a Ca2+-activated TRPM4 current. RT-PCR and Western blot analysis confirmed the expression of TRPM7 and TRPM4 channels in human atria. Moreover, we found TRPM7 protein, but not TRPM4 protein was significantly up-regulated in human atria with atrial fibrillation, suggesting the potential participation of TRPM7 channels in atrial remodeling of human atria with atrial fibrillation.
Collectively, this PhD thesis project has demonstrated for the first time that human cardiac Itois modulated by EGFR kinase and Src kinases via phosphorylating Y136and Y108, respectively. TRPC1 channels mediate the nonselective cation current and SOCs.TRPM7 channels are expressed in human atrial myocytes. The up-regulation of TRPC1, STIM1, and TRPM7 channels in human atria with atrial fibrillation suggest that they are likely involved in atrial electrical and/or structure remodeling in patients with atrial fibrillation.<br>published_or_final_version<br>Medicine<br>Doctoral<br>Doctor of Philosophy
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Binkley, Sarah L. "Re(I) Tri-Carbonyl Based Radiopharmaceuticals; Synthesis, in vitro Studies, and Protein Complexation." University of Akron / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=akron1469473412.
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TAUBENBLATT, PATRICE. "Tri intracellulaire de la vamp et etude de la proteine moteur kif 1a." Paris 11, 2001. http://www.theses.fr/2001PA112142.
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La vamp 2 est une proteine de la vesicule synaptique essentielle au phenomene d'exocytose. La formation d'un complexe entre la vamp et 2 proteines de la membrane presynaptique (syntaxine et snap 25) va permettre la fusion entre ces 2 structures membranaires et la liberation du neurotransmetteur. Dans un premier temps, nous nous sommes interesses a la localisation subcellulaire de la vamp a la terminaison nerveuse. Grace a une technique de marquages apres cryofracture, nous montrons que la vamp est associee a la membrane presynaptique. Ces resultats suggerent qu'en plus d'une localisation vesiculaire, la vamp est localisee au niveau de la membrane presynaptique. Cette localisation n'est pas due a une fusion des vesicules synaptiques avec la membrane presynaptique puisque la presence de la vamp n'est pas correlee avec celle d'autres marqueurs vesiculaires tels que la synaptophysine, sv2 ou vacht. Sur la preparation de membrane presynaptique, on peut mettre en evidence un complexe sds-resistant entre la vamp, la syntaxine et la snap 25. Suite a ce travail nous nous sommes demandes si des la sortie du trans golgi network, la vamp est cotransportee vers la terminaison nerveuse avec les autres proteines vesiculaires ou s'il y a deja eu une etape de tri. En immunopurifiant le precurseur des vesicules synaptiques via un anticorps anti-sv2, nous mettons en evidence la presence de proteines vesiculaires mais pas de la vamp (ni des t-snares). Toujours dans la logique de l'etude du trafic intracellulaire, nous nous sommes interesses a la kif 1a, proteine moteur impliquee dans le transport du precurseur des vesicules synaptiques vers la terminaison nerveuse. Nous avons tout d'abord clone le gene de la kif 1a. Apres avoir determiner la repartition cellulaire et subcellulaire de la kif 1a, notre problematique a ete de savoir comment est regulee l'accrochage/decrochage de la kif 1a a son cargo et aussi qu'elle est l'identite du recepteur responsable de la specificite d'accrochage.
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Ghoorah, Anisah W. "Extraction de connaissances pour la modélisation tri-dimensionnelle de l'interactome structural." Electronic Thesis or Diss., Université de Lorraine, 2012. http://www.theses.fr/2012LORR0204.
Full textAbstract:
L'étude structurale de l'interactome cellulaire peut conduire à des découvertes intéressantes sur les bases moléculaires de certaines pathologies. La modélisation par homologie et l'amarrage de protéines ("protein docking") sont deux approches informatiques pour modéliser la structure tri-dimensionnelle (3D) d'une interaction protéine-protéine (PPI). Des études précédentes ont montré que ces deux approches donnent de meilleurs résultats quand des données expérimentales sur les PPIs sont prises en compte. Cependant, les données PPI ne sont souvent pas disponibles sous une forme facilement accessible, et donc ne peuvent pas être re-utilisées par les algorithmes de prédiction. Cette thèse présente une approche systématique fondée sur l'extraction de connaissances pour représenter et manipuler les données PPI disponibles afin de faciliter l'analyse structurale de l'interactome et d'améliorer les algorithmes de prédiction par la prise en compte des données PPI. Les contributions majeures de cette thèse sont de : (1) décrire la conception et la mise en oeuvre d'une base de données intégrée KBDOCK qui regroupe toutes les interactions structurales domaine-domaine (DDI); (2) présenter une nouvelle méthode de classification des DDIs par rapport à leur site de liaison dans l'espace 3D et introduit la notion de site de liaison de famille de domaines protéiques ("domain family binding sites" ou DFBS); (3) proposer une classification structurale (inspirée du système CATH) des DFBSs et présenter une étude étendue sur les régularités d'appariement entre DFBSs en terme de structure secondaire; (4) introduire une approche systématique basée sur le raisonnement à partir de cas pour modéliser les structures 3D des complexes protéiques à partir des DDIs connus. Une interface web (http://kbdock.loria.fr) a été développée pour rendre accessible le système KBDOCK<br>Understanding how the protein interactome works at a structural level could provide useful insights into the mechanisms of diseases. Comparative homology modelling and ab initio protein docking are two computational methods for modelling the three-dimensional (3D) structures of protein-protein interactions (PPIs). Previous studies have shown that both methods give significantly better predictions when they incorporate experimental PPI information. However, in general, PPI information is often not available in an easily accessible way, and cannot be re-used by 3D PPI modelling algorithms. Hence, there is currently a need to develop a reliable framework to facilitate the reuse of PPI data. This thesis presents a systematic knowledge-based approach for representing, describing and manipulating 3D interactions to study PPIs on a large scale and to facilitate knowledge-based modelling of protein-protein complexes. The main contributions of this thesis are: (1) it describes an integrated database of non-redundant 3D hetero domain interactions; (2) it presents a novel method of describing and clustering DDIs according to the spatial orientations of the binding partners, thus introducing the notion of "domain family-level binding sites" (DFBS); (3) it proposes a structural classification of DFBSs similar to the CATH classification of protein folds, and it presents a study of secondary structure propensities of DFBSs and interaction preferences; (4) it introduces a systematic case-base reasoning approach to model on a large scale the 3D structures of protein complexes from existing structural DDIs. All these contributions have been made publicly available through a web server (http://kbdock.loria.fr)
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De, Stefano Vittorio. "Origins of specificity in protein modification, reaction patterns of tris-trimesates with human hemoglobin A, water, and n-propylamine." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0015/NQ45655.pdf.
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Rüßmann, Florian Verfasser], and Franz-Ulrich [Akademischer Betreuer] [Hartl. "The eukaryotic chaperonin TRiC domain-wise folding of multi-domain proteins / Florian Rüßmann. Betreuer: Franz-Ulrich Hartl." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2013. http://d-nb.info/1035066866/34.
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Rüßmann, Florian [Verfasser], and Franz-Ulrich [Akademischer Betreuer] Hartl. "The eukaryotic chaperonin TRiC domain-wise folding of multi-domain proteins / Florian Rüßmann. Betreuer: Franz-Ulrich Hartl." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2013. http://nbn-resolving.de/urn:nbn:de:bvb:19-157246.
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Becher, Peter Moritz [Verfasser]. "Die Bedeutung des TIR-domain-containing adaptor protein inducing Interferon-ß (TRIF) bei der viralen Myokarditis im murinen Tiermodell / Peter Moritz Becher." Berlin : Medizinische Fakultät Charité - Universitätsmedizin Berlin, 2012. http://d-nb.info/1026789435/34.
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Forsthoefel, David J. "A molecular genetic analysis of the role of the Guanine Nucleotide Exchange Factor Trio during Axon Pathfinding in the Embryonic CNS of Drosophila melanogaster." Connect to resource, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1127241654.
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Ghoorah, Anisah. "Extraction de Connaissances pour la Modelisation tri-dimensionnelle de l'Interactome Structural." Phd thesis, Université de Lorraine, 2012. http://tel.archives-ouvertes.fr/tel-00762444.
Full textAbstract:
L'étude structurale de l'interactome cellulaire peut conduire à des découvertes intéressantes sur les bases moléculaires de certaines pathologies. La modélisation par homologie et l'amarrage de protéines ("protein docking") sont deux approches informatiques pour modéliser la structure tri-dimensionnelle (3D) d'une interaction protéine-protéine (PPI). Des études précédentes ont montré que ces deux approches donnent de meilleurs résultats quand des données expérimentales sur les PPIs sont prises en compte. Cependant, les données PPI ne sont souvent pas disponibles sous une forme facilement accessible, et donc ne peuvent pas être re-utilisées par les algorithmes de prédiction. Cette thèse présente une approche systématique fondée sur l'extraction de connaissances pour représenter et manipuler les données PPI disponibles afin de faciliter l'analyse structurale de l'interactome et d'améliorer les algorithmes de prédiction par la prise en compte des données PPI. Les contributions majeures de cette thèse sont de : (1) décrire la conception et la mise en oeuvre d'une base de données intégrée KBDOCK qui regroupe toutes les interactions structurales domaine-domaine (DDI); (2) présenter une nouvelle méthode de classification des DDIs par rapport à leur site de liaison dans l'espace 3D et introduit la notion de site de liaison de famille de domaines protéiques ("domain family binding sites" ou DFBS); (3) proposer une classification structurale (inspirée du système CATH) des DFBSs et présenter une étude étendue sur les régularités d'appariement entre DFBSs en terme de structure secondaire; (4) introduire une approche systématique basée sur le raisonnement à partir de cas pour modéliser les structures 3D des complexes protéiques à partir des DDIs connus. Une interface web (http://kbdock.loria.fr) a été développée pour rendre accessible le système KBDOCK. Le système KBDOCK couvre plus de 2,700 hetero DDIs non-redondantes correspondant à 1,439 DFBSs localisés sur 947 domaines Pfam distincts. KBDOCK a permis de réaliser plusieurs études étendues. Par exemple, KBDOCK a été utilisé pour montrer que: (1) après de 70% de familles de domaines protéiques n'ont qu'un seul DFBS et les autres familles en ont un petit nombre seulement, ce qui suggère que les DDIs re-utilisent souvent les mêmes sites de liaison; (2) plus de 80% de DFBSs interagissent avec une seule famille de domaines protéiques et les autres DFBSs interagissent avec un petit nombre de familles, ce qui indique que la plupart des DFBSs sont principalement monogames dans leur interactions avec les autres domaines protéiques; (3) les DFBSs impliqués dans des interactions présentent des régularités en terme de structure secondaire, ce qui pourrait servir comme un descripteur complémentaire dans la prédiction d'interaction; (4) lorsque les domaines re-utilisent leur DFBS, le docking orienté vient améliorer les prédictions. Ainsi, KBDOCK constitue une ressource unifiée qui permet d'enrichir les connaissances sur l'interactome structural.
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Bravo, Silvina Alejandra. "The di/tri-peptide transporters PEPT1 and PEPT2 : expression and regulation in the intestinal Caco-2 and renal SKPT0193 cl.2 cell lines /." Cph. : Department of Pharmaceutics, The Danish University of Pharmaceutical Sciences, 2004. http://www.dfh.dk/phd/defences/silvinabravo.htm.
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Confavreux, Antoine. "Optimisation des conditions de migration et de détachement de lignées cancéreuses du cancer du sein en vue de leur tri fonctionnel." Thesis, Lyon 1, 2014. http://www.theses.fr/2014LYO10209/document.
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Cette thèse concerne l'étude des propriétés de migration et de détachement de lignées cancéreuses du cancer du sein de type mésenchyme, très métastatique et invasif (MDA-MB-231), ou au contraire de type épithélial et peu invasif (MCF-7). Des techniques de vidéomicroscopie et d'analyse d'images automatisées ont été utilisées afin de tirer des informations sur la dynamique cellulaire sur de grandes populations. Nos expériences sur la migration aléatoire des cellules MDA-MB-231 montrent que les propriétés de déplacement de celles-ci sont liées à la fois à la composition de leur milieu environnant, mais aussi à la nature et la quantité de protéines d'adhésion. Nous avons notamment mis en évidence un comportement biphasique de la distance migrée au cours du temps en fonction de la densité de protéines adsorbées sur des surfaces pour deux types de protéines d'adhésion (collagène type IV et fibronectine). Selon le type de protéines d'adhésion, nous avons également mis en évidence un phénotype cellulaire très différent en termes de forme, d'adhésion et de mode de déplacement. Nous avons ensuite utilisé ces résultats pour mettre en place un protocole de migration dirigée de cellules cancéreuses dans un gradient chimiotactique généré par un système microfluidique. Ainsi, en faisant varier les paramètres du système (protéines de surface, concentration maximale en chimioattractants, …), nous avons pu caractériser les bonnes conditions d'obtention de la migration dirigée. Pour finir, nous avons montré la faisabilité d'un tri cellulaire entre cellules de type mésenchyme et épithéliales en utilisant la chimiotaxie à partir de ces systèmes<br>This thesis investigates migration and detachement properties of different types of breast cancer cell lines : metastatic, invasive MDA-MB-231 and epithelial, low-invasive MCF-7 celles. Videomicroscopy and image analysis techniques were used to obtain dynamic information for large cell populations. Random migration assays performed on MDA-MB-231 cells reveal that their migration properties are related to both medium and surface (substrate adhesion protein type and quantity) conditions. A biphasic behavior for the migrated distance through time was observed to be dependent on the density of adsorbed protein (collagen type IV or fibronectin) on the substrate. Cell shape, detachement and moving properties were also computed as a function of the surface protein characteristics. These results were then used to perform directed migration assays in a chemotactic gradient generated in a microfluidic chamber. Optimal conditions for directed migration of cells were determined by varying the parameters of the system such as gradient maximum concentration, substrate adhesion protein… Lastly, it was experimentally proved that it is possible to separate cancer epithelial cell lines from mesenchymal ones by using chemotactic microfluidic chambers
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Dugast, Marc. "Mécanismes de tri impliqués dans le trafic intracellulaire des molécules du CMH II et dans les effets de Nef du VIH-1 sur les CMH et CD4." Paris 7, 2005. http://www.theses.fr/2005PA077016.
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Schächterle, Carolin. "Der strukturelle und funktionelle Einfluss des Cytokins IFNgamma auf die Modulation proteasomaler Komplexsubtypen." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2013. http://dx.doi.org/10.18452/16849.
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Das 20S Proteasom ist das Kernelement des Ubiquitin-Proteasom-Systems und baut fehlerhafte, nicht mehr benötigte und oxidierte Proteine ab, wobei drei katalytisch aktive Untereinheiten die Polypeptidkette schneiden. Das proinflammatorische Cytokin IFNg induziert die Expression und Inkorporation der alternativen katalytisch aktiven Immunountereinheiten, was in variablen Isoformen des 20S Proteasoms resultiert. Die zusätzliche Assoziation des 19S Regulators, bzw. des PA28 und des PA200 Aktivators an eine Isoform erweitert das Sortiment an proteasomalen Komplexsubtypen. Der zeitliche Verlauf einer IFNg Stimulation zeigte, dass die Aktivatoren PA28 und PA200 antagonistisch an das 20S Proteasom assoziieren und niedermolekulare Komplexsubtypen bilden, sodass in dieser Studie auch zum ersten Mal eine IFNg abhängige Assoziation des PA200 Monomers an das 20S Proteasom detektiert wurde. Ex vivo Versuche zeigten, dass die Defizienz der Immunountereinheit LMP7 mit der Assoziation des PA28-Aktivators an das 20S-19S Proteasom kompensiert wird, wobei die funktionelle Wirksamkeit aber offen bleibt. In einer monozytären Zelllinie wird ein sehr hochmolekularer, chymotryptisch aktiver Komplex assembliert und massenspektrometrische Analysen detektierten proteasomale Untereinheiten und viele Komponenten der Proteinbiosynthese, was für eine Assoziation des Proteasoms mit dem Polysom spricht. Diese Möglichkeit der kotranslationalen Degradation kann auch die Assoziation des detektieren Chaperonins TriC erklären, wobei dieser Komplex, der ATP abhängig Proteine faltet, möglicherweise auch direkt mit dem Proteasom interagieren könnte, wie elektronenmikroskopische Aufnahmen belegten. Neben den neuen strukturellen Ergebnissen, bestätigte die funktionelle Analyse den Abbau polyubiquitinierter Substrate durch 19S-Regulator assoziierte Komplexsubtypen, doch das 19S-20S-19S Proteasom konnte das Modellsubstrat HA-Ubi-IkBa-flag besser abbauen und deubiquitinieren als das 20S-19S Proteasom.<br>The 20S proteasome is the core element of the ubiquitin-proteasome-system, which degrades defective, unneeded and oxidized proteins, while three catalytically active subunits hydrolyze the peptide bonds of the polypeptide. The proinflammatory cytokine IFNg induces the expression and incorporation of three alternative, catalytically active immunosubunits resulting in variable isoforms of the 20S proteasome. The additional association of the 19S regulator, or the PA28 and PA200 activator, respectively, expands the range of proteasome complex subtypes. The time course of IFNg stimulation showed that the proteasomal association of PA28 and PA200 occurs antagonistically, forming low molecular weight complex subtypes. Furthermore, this study revealed for the first time an IFNg dependent association of the PA200 monomer to the 20S proteasome. Ex vivo experiments showed that the deficiency of the immunosubunit LMP7 is compensated by the association of the PA28 activator to the 20S-19S proteasome, whereas the functional efficacy remains elusive. In a monocytic cell line, a chymotryptic active complex with a very high molecular weight was detected, and mass spectrometry confirmed proteasomal subunits and components of the protein synthesis machinery, suggesting an association of the proteasome with the polysome. The fact of cotranslational degradation may also explain the association of the chaperonin TriC, an ATP dependent protein folding chaperonin. Electron micrographs could reveal that TriC possibly interacts directly with the proteasome. Next to the new structural results, the functional analysis confirmed the degradation of polyubiquitinated substrates by 19S regulator associated complex subtypes, and in addition to it, the 19S-20S-19S proteasome degraded and deubiquitinated the model substrate HA-Ubi-IkBa-flag better than the 20S-19S proteasome.
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Ecard, Jason. "Mécanismes de tri et voies de transport intracellulaire des protéines de la membrane du lysosome." Electronic Thesis or Diss., Sorbonne université, 2019. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2019SORUS094.pdf.
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Plus d’une soixantaine de protéines différentes sont insérées dans la membrane du lysosome et participent aux différentes fonctions de cet organite. Mais les voies de transport intracellulaire qui mènent les protéines membranaires lysosomales (LMP) jusqu’à cet organite ne sont pas bien comprises. De façon intéressante, certaines LMP présentent des localisations intracellulaires anormales dans certains cancers. C’est notamment le cas de la glycoprotéine LAMP1 qui s’avère surexposée à la surface cellulaire dans plusieurs cancers, où elle y joue plusieurs rôles dans l’agressivité tumorale. Grâce au système RUSH (pour Retention Using Selective Hooks), permettant la synchronisation du transport le long de la voie de sécrétion, nous avons montré que LAMP1, après néosynthèse, passe par la membrane plasmique avant d’accéder aux endosomes. La comparaison des voies empruntées par différentes LMP a aussi permis de révéler que LAMP1 et LIMP2 sont triées au niveau de l’appareil de Golgi, LIMP2 étant concentrée dans des structures vésiculaires caractéristiques et dépourvues de clathrine. Nous avons aussi montré que, de façon surprenante, ce tri au niveau de l’appareil de Golgi est indépendant des signaux de recrutement d’adaptateurs à la clathrine portés dans les queues C-terminales de ces deux LMP. Afin d’étudier quels mécanismes pourraient être impliqués dans la surexposition de LAMP1 à la surface cellulaire de certains cancers, nous avons aussi réalisé un criblage d’inactivation de gènes basé sur la technologie CRISPR-Cas9. Nous avons sélectionné les gènes dont l’inactivation affectait les niveaux de LAMP1 en surface et nous avons obtenu de nombreux gènes candidats qui sont à l’étude<br>More than sixty different proteins are inserted into the membrane of the lysosome, participating in the various functions of this organelle. But the intracellular trafficking pathways that lead lysosomal membrane proteins (LMPs) to this organelle are not well understood. Interestingly, some LMPs exhibit abnormal intracellular localisations in some cancers. This is the case of the glycoprotein LAMP1 which is overexpressed at the cell surface in several cancers, from where it plays several roles in tumour aggressiveness. Thanks to the Retention Using Selective Hooks (RUSH) system, allowing the synchronisation of the transport along the secretory pathway, we have shown that neosynthesized LAMP1 reaches the plasma membrane before entering endosomes. Comparing the routes followed by different LMPs also revealed that LAMP1 and LIMP2 are sorted at the Golgi apparatus, LIMP2 being concentrated in characteristic vesicular and clathrin-free structures. We have also shown that, surprisingly, this sorting at the level of the Golgi apparatus is independent of clathrin adapters recruitment signals carried in the C-terminal tails of these two LMPs. To investigate what mechanisms might be involved in the overexposure of LAMP1 at the cell surface of certain cancers, we also performed a gene knock-out screen based on CRISPR-Cas9 technology. We selected genes whose inactivation affected LAMP1 levels at the surface and obtained many candidate genes that are under study
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Collins, Karl Daniel. "The development and application of radical and anionic cyclisations mediated by samarium(II) diodide and protic co-solvents." Thesis, University of Manchester, 2012. https://www.research.manchester.ac.uk/portal/en/theses/the-development-and-application-of-radical-and-anionic-cyclisations-mediated-by-samariumii-diodide-and-protic-cosolvents(0e807a8c-d40f-45bb-8d83-26e79ebe9388).html.
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The development of selective SmI2-H2O-mediated mono-reductions of cyclic-1,3-diesters to the corresponding 3-hydroxy acids is described. The reaction proceeds with complete selectivity for cyclic-1,3-diesters over acyclic esters. Sequential one-pot conjugate reduction-ester reduction of alkylidene cyclic-1,3-diesters is also reported. Furthermore, we describe the exploitation of the unusual ketyl radical intermediates formed via single electron reduction of the ester carbonyl in unprecedented 5-exo-trig cyclisations providing access to highly substituted, stereo-defined, cyclopentanols and cyclopentanones. Also described is the use of a silicon control element to direct the stereochemical outcome of the SmI2-MeOH-mediated conjugate reduction-intramolecular aldol cyclisations of α,β-unsaturated lactones. These cyclisations generate two contiguous quaternary centres with complete diastereocontrol; the utility of the silicon-directing group as a synthetic handle for derivatisation of the cyclisation products has also been demonstrated. These cyclisations have been applied in a model approach to the anti-mitotic natural product pseudolaric acid B.
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Huang, Shu-Yu, and 黃書毓. "Structural Characterization and Molecular Interaction with the TRIM Domains of Promyelocytic Leukemia Protein." Thesis, 2015. http://ndltd.ncl.edu.tw/handle/40271052944316786419.
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博士<br>國立臺灣大學<br>生化科學研究所<br>103<br>PML protein is mainly present inside the nucleus in the form of PML nuclear bodies (PML-NBs) and serves as a SUMO E3 ligase which facilitates SUMOylation on PML itself and proteins in PML-NBs. PML has a conserved N-terminal TRIM/RBCC region comprised of a RING finger domain, two B-boxes and a coiled-coil region. The purpose of this study is to investigate the structural basis of SUMOylation on PML TRIM domains which is essential in the formation of PML-NBs. However, not much of the structural information of PML is known today. In this work we solved the structures of RING finger and B-box 1 of dimer by advanced NMR techniques. We identified the residues involved in the binding of SUMO E2 enzyme Ubc9 and PML TRIM domains. The result of SPR indicated that dimeric domain RB1 showed much stronger interaction with Ubc9 (KD=16uM) than any single domain (KD=490uM for RING finger and KD=94uM for B-box 1), suggesting that RING finger and B-box 1 bound with Ubc9 in synergy. Here, we provide the structures of PML TRIM domains and the bindings with Ubc9 at molecular level in order to understand the SUMOylation mechanism on PML TRIM domains.
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Späth, Kerstin [Verfasser]. "Untersuchungen zur funktionellen Charakterisierung von regulatory-protein T-lymphocyte-1 (rpt-1, Trim 30) / vorgelegt von Kerstin Späth." 2005. http://d-nb.info/973945087/34.
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Chang, Chia-Ling, and 張嘉玲. "I. Studies of a Rice Sterile Mutant sstl from Taiwan Rice Insertional Mutants (TRIM) CollectionII. Multifunctional Roles of Rice Yellow Mottle Virus (RYMV) P1 Protein in Host Infection." Thesis, 2019. http://ndltd.ncl.edu.tw/handle/dbh86b.
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博士<br>國立臺灣大學<br>農藝學研究所<br>107<br>Rice (Oryza sativa) is one of the main crops in the world. By 2025, more than 3.9 billion people count rice as daily food energy especially in Asia and Africa. Because of the increased population, the production of rice is still far away behind requirements. Meanwhile, the food safety issue related to feed the world continuously, to adjust crop adaptation in climate change, to establish sustainable agriculture, etc. are urgent to be solved. My study in this thesis will cover two different topics described as followings: First, studies of a rice sterile mutant (semi-sterile; sstl) from the TRIM collection and the second investigation, multifunctional roles of rice yellow mottle virus (RYMV) P1 protein in host infection.
I. Studies of a rice sterile mutant sstl from the TRIM collection
Sterility significantly affects rice production and leads to yield defects. The undeveloped anthers or abnormal pollens represent serious defects in rice male sterility. Therefore, understanding the mechanism of male sterility is an important task. Here, we identified an untagged T-DNA insertion mutant sstl based on its semi-sterile morphology of rice development. We investigated the fully sterile mutants (sstl-s) of sstl segregated progeny showed defective pollens and abnormal anthers. Transcriptomic analysis of sterile sstl-s revealed significant differences in several biosynthesis pathways, such as downregulated cell wall, lipids, secondary metabolism, and starch synthesis. The downregulation of gene expression is consistent with the morphological characterization of sstl-s anthers with irregular exine, absence of intine, lack of starch accumulation in pollen grains and no accumulation of flavonoids in anthers. Moreover, defective microsporangia development led to abnormal anther locule and aborted microspores. The downregulated expression of lipids, starch, and cell wall synthesis-related genes resulted in loss of fertility. In summary, the analysis of sstl-s mutant pointed out the importance of microsporangia in the development of anthers and functional microspores.
II. Multifunctional roles of RYMV P1 protein in host infection
Rice yellow mottle virus (RYMV), a virus spread all over African countries, has caused significant damage to rice plant and resulted in dramatic decrease of yield in Africa. ORF1 of RYMV encodes P1 protein which belongs to a novel zinc finger family with its conformation regulated by redox switches. P1 protein was suggested as suppressor after virus infection; however, the function of P1 in virus transition is still unclear. In the present study, we explored the possible mechanisms of P1 in virus replication rate, movement ability, and suppression of host defense. We showed that mutated P1 RYMV still could replicate but at less replication rate than that of normal RYMV after transfection into rice protoplast. All replication rate with mutated P1 RYMV infection decreased from 24 hrs to 48 hrs after inoculation. This result indicated that functional P1 not only could regulate RYMV replication production but also maintain viral RNA transcription stability. In addition, mutated P1 RYMV showed no virus accumulation after infection into rice plant and none of the infected plant displayed virus accumulation. This indicated P1 could help regulate virus spread after infection. P1 protein co-localized with ER marker suggested this protein might participate in virus spread in the cell. Meanwhile, P1-eGFP fusion protein was transmitted between two adjacent cells and thus illustrating P1 mobility. Heat-inducible transgenic rice also displayed P1 transcript moving from lower leaf to non-heat treated upper leaf after heat treatment. This evidence strongly suggested that P1 RNA could be involved in virus long-distance movement. In additional to virus infection ability, the virulence can also be affected by host defense. Our data suggested functional P1 protein might help virus resist host defense by decreasing the expression of biotic-related genes such as PR10A and CPR5. Moreover, P1 could hijack host silencing pathway through down-regulating DCL-like and AGO expression to make host susceptible. Taken together, these results illustrate that P1 protein may serve as multifunctional roles to participate in virus replication, movement, as well as counterattack.
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Chang, Jian-Sheng, and 張建盛. "Protein Expression, Purification, and Structural Characterization of Truncated Human TREM-Like Transcript-2." Thesis, 2007. http://ndltd.ncl.edu.tw/handle/39999279592359434152.
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碩士<br>國立清華大學<br>生物資訊與結構生物研究所<br>95<br>TREMs, triggering receptor expressed on myeloid cells, belong to a rapidly expanding family of receptors that include activating and inhibitory isoforms encoded by a gene cluster linked to the major histocompatibility complex (MHC) on human chromosome 6. Human TREM-like transcript-2 (hTLT-2), one kind of TREM gene family with 321 amino acids, is a membrane protein and signal receptor expressed on neutrophils, macrophages, and B lymphocytes in innate and adaptive immune system. Until now, the characterization and structural analysis of hTLT-2 remain unclear. In this study, the N-terminus extracellular domain of hTLT-2 was truncated to 26-kDa (from 14-Q to 265-D) and 13-kDa (from 14-Q to 132-N) fragments and cloned into expression vectors pET-28a and pGEX-6P-3. The two partial fragments of hTLT-2 were expressed in competent cells, such as E. coli BL21 (DE3), BL21-Gold (DE3), and Rosetta (DE3). Tag of target proteins were His-tag and GST-tag and the two truncated hTLT-2 proteins were purified with Ni-column and GSTrap FF column, respectively. Guanidine hydrochloride (Gdn-HCl) was used to dissolving the truncated hTLT-2 involved in inclusion body and the target proteins were refolded by dialysis for removing Gdn-HCl in the buffer. The results demonstrate that the larger size of 26-kDa of outer-membrane region of truncated hTLT-2 proteins are difficult to be expressed in E. coli expression system and tend to aggregate with other proteins in inclusion body. According to circular dichroism spectrum, the secondary structure of this 16-kDa of His-tagged hTLT-2 fragment is composed of about 5% alpha helix, 47% beta sheet, and 48% random coil. Thus, the secondary structure of outer-membrane region of 16-kDa of truncated hTLT-2 like TREM-1 and TLT-1 of TREM family mainly comprises beta sheets.
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Lin, Yin-Ling, and 林易鈴. "A Trip to Protect Your Heart：Studies of Cardiovascular Nursing Care." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/qx42zw.
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碩士<br>國立陽明大學<br>科技與社會研究所<br>106<br>This study explores cardiovascular nursing care from the perspectives of gender and technology studies. I review studies of cardiovascular epidemiology, medical guideline of heart diseases, and cardiovascular nursing education in school and the hospital. I also review literatures of nurse-patient relationship, nursing guidance, and "gender innovation" studies on female heart diseases. I use multiple research methods in this studies. The empirical data in this study includes my own clinical practice of cardiovascular nursing care, and in-depth interviews of my colleagues. Secondary data includes health education information of cardiovascular nursing care collected from five teaching hospitals. The contents of this thesis is divided into three chapters. In Chapter II, I describe the clinical treatments of heart disease in Taiwan. In Chapter III, I compare the differences between school nursing education and clinical practice in cardiology. I use pain assessment in cardiology for an example to explore gender differences in cardiology. In Chapter IV, I analyze the health education information of cardiovascular care from five medical centers. I analyze and compare their writers, forms of transmission, timing of use, and their differences concerning sex, gender and gender differences. I conclude my thesis with "seeing your heart" and " put your heart in my heart". I believe that the perspectives of gender and technology studies can lead us to a better cardiovascular nursing care.
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Liu, Sunbin [Verfasser]. "Investigation of protein-protein interactions within the human spliceosomal U4/U6.U5 tri-snRNP particle / vorgelegt von Sunbin Liu." 2005. http://d-nb.info/97621802X/34.
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Rold, Christopher James. "The role of the cellular proteasome and ubiquitin in post-entry restriction of retroviruses by TRIM5[alpha]." Diss., 2009. http://etd.library.vanderbilt.edu/available/etd-03302009-150129/.
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Chang, Po-Chih, and 張博智. "Synthesis and Reactivity Study of Tris(1-pyrazolyl)methane Copper(I) Complexes Relating to the Copper Protein Active Site Modeling Complexes." Thesis, 2004. http://ndltd.ncl.edu.tw/handle/19584927692376547912.
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碩士<br>國立中山大學<br>化學系研究所<br>92<br>Nitrous oxide is a greenhouse gas produced in large quantity by several industrial processes. Efficient means of eliminating N2O are therefore of interest. The denitrification enzyme nitrous oxide reductase (N2OR), which reduces N2O to N2 and water , has recently been shown to contain an unprecedented [Cu4-µ4S] active site. Multinuclear copper sulfide compounds are known but have not been studied in the context of modeling N2OR or as N2O reduction catalysts. The synthesis of new tetranuclear [Cu4-µ4S] compounds is proposed to model the N2OR active site.The purpose of our research is to synthesize [Cu2-µ2S] complex, which original compound of [Cu4-µ4S] complex. This can be groundwork for mimicking the copper protein active site.
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Choonara, Bibi Fatima. "A Tri-Functionalized Oral Core-Melt Tablet (OCMT) for enhanced delivery of gastro-sensitive proteins and synthetic peptides." Thesis, 2017. https://hdl.handle.net/10539/24911.
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A thesis submitted to the Faculty of Health Sciences, University of the Witwatersrand, in fulfillment of the requirements for the degree of Doctor of Philosophy. Department of Pharmacy and Pharmacology, University of the Witwatersrand,
South Africa
Johannesburg, 2017.<br>The global pharmaceutical biotechnology industry is continually growing and increased amounts of protein and peptide-based therapeutics are entering into the market. Conventionally, these therapeutic proteins and peptides are administered intravenously, subcutaneously or intramuscularly as oral routes of administration may result in their degradation in the gastrointestinal tract (O’ Connor, 2009). The parenteral route limits patient acceptability and convenience. Oral dosage forms, particularly tablets, are considered one of the most common and widely used routes of drug administration and accounts for approximately 50% of all dosage forms on the market (Oh et al., 2012). Thus, the development of oral technologies for therapeutic proteins and peptides remain a dynamic research field despite its many challenges. Successful oral delivery of proteins and peptides require the accomplishment of three key tasks: protection of the macromolecules from degradation in the gastrointestinal tract (GIT), permeation through the intestinal barrier and the absorption of molecules into the systemic circulation. Currently, no clinically useful oral formulations have been approved but several attempts have been made to overcome the challenges of low oral bioavailability resulting from poor absorption, poor permeation and enzymatic degradation of the proteins and peptides in the GIT. Present strategies attempt to provide structural protection of the proteins and peptides and improved absorption through the use of enzyme inhibitors, absorption enhancers, novel polymeric delivery systems and chemical modification. However, each of these technologies possesses limitations that preclude the successful oral delivery of proteins and peptides.
The design and development of the novel Tri-functionalized OCMT attempts to breakthrough this market by triple targeting the major challenges governing successful oral delivery of proteins and peptides. Essentially, the Tri-functionalized OCMT is made up of three distinct functional components; the core-eutectic region, the outer polymer shell and the ‘smart’ polymeric sheet. Triple targeting was achieved by incorporating the bioactive into a core-melt archetype within the tablet and facilitating the process of in situ crosslinking which significantly affects the way the bioactive is protected within the compressed tablet matrix as well providing desirable bioactive release kinetics. In addition, the incorporation of a co-inhibitory ‘smart’ polymeric sheet provided added protection and enabled an improved absorption by virtue of its intrinsic properties and co-inhibition of the major determinants, CYP3A4 and Pgp, of poor absorption and low oral bioavailability. Lastly, targeting of enzymatic degradation was achieved by incorporation of a pH modifier that functions to transiently lower the micro-environmental pH and reduce the optimal environment for enzyme activity.
The combination of the distinct formulatory components contained within the Tri-functionalized OCMT was extensively evaluated through in-depth in vitro physicochemical and physicomechanical characterization, ex vivo analyses and in vivo performance. In vitro and ex vivo characterization enabled the optimization of design variables and promoted the achievement of desirable functionalities for the attainment of optimum in vivo performance. In vivo analyses of the Tri-functionalized OCMT in the Large White pig model revealed an enhanced oral bioavailability of the incorporated peptides, octreotide and exenatide, following oral administration, as compared to their conventionally administered subcutaneous counterparts. In addition, pharmacokinetic analysis of the Tri-functionalized OCMT confirmed the maintenance of sustained, therapeutic levels of both octreotide and exenatide over the 24 hour period, supporting a convenient once-daily dosing.
The rate at which protein and peptide-based therapeutics are developing is astounding, and this consequently increases the demand and focus towards achieving a simpler and more effective oral delivery of therapeutic proteins and peptides. The Tri-functionalized OCMT has successfully demonstrated its feasibility in enhancing the oral delivery of therapeutic proteins and peptides up to a preclinical stage. It may potentially serve as a viable alternative to the conventional parenteral route of administration for the treatment of various disease conditions by incorporating a multitude of proteins and peptides into its versatile design. The advancement of the Tri-functionalized OCMT to the clinical stage and beyond may ultimately improve patient outcomes and change the face of therapeutic protein and peptide delivery globally.<br>LG2018
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Häcker, Irina. "Electron microscopic localization of tagged proteins in the yeast S. cerevisiae spliceosomal U4/U6.U5 trisnRNP." Doctoral thesis, 2008. http://hdl.handle.net/11858/00-1735-0000-0006-AD0F-E.
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Narita, Vanny. "Molecular, genetic, and functional analysis of Ptr3p, a novel protein involved in amino acid and dipeptide regulation of di/tri-peptide transport system in Saccharomyces cerevisiae." 2002. http://etd.utk.edu/2002/NaritaVanny.pdf.
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Thesis (Ph. D.)--University of Tennessee, Knoxville, 2002.<br>Title from title page screen (viewed Oct. 3, 2002). Thesis advisor: Jeffrey M. Becker. Document formatted into pages (xiv, 250 p. : ill. (some col.)). Vita. Includes bibliographical references.
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Müllers, Nina. "Struktur-Funtionsbeziehung in den spleißosomalen Proteinen des U4/U6•U5 tri-snRNP." Doctoral thesis, 2006. http://hdl.handle.net/11858/00-1735-0000-0006-AC43-D.
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