Дисертації з теми "Cryo-EM structures"
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Wilkes, Martin [Verfasser], Christine [Akademischer Betreuer] [Gutachter] Ziegler, and Clemens [Gutachter] Glaubitz. "Single-particle cryo-EM structures of oligomeric membrane protein complexes / Martin Wilkes ; Gutachter: Clemens Glaubitz, Christine Ziegler ; Betreuer: Christine Ziegler." Frankfurt am Main : Universitätsbibliothek Johann Christian Senckenberg, 2016. http://d-nb.info/1120493412/34.
Повний текст джерелаPreis, Anne [Verfasser], and Roland [Akademischer Betreuer] Beckmann. "Cryo-EM structures of eukaryotic translation termination and ribosome recycling complexes containing eRF1, eRF3 and ABCE1 / Anne Preis ; Betreuer: Roland Beckmann." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2020. http://d-nb.info/1213658837/34.
Повний текст джерелаZhou, Yu. "Structural study of eIF2B by electron microscopy." Thesis, University of Manchester, 2016. https://www.research.manchester.ac.uk/portal/en/theses/structural-study-of-eif2b-by-electron-microscopy(feacd470-3139-4648-9812-c152168c930d).html.
Повний текст джерелаAbdelkareem, Moamen. "Structural basis of transcription : RNA polymerase backtracking and its reactivation." Thesis, Strasbourg, 2019. http://www.theses.fr/2019STRAJ062.
Повний текст джерела[...]My Ph.D. was focused on the understanding of a transcriptional phenomenon, termed backtracking, which inactivates RNAP and halts transcription. Reactivation of halted RNAP complexes and transcription resumption, requires a protein factor called GreB. The objective of the project was to gain structural information on: i) how backtracking inactivates RNAP inE. coli; and ii) how GreB rescues backtracked RNAP to continue transcription. Using SP cryo- EM, I captured four snapshots of RNAP at different states covering the backtracking and reactivation cycle. My results show that the RNA is no longer aligned with the active center, explaining the transcription halt. Furthermore, as a result of backtracking, RNAP adopts new conformational changes allowing GreB binding. As a consequence, the NTD of GreB contacts RNAP active center and donates acidic residues that increase the affinity towards a magnesium ion, which is required for cleavage catalysis of the misaligned RNA. These four reconstructions give insights on the catalytic mechanism and dynamics of RNA cleavage and extension. [...]
Brito, Querido Jailson Fernando. "Structural study of mRNA translation in kinetoplastids by Cryo-electron microscopy." Thesis, Strasbourg, 2017. http://www.theses.fr/2017STRAJ108.
Повний текст джерелаKinetoplastid is a group of flagellated protozoans, which threatens more than 400 million people world-wide. They possess unusual large rRNA expansion segments (ES) in the 40S, such as ES6S, ES7S and ES9S and their location suggests an involvement in the initiation process. Furthermore, all mature mRNAs possess a conserved 5’ spliced-leader. Here, we purified from T. cruzi cell lysates native initiation complexes and native 40S subunits that we then analysed by cryo-EM. The structure of native initiation complexes reveals several kinetoplastid-specific aspects of translation, such as an intricate interaction network between eIF3 and ES6S and ES7S. Furthermore, it reveals the role of DDX60 in translation initiation in kinetoplastids. The structure of native 40S subunits reveals the existence of an uncharacterized factor (termed ηF) bound at platform of the 40S. The binding site of ηF suggests a role in translational control. Moreover, we reported a novel kinetoplastid-specific ribosomal (r-) protein (KSRP) bound to the 40S subunit. Our work represents the first structural characterization of kinetoplastids-specific aspects of translation initiation
Spikes, Tobias Edward. "Structural studies of the mitochondrial F-ATPase." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/274349.
Повний текст джерелаHe, Shaoda. "Helical reconstruction in RELION." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/284086.
Повний текст джерелаNojima, Shingo. "Cryo-EM Structure of the Prostaglandin E Receptor EP4 Coupled to G Protein." Doctoral thesis, Kyoto University, 2021. http://hdl.handle.net/2433/263574.
Повний текст джерелаTorchy, Morgan. "Etude structure-fonction du complexe de remodelage de la chromatine NuRD." Thesis, Strasbourg, 2014. http://www.theses.fr/2014STRAJ113/document.
Повний текст джерелаAn integrative structural biology approach has been used to study the structural organization of the NuRD complex.My work focused especially on three subunits of this complex: MBD3, RbAp46 and RbAp48. I set up the preparation of the individual subunits and characterized them by various biophysical methods. We next carried out binding assays with homemade human nucleosomes. For MBD3, optimization of the complex led to crystals diffracting up to 7 Å. In parallel, a preliminary 3-D reconstruction at 25 Å resolution has been solved in cryo-EM. For RbAp46/48, crystal we were able to show that these proteins form stable complexes with the nucleosome, paving the way for future structural analysis by cryo-EM or X-ray crystallography
Guo, Xieyang. "Regulation of transcription : structural studies of an RNA polymerase elongation complex bound to transcription factor NusA." Thesis, Strasbourg, 2018. http://www.theses.fr/2018STRAJ071/document.
Повний текст джерелаTranscriptional pausing by RNA polymerases (RNAPs) is a key mechanism to regulate gene expression in all kingdoms of life and is a prerequisite for transcription termination. The essential bacterial transcription factor NusA stimulates both pausing and termination of transcription, thus playing a central role. Here, I present single-particle electron cryo-microscopy (cryo-EM) reconstructions of NusA bound to paused elongation complexes with and without a pause-enhancing hairpin in the RNA exit channel. The structures reveal four interactions between NusA and RNAP that suggest how NusA stimulates RNA folding, pausing, and termination. An asymmetric translocation intermediate of RNA and DNA converts the active site of the enzyme into an inactive state, providing a structural explanation for the inhibition of catalysis. Comparing RNAP at different stages of pausing provides insights on the dynamic nature of the process and the role of NusA as a regulatory factor
Busselez, Johan. "Structure et oligomérisation de complexes membranaires photosynthétique bactériens : une analyse par cryo-microscopie électronique." Paris 6, 2007. http://www.theses.fr/2007PA066094.
Повний текст джерелаThonghin, Nopnithi. "Structural studies of the multi-drug resistance protein P-glycoprotein (ABCB1)." Thesis, University of Manchester, 2018. https://www.research.manchester.ac.uk/portal/en/theses/structural-studies-of-the-multidrug-resistance-protein-pglycoprotein-abcb1(9f3d4a87-4d43-4984-9e41-3db5fc2be66a).html.
Повний текст джерелаPolovinkin, Lucie. "Etudes structurales du récepteur 5-HT3." Thesis, Université Grenoble Alpes (ComUE), 2019. http://www.theses.fr/2019GREAV028.
Повний текст джерелаCys-loop receptors are pentameric ligand-gated ion channels (pLGIC), which play a crucial role in rapid neurotransmission. They are the targets of a legion of drugs (antiemetics, general anesthetics, benzodiazepines, smoke cessation drugs, etc.) and their physiological properties are intensively studied. When pLGICs bind neurotransmitters, they undergo conformational changes, from a resting closed-pore state to a transient open-pore state; they can also enter a ligand-bound, closed-pore, desensitized state. Moreover, the gating properties of pLGICs can be influenced by a variety of compounds (e.g. lipids, competitive inhibitors, allosteric modulators, ions such as Ca2+), which makes them flexible receptors capable of integrating different signals into conformational changes.In this thesis we focus on structural studies of the mouse serotonin type 3 receptor (m5-HT3R). The first structure of the m5-HT3R, obtained by X-ray crystallography using stabilizing nanobodies, was a closed-pore inhibited conformation {Hassaine:2014de}. As a follow-up, we aimed to obtain structures of the m5-HT3R in other conformations, in order to elucidate its gating mechanism. For this purpose we used both X-ray crystallography and cryo-electron microscopy and thus the whole thesis follows two story-lines.A general introduction of the pLGIC family is followed by a detailed structural description of the m5-HT3R. In the results section, we present the optimized protocol for the receptor purification, we report that limiting diffraction is a bottleneck in the crystallographic trials and we emphasize limits met using nanobodies for conformational stabilization of the receptor. In the electron microscopy results part we present the optimization of the sample and grid preparation that ultimately permitted data collection. We report four different structures representing distinct functional states of the m5-HT3R: an inhibited tropisetron-bound closed conformation, an open-pore state and a putative pre-active state obtained in the presence of serotonin, and finally a closely-related putative pre-active state in the presence of serotonin and of the allosteric modulator TMPPAA. We compare our data with structures of the same receptor obtained by other laboratory.It was shown for the first time in our work how the antagonist (tropisetron) and the neurotransmitter (serotonin) bind to the full-length m5-HT3R. And our structures deepen the knowledge of the receptor's gating mechanism
Lobo, Joshua J. "3D RECONSTRUCTION OF RyR1 AND STRUCTURAL VALIDATION UNDER DIFFERENT LEVELS OF NOISE." VCU Scholars Compass, 2014. http://scholarscompass.vcu.edu/etd/3633.
Повний текст джерелаRamsay, Ewan. "Structural and mutational characterisation of human retinoschisin." Thesis, University of Manchester, 2017. https://www.research.manchester.ac.uk/portal/en/theses/structural-and-mutational-characterisation-of-human-retinoschisin(affc298b-83fe-4494-9456-f827177d578d).html.
Повний текст джерелаGomez, de Segura Jesus. "Caractérisation structurale et fonctionnelle des NuRD Complexes." Thesis, Université Grenoble Alpes (ComUE), 2019. https://thares.univ-grenoble-alpes.fr/2019GREAV063.pdf.
Повний текст джерелаThe nucleosome remodeling and histone deacetylase (NuRD) complex is one of the main epigenetic regulators of the genome. It contributes to the formation and maintenance of the heterochromatin, a tightly packed structure of DNA and proteins that represses transcription. NuRD plays a central role in relevant biological processes such as pluripotency regulation or tumorigenesis. Despite that, its structure and action mechanism remain unknown. This is largely due to the inherent compositional and conformational hetesrogeneity of NuRD. In this PhD work we tried to overcome these challenges using a multidisciplinary approach. We combined affinity purification of endogenous and recombinant NuRD complexes and subunits, cross-linking, electron cryo-microscopy and mass spectrometry. Thanks to that we were able to identify a stable histone deacetylase subcomplex with independent activity (PMMR) and solve its structure at 16.6 Å. We also obtained low resolution structures of several smaller subcomplexes. Studying these subcomplexes allowed us to propose a Holo-NuRD assembly pathway, leading to the publication of a scientific paper.Key words: NuRD, Epigenetic regulation, Chromatin remodeling, Histone deacetylase, Cryo-EM
Müller, Claudia [Verfasser], and Daniel [Akademischer Betreuer] Wilson. "Structural insights into bacterial ribosome rescue using cryo-EM / Claudia Müller ; Betreuer: Daniel Wilson." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2020. http://d-nb.info/1218466405/34.
Повний текст джерелаKhusainov, Iskander. "Structural studies of the Staphylococcus aureus ribosome." Thesis, Strasbourg, 2015. http://www.theses.fr/2015STRAJ071/document.
Повний текст джерелаThe ribosome is a large cellular machinery that performs the protein synthesis in every living cell. Therefore, the ribosome is one of the major targets of naturally produced antibiotics, which can kill bacterial cells by blocking protein synthesis. However, some bacteria are resistant to these antibiotics due to small modifications of their ribosomes. Among them, Staphylococcus aureus (S. aureus) is a severe pathogen that causes numerous infections in humans. The crystal structures of complexes of antibiotics with ribosomes from Gram-negative non-pathogenic non-resistant bacteria have provided unparalleled insight into mechanisms of antibiotics action. However, the structure of the ribosome from Gram-positive pathogenic and highly resistant bacteria such as S. aureus was still unidentified.In this study we present the first high resolution structure of the ribosome from S. aureus solved at 3.9 Å by cryo-electron microscopy (cryo-EM). We demonstrate several features of the ribosome organization which are unique for Gram-positive bacteria. We also describe the protocol of purification and crystallization of S. aureus ribosome for future cryo-EM and X-ray crystallography studies.All the results obtained in this work will help to describe S. aureus ribosome and its functional complexes at the atomic level in the nearest future. The combination of X-ray crystallography and cryo-EM methods will help to achieve this aim. The obtained results will provide a foundation for the development of new compounds against the pathogenic and extremely resistant bacteria S. aureus
Albanese, Pascal. "Structure and structural dynamics of Photosystem II supercomplex in higher plants." Doctoral thesis, Università degli studi di Padova, 2017. http://hdl.handle.net/11577/3423249.
Повний текст джерелаLa fotosintesi è indubbiamente il processo biologico principale che introduce energia chimica e biomassa negli ecosistemi ossidando l’acqua e riducendo l'anidride carbonica in composti organici. Il fotosistema II (PSII) è un complesso proteico presente nelle membrane tilacoidali di tutti gli organismi fotosintetici, l’unico in grado di catalizzare la reazione di lisi dell'acqua utilizzando la luce solare come forza motrice e di conseguenza responsabile della generazione di tutto l'ossigeno molecolare presente nell'atmosfera da più di tre miliardi di anni. Nonostante il centro catalitico del PSII sia rimasto fondamentalmente inalterato nel corso dell'evoluzione dai cianobatteri alle piante superiori, la necessità di far fronte alla continua variazione delle condizioni di luce ambientali ha portato all’evoluzione di sistemi di antenne periferiche altamente differenziate, distinte in ficobilisomi estrinseci nei cianobatteri e complessi di membrana intrinseci (LHCII) in alghe verdi e piante superiori. Gli LHCII sono complessi proteici di membrana presenti come etero-trimeri composti dalle subunità Lhcb1-2-3 e subunità monomeriche Lhcb4-5-6 associate perifericamente con il centro catalitico del PSII in numero variabile, formando così associazioni supramolecolari chiamate supercomplessi PSII-LHCII. L'unità funzionale minima, presente in ogni condizione di luce, detta C2S2, è costituita da un PSII centro di reazione dimerico (C2) legato strettamente a due complessi antenna trimerici (S2), composti da Lhcb1 e Lhcb2, mediante due subunità monomeriche Lhcb4 e Lhcb5. In condizioni di luce limitante il C2S2 può ulteriormente associare uno o due complessi antenna trimerici legati moderatamente (M2), costituiti dalle subunità Lhcb1, Lhcb2 e Lhcb3, mediante una peculiare subunità monomerica che si trova solo nelle piante superiori, Lhcb6, generando supercomplessi di tipo C2S2M1-2. I supercomplessi PSII-LHCII possono ulteriormente interagire lateralmente all'interno del piano della membrana tilacoidale formando megacomplessi PSII-LHCII o più estesi arrangiamenti ordinati semicristallini. I complessi antenna LHCII svolgono un duplice ruolo, la dissipazione efficiente dell'energia luminosa, spesso in eccesso negli ambienti naturali, e l’ottimizzazione della sua raccolta negli ambienti in cui vi è concorrenza tra organismi e ombreggiatura reciproca. Il riassetto del sistema di antenne modulari del PSII attraverso la sua interazione dinamica con il centro catalitico sembra quindi essere un processo chiave nella regolazione della raccolta della luce. Inoltre, i PSII e LHCII nelle piante sono spazialmente e funzionalmente segregati in dischi impilati di membrane tilacoidi (grana), dove occupano l'80% della superficie. La loro disposizione strutturale in supercomplessi PSII-LHCII che interagiscono dinamicamente tra loro sembra essere determinante per l'architettura complessiva della membrana tilacoidale e quindi per l'efficienza della fotosintesi. Sebbene la struttura del supercomplesso base C2S2 delle piante sia stata recentemente risolta ad una risoluzione quasi atomica, c'è ancora una lacuna conoscitiva riguardo al ri-arrangiamento strutturale dei PSII-LHCII che avviene in diverse condizioni di luce e alla loro interazione reciproca nel piano della membrana e tra membrane adiacenti dei grana. Durante il lavoro svolto in questa tesi, siamo stati in grado di purificare super- e megacomplessi PSII-LHCII isolati da piante di pisello coltivate in luce moderata mediante la completa solubilizzazione delle membrane tilacoidali. La caratterizzazione biochimica dei supercomplessi PSII-LHCII isolati, complementata da accurate analisi proteomiche, è stata accoppiata con studi strutturali al fine di comprendere la loro architettura funzionale. La caratterizzazione strutturale, eseguita mediante microscopia elettronica a trasmissione (TEM) in condizioni criogeniche (cryo-EM) e successiva analisi d’immagine sulle singole particelle, ha portato ad una nuova struttura tridimensionale (3D) a circa 14 Å di risoluzione del supercomplesso di tipo C2S2M. La mappa di densità elettronica ottenuta ha rivelato che, in condizioni di luce di crescita di intensità moderata, la maggior parte dei supercomplessi è di tipo C2S2M. Essi sono disposti in maniera accoppiata, interagendo mediante collegamenti fisici attraverso l’intervallo stromatico, verosimilmente di membrane adiacenti. La sovrapposizione specifica degli LHCII trimerici, uno di fronte all'altro in supercomplessi accoppiati, come già osservato in altri studi, suggerisce che questa conformazione potrebbe essere rappresentativa del loro stato nativo all'interno delle membrane. I collegamenti fisici osservati nell’intervallo stromatico potrebbero essere attribuibili all'interazione reciproca tra le lunghe porzioni N-terminali di subunità monomeriche Lhcb4 adiacenti. Queste subunità occupano una posizione chiave nella mappa 3D dei supercomplessi accoppiati e le densità elettroniche che attraversano l’intervallo stromatico connettendo i due supercomplessi sono chiaramente attribuibili alle loro porzioni flessibili N-terminali. La sequenza amminoacidica di questa regione, nonostante la sua flessibilità, è sorprendentemente conservata anche in organismi fotosintetici filogeneticamente distanti, il che suggerisce un suo coinvolgimento in dinamiche strutturali fisiologicamente rilevanti per l’apparato fotosintetico. L'interazione specifica osservata nei supercomplessi appaiati sembra essere mediata dai cationi presenti all'interno del cloroplasto in concentrazioni fisiologiche. La loro rimozione dai tamponi utilizzati per l'isolamento, infatti, ne provoca la dissociazione in singoli supercomplessi. Questa evidenza è inoltre sostenuta dalla stima della connettività funzionale misurata in-vivo tramite tecniche di induzione di fluorescenza. Nei supercomplessi appaiati infatti si è evidenziato un potenziale trasferimento di energia maggiore se confrontato con i supercomplessi singolarizzati mediante semplice diluizione dei cationi presenti. L’ appaiamento sul lato stromatico mediato da cationi è stato osservato anche in forme isolate di PSII-LHCII con forme di oligomerizzazione superiore ai supercomplessi, in cui due supercomplessi accoppiati interagiscono lateralmente tra loro nel piano di membrana, formando così megacomplessi appaiati. Questa nuova struttura è stata ottenuta con TEM e ricostruzione bidimensionale a partire da particelle colorate negativamente. Nonostante la bassa risoluzione ottenuta, questa struttura rivela come i supercomplessi PSII-LHCII possono interagire reciprocamente in modi diversi, sia lateralmente che attraverso l’intervallo stromatico. L'osservazione della potenziale sovrapposizione degli LHCII trimerici in megacomplessi accoppiati, così come la presenza di diverse geometrie di interazione tra supercomplessi all'interno del piano di membrana e tra megacomplessi nelle membrane adiacenti, forniscono informazioni interessanti su come PSII e LHCII potrebbero interagire in modo stabile e specifico all'interno della membrana tilacoidale e tra i vari dischi dei grana. Al fine di studiare il rimodellamento dei supercomplessi PSII-LHCII nel contesto di un continuo cambiamento delle condizioni ambientali di luce, sono stati isolati supercomplessi PSII-LHCII da piante di pisello cresciute a diverse intensità di luce: bassa (LL), moderata (CL) e alta (HL). La valutazione in-vivo delle dimensioni dell'antenna funzionale del PSII (ASII) è stata accoppiata con l’identificazione e la quantificazione, mediante analisi proteomiche, delle diverse subunità di LHCII presenti sia nei supercomplessi isolati che nei tilacoidi nativi. All’aumentare dell’intensità di luce di crescita, si evince il rimodellamento strutturale dell’antenna modulare del PSII dovuto alla riduzione della quantità di LHCII trimerici di tipo “M” nei complessi isolati, attestata da una ridotta presenza di Lhcb3 e Lhcb6. Questo rimodellamento specifico non avviene però con le stesse modalità in tutta la membrana tilacoidale. Infatti, la quantità totale di LHCII nei tilacoidi viene significativamente ridotta solo in piante cresciute in HL, suggerendo la presenza di diverse strategie di acclimatazione in grado di ridurre l’antenna funzionale nei tilacoidi. La notevole diminuzione dell’ASII osservata sia nei supercomplessi isolati che nelle membrane tilacoidi di piante cresciute in HL, rispetto alle piante LL, può essere attribuita al significativo incremento di Lhcb4.3, una isoforma di Lhcb4. A differenza delle isoforme Lhcb4.1-2, l'isoforma Lhcb4.3, la cui trascrizione è nota aumentare in seguito all'esposizione ad HL, presenta l’estremità C-terminale troncata. Questa porzione della proteina nella struttura del supercomplesso C2S2M si trova a livello dell’interfaccia di legame con Lhcb6, la subunità monomerica che funge da connettore specifico per l’LHCII trimerico di tipo “M”. L'incorporazione di Lhcb4.3 nel supercomplesso PSII-LHCII sembrerebbe svolgere quindi un ruolo importante nel ridurre le dimensioni dell'antenna funzionale, riducendo l’affinità di legame di antenne aggiuntive (tipo “M”) per ridurre l’efficienza di raccolta della luce già ad intensità moderate. L'esposizione ad HL invece, oltre ad indurre la diminuzione dell'antenna del PSII in supercomplessi isolati, determina anche la riduzione parziale di tutte le antenne del PSII presenti nelle membrane tilacoidi, impedendo quindi danni al centro di reazione quando la luce incidente supera costantemente la sua capacità di utilizzarla efficientemente. Questi risultati contribuiscono ad aumentare le conoscenze su come il sistema di antenne associate al PSII è attivamente regolata a lungo termine modulando l’espressione genica in piante acclimatate a diverse intensità di luce. La flessibilità del sistema modulare di antenne del PSII e la sua interazione strutturale con il centro catalitico, oltre ad essere fondamentale per l’architettura tridimensionale delle membrane tilacoidi delle piante, ha certamente giocato un ruolo chiave nel determinare la loro notevole diversificazione nel corso dell’evoluzione. Nel complesso questi risultati potrebbero fornire nuovi spunti per ampliare la conoscenza di come le associazioni di PSII e LHCII e la loro reciproca interazione contribuiscono a mantenere la complessa architettura delle membrane tilacoidi e quindi l'efficienza complessiva della fotosintesi in condizioni ambientali in continuo mutamento.
Francy, Christopher Alfred. "Investigating the Functional Role of Drp1 in Mitochondrial Fission." Case Western Reserve University School of Graduate Studies / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=case1480952643685349.
Повний текст джерелаChen, Ichia. "Structural basis for the dual transport-channel functions of SLC1A transporters." Thesis, The University of Sydney, 2021. https://hdl.handle.net/2123/26804.
Повний текст джерелаSantosh, Vishaka. "Rep-DNA complexes and their role in AAV DNA transactions." VCU Scholars Compass, 2018. https://scholarscompass.vcu.edu/etd/5648.
Повний текст джерелаGuyomar, Charlotte. "Études structurales de la trans-traduction, cible privilégiée pour le développement de nouveaux antibiotiques." Thesis, Rennes 1, 2018. http://www.theses.fr/2018REN1B039.
Повний текст джерелаThis work is focused on a biological process which controls bacterial protein synthesis, trans-translation. This all-in-one process allows the rescuing of ribosomes stalled on defective mRNA, the degradation of the problematic peptides and mRNA. It is driven by two principal actors that interact with the ribosome: transfer-messenger RNA (tmRNA) and Small protein B (SmpB). In a first chapter, by a cryo-electron microscopic (cryo-EM) study, two near-atomic resolution structures, involving the ribosome and various trans-translation actors, were obtained. The first one highlights the interactions between RNase R, an enzyme responsible for mRNA degradation during trans-translation, and the bacterial ribosome. The second one corresponds to the characterization of two early trans-translation states at a near-atomic resolution. New interactions have been observed between SmpB and tmRNA H5 helix. In a second chapter, trans-translation is used as a target for the development of new antibiotic molecules. Indeed, this pathway is often necessary for bacterial survival and pathogenicity. Towards this aim, we designed and set up a new in vitro assay for high-throughput screening assays. This efficient system is based on fluorescence measurements of a GFP reassembled through trans-translation by a mutated tmRNA. This system has been validated and will be used for the discovery of new anti-trans-translation compounds
Braun, Tatjana [Verfasser], Gunnar [Gutachter] Schröder, and Georg [Gutachter] Groth. "Protein Structure Modelling using Evolutionary Information and Cryo-EM Data / Tatjana Braun ; Gutachter: Gunnar Schröder, Georg Groth." Düsseldorf : Universitäts- und Landesbibliothek der Heinrich-Heine-Universität Düsseldorf, 2017. http://d-nb.info/1139891170/34.
Повний текст джерелаSchenk, Carla [Verfasser], Gunnar [Gutachter] Schröder та Dieter [Gutachter] Willbold. "Structure Determination of Amyloid-β1-42 Fibrils by Cryo-EM / Carla Schenk ; Gutachter: Gunnar Schröder, Dieter Willbold". Düsseldorf : Universitäts- und Landesbibliothek der Heinrich-Heine-Universität Düsseldorf, 2019. http://d-nb.info/1195775385/34.
Повний текст джерелаAbdelshahid, Maha William Eissa [Verfasser], and Daniel [Akademischer Betreuer] Wilson. "Structural studies of stringent response mechanisms in bacteria using cryo-EM / Maha William Eissa Abdelshahid ; Betreuer: Daniel Wilson." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2019. http://d-nb.info/1215499728/34.
Повний текст джерелаJohnson, Matthew C. "Identifying key factors in two-dimensional crystal production and sample preparation for structure-function studies of membrane proteins by cryo-EM." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/52974.
Повний текст джерелаClinton, Ryan William. "Investigating Factors That Regulate the Direct Drp1-Mff Interaction." Case Western Reserve University School of Graduate Studies / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=case1529683123350889.
Повний текст джерелаJames, Nathan Rhys. "Structural insights into noncanonical mechanisms of translation." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/267783.
Повний текст джерелаSousa, Joana S. [Verfasser], Volker Gutachter] Dötsch, and Werner [Gutachter] [Kühlbrandt. "Structural characterization of membrane protein complexes by single-particle cryo-EM / Joana Sofia de Sousa ; Gutachter: Volker Dötsch, Werner Kühlbrandt." Frankfurt am Main : Universitätsbibliothek Johann Christian Senckenberg, 2019. http://d-nb.info/1202297900/34.
Повний текст джерелаPochopień-Pobel, Agnieszka [Verfasser], and Roland [Akademischer Betreuer] Beckmann. "Structural insights into yeast translation elongation and the integrated stress response using cryo-EM / Agnieszka Pochopień-Pobel ; Betreuer: Roland Beckmann." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2021. http://d-nb.info/1238017355/34.
Повний текст джерелаSousa, Joana Sofia de Verfasser], Volker [Gutachter] Dötsch, and Werner [Gutachter] [Kühlbrandt. "Structural characterization of membrane protein complexes by single-particle cryo-EM / Joana Sofia de Sousa ; Gutachter: Volker Dötsch, Werner Kühlbrandt." Frankfurt am Main : Universitätsbibliothek Johann Christian Senckenberg, 2019. http://d-nb.info/1202297900/34.
Повний текст джерелаRighetto, Ricardo Diogo 1986. "Validation of structural heterogeneity in Cryo-EM datasets by cluster ensembles = Validação de heterogeneidade estrutural em dados de Crio-ME por comitês de agrupadores." [s.n.], 2014. http://repositorio.unicamp.br/jspui/handle/REPOSIP/259094.
Повний текст джерелаDissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Elétrica e de Computação
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Resumo: Análise de Partículas Isoladas é uma técnica que permite o estudo da estrutura tridimensional de proteínas e outros complexos macromoleculares de interesse biológico. Seus dados primários consistem em imagens de microscopia eletrônica de transmissão de múltiplas cópias da molécula em orientações aleatórias. Tais imagens são bastante ruidosas devido à baixa dose de elétrons utilizada. Reconstruções 3D podem ser obtidas combinando-se muitas imagens de partículas em orientações similares e estimando seus ângulos relativos. Entretanto, estados conformacionais heterogêneos frequentemente coexistem na amostra, porque os complexos moleculares podem ser flexíveis e também interagir com outras partículas. Heterogeneidade representa um desafio na reconstrução de modelos 3D confiáveis e degrada a resolução dos mesmos. Entre os algoritmos mais populares usados para classificação estrutural estão o agrupamento por k-médias, agrupamento hierárquico, mapas autoorganizáveis e estimadores de máxima verossimilhança. Tais abordagens estão geralmente entrelaçadas à reconstrução dos modelos 3D. No entanto, trabalhos recentes indicam ser possível inferir informações a respeito da estrutura das moléculas diretamente do conjunto de projeções 2D. Dentre estas descobertas, está a relação entre a variabilidade estrutural e manifolds em um espaço de atributos multidimensional. Esta dissertação investiga se um comitê de algoritmos de não-supervisionados é capaz de separar tais "manifolds conformacionais". Métodos de "consenso" tendem a fornecer classificação mais precisa e podem alcançar performance satisfatória em uma ampla gama de conjuntos de dados, se comparados a algoritmos individuais. Nós investigamos o comportamento de seis algoritmos de agrupamento, tanto individualmente quanto combinados em comitês, para a tarefa de classificação de heterogeneidade conformacional. A abordagem proposta foi testada em conjuntos sintéticos e reais contendo misturas de imagens de projeção da proteína Mm-cpn nos estados "aberto" e "fechado". Demonstra-se que comitês de agrupadores podem fornecer informações úteis na validação de particionamentos estruturais independetemente de algoritmos de reconstrução 3D
Abstract: Single Particle Analysis is a technique that allows the study of the three-dimensional structure of proteins and other macromolecular assemblies of biological interest. Its primary data consists of transmission electron microscopy images from multiple copies of the molecule in random orientations. Such images are very noisy due to the low electron dose employed. Reconstruction of the macromolecule can be obtained by averaging many images of particles in similar orientations and estimating their relative angles. However, heterogeneous conformational states often co-exist in the sample, because the molecular complexes can be flexible and may also interact with other particles. Heterogeneity poses a challenge to the reconstruction of reliable 3D models and degrades their resolution. Among the most popular algorithms used for structural classification are k-means clustering, hierarchical clustering, self-organizing maps and maximum-likelihood estimators. Such approaches are usually interlaced with the reconstructions of the 3D models. Nevertheless, recent works indicate that it is possible to infer information about the structure of the molecules directly from the dataset of 2D projections. Among these findings is the relationship between structural variability and manifolds in a multidimensional feature space. This dissertation investigates whether an ensemble of unsupervised classification algorithms is able to separate these "conformational manifolds". Ensemble or "consensus" methods tend to provide more accurate classification and may achieve satisfactory performance across a wide range of datasets, when compared with individual algorithms. We investigate the behavior of six clustering algorithms both individually and combined in ensembles for the task of structural heterogeneity classification. The approach was tested on synthetic and real datasets containing a mixture of images from the Mm-cpn chaperonin in the "open" and "closed" states. It is shown that cluster ensembles can provide useful information in validating the structural partitionings independently of 3D reconstruction methods
Mestrado
Engenharia de Computação
Mestre em Engenharia Elétrica
Bertram, Karl [Verfasser], Holger [Akademischer Betreuer] Stark, Reinhard [Gutachter] Lührmann, Henning [Gutachter] Urlaub, and Juliane [Gutachter] Liepe. "High-resolution structure determination of human spliceosome complexes by cryo-EM / Karl Bertram ; Gutachter: Reinhard Lührmann, Henning Urlaub, Juliane Liepe ; Betreuer: Holger Stark." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2019. http://d-nb.info/1178115836/34.
Повний текст джерелаMacé, Kévin. "Le contrôle qualité de la synthèse protéique comme cible pour le développement de nouveaux antibiotiques." Thesis, Rennes 1, 2016. http://www.theses.fr/2016REN1B034/document.
Повний текст джерелаThe current PhD work brings together various studies linked to bacterial protein synthesis. The first chapter is about the origins of protein synthesis at the time of the RNA world. This theoretical work continues with the presentation of a high-resolution structure of the elongation factor G (EF-G) in complex with the ribosome by cryo-electron transmission microscopy (cryo-TEM). We describe for the first time EF-G bound to the ribosome in the absence of any inhibitor. This particular structure of EF-G displays a yet unseen positioning of its third domain, which becomes very flexible. This study helps to understand the way the antibiotic fusidic acid blocks translation. The work then switches to a study of trans-translation, the main rescuing system of stalled ribosomes in bacteria. Trans-translation is generally vital or at least necessary for bacterial virulence. We conducted a preliminary structural study on the way faulty mRNAs are degraded during this process. This is why we present a study of trans-translation as a target for the development of new antibiotics. For this we developed and validated a reporter system for trans-translation, which is used to screen molecules targeting trans-translation
Leonard, Daniel J. "ORCHESTRATING PP2A HOLOENZYME ASSEMBLY: FROM NORMAL TO ABNORMAL AND THE THERAPEUTIC OPPORTUNITY IN BETWEEN." Case Western Reserve University School of Graduate Studies / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=case1619527891708312.
Повний текст джерелаChen, Wenbo [Verfasser], Misha [Gutachter] Kudryashev, and Klaas Martinus [Gutachter] Pos. "Structure and function of integral and peripheral membrane proteins by cryo-EM: RyR1 and SidE family proteins / Wenbo Chen ; Gutachter: Misha Kudryashev, Klaas Martinus Pos." Frankfurt am Main : Universitätsbibliothek Johann Christian Senckenberg, 2020. http://d-nb.info/1221184938/34.
Повний текст джерелаWeyers, Birte [Verfasser], Stefan [Akademischer Betreuer] Raunser, and Daniel [Gutachter] Summerer. "Structural investigations on cholesterol binding membrane proteins SREBP cleavage-activating protein (Scap) and Patched1 by cryo-EM / Birte Weyers ; Gutachter: Daniel Summerer ; Betreuer: Stefan Raunser." Dortmund : Universitätsbibliothek Dortmund, 2021. http://d-nb.info/1230628665/34.
Повний текст джерелаLambrecht, Felix [Verfasser], Holger [Akademischer Betreuer] Stark, Helmut [Gutachter] Grubmüller, Michael [Gutachter] Habeck, Kai [Gutachter] Tittmann, and Sarah [Gutachter] Adio. "Computational methods for the structure determination of highly dynamic molecular machines by cryo-EM / Felix Lambrecht ; Gutachter: Helmut Grubmüller, Michael Habeck, Kai Tittmann, Sarah Adio ; Betreuer: Holger Stark." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2019. http://d-nb.info/1178792099/34.
Повний текст джерелаSingh, Kashish [Verfasser], Holger [Akademischer Betreuer] Stark, Holger [Gutachter] Stark, Kai [Gutachter] Tittmann, Ralf [Gutachter] Ficner, Markus [Gutachter] Zweckstetter, Alexander [Gutachter] Stein, and Alex [Gutachter] Faesen. "New sample preparation techniques of macromolecular complexes for high resolution structure determination using cryo-EM / Kashish Singh ; Gutachter: Holger Stark, Kai Tittmann, Ralf Ficner, Markus Zweckstetter, Alexander Stein, Alex Faesen ; Betreuer: Holger Stark." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2020. http://d-nb.info/1208221809/34.
Повний текст джерелаAyranci, Diyar. "Design, expression and purification of virus-like particles derived from metagenomic studies : Virus-like Particles (VLP) of novel Partitiviridae species, Hubei.PLV 11, and novel Soutern pygmy squid flavilike virus were designed, expressed using the bac-to-bac expression system and then pruified using various methods." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-452049.
Повний текст джерелаRavikumar, Ashraya. "Stereochemical studies on peptide and protein structures: Implications for validation, flexibility, and dynamics." Thesis, 2020. https://etd.iisc.ac.in/handle/2005/5049.
Повний текст джерелаRakesh, Ramachandran. "Structural and Mechanistic Features of Protein Assemblies with Special Reference to Spliceosome." Thesis, 2016. http://etd.iisc.ac.in/handle/2005/2871.
Повний текст джерелаRakesh, Ramachandran. "Structural and Mechanistic Features of Protein Assemblies with Special Reference to Spliceosome." Thesis, 2016. http://hdl.handle.net/2005/2871.
Повний текст джерелаSheng-ZheFu and 傅晟哲. "The cryo-EM structure of Zika virus-like particle." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/8msrj5.
Повний текст джерелаTuhman-Mushkin, Jana. "Structural Studies of Saccharomyces cerevisiae V1-ATPase in the Stationary Phase of Yeast Cell Culture." Thesis, 2012. http://hdl.handle.net/1807/32635.
Повний текст джерела(6589034), Matthew D. Therkelsen. "Structural Asymmetry of Flaviviruses." Thesis, 2019.
Знайти повний текст джерелаFlaviviruses are enveloped, positive-strand RNA viruses that
are spread by mosquitoes and ticks and can cause serious disease in humans.
Flavivirus virions undergo extensive structural changes during their life
cycle, including during maturation and fusion. Flaviviruses are initially
assembled at the endoplasmic reticulum in a non-infectious, immature state, and
then traffic to the trans-Golgi network, where a pH drop triggers a structural
rearrangement of glycoproteins prM and E on the virus surface from 60 trimers
to 90 dimers. A host protease, furin, then cleaves prM which makes the
transition irreversible. Upon exiting the host cell, pr disassociates from the
virus and the infectious, mature virus is able to enter a new cell.
In Chapter 1, an overview of flaviviruses is presented, including a brief history of their discovery and interaction with humans, followed by what is known about their life cycle and the maturation process. The structure of a mature flavivirus is then described, including the symmetrical arrangement of glycoproteins on the virion surface, the lipid membrane, and the nucleocapsid core, followed by an introduction of the structural proteins that assemble into the virion. The structure of the immature flavivirus is then described. The chapter concludes with a description of the dynamics and heterogeneity observed for flaviviruses.
The conformational rearrangements that occur during flavivirus maturation remain unclear. The structures of immature and mature flaviviruses determined with cryo-electron microscopy (cryo-EM) demonstrated that flaviviruses are icosahedral particles with 180 copies of glycoproteins on their surface. Icosahedral viruses typically have a quasi-equivalent arrangement of glycoproteins, but flaviviruses lack quasi-equivalence and instead the three subunits within an asymmetric unit occupy different chemical environments. Although the subunits are the same proteins, the unique environment of each subunit can be exploited for tracking subunits during conformational rearrangements. For example, the unique labeling of a subunit can be used to identify it in the immature and mature virion.
In Chapter 2, the maturation process was studied by
developing tools to differentially label protein subunits and trap potential
intermediates of maturation. The tools included heavy-atom compounds and
antibody Fabs, which were used to probe Kunjin virus (KUNV), an Australian
subtype of West Nile virus (WNV). One heavy-atom compound, potassium
tetranitroplatinate(II), was found to derivatize immature KUNV, likely at sites
on both E and prM. Higher-resolution studies will be required to determine if
the compound differentially labeled the three subunits. The other tool
developed was the E16 Fab. E16 Fab, originally isolated from a mouse immunized
with WNV E and found to bind to two out of three subunits on mature WNV, was
used to differentially label subunits in immature KUNV. Based on poor epitope
accessibility on immature KUNV, E16 Fab was hypothesized to trap an
intermediate state of maturation. In the cryo-EM reconstruction of E16 Fab
bound to immature KUNV it was found that the virion had localized distorted density
and apparent non-uniform binding of the E16 Fab. Based on this result it was
proposed that flaviviruses had imperfect icosahedral symmetry.
The structural asymmetry of immature and mature flaviviruses was investigated in Chapter 3. Icosahedral symmetry has always been imposed during cryo-EM reconstructions of flaviviruses, as it led to stable convergence of orientations. When reconstructions of immature KUNV and ZIKV were performed without imposing symmetry, the reconstructions showed that the flaviviruses had an eccentric nucleocapsid core, which was positioned closer to the membrane at one pole. At the opposite pole, the glycoprotein and inner leaflet densities were weak and distorted. Furthermore, there were protrusions from the core that contacted the transmembrane helices of the glycoproteins. In the asymmetric reconstruction of mature KUNV, the core was positioned concentric with the glycoprotein shell, in contrast to the immature virion, indicating that maturation alters the interactions between the core and the glycoproteins. The asymmetric reconstructions suggested that there is variable contact between the core and glycoproteins during assembly, which may be due to membrane curvature restrictions in the budding process.
In Chapter 4, extracellular vesicles (EVs) that were released during dengue virus (DENV) infection were characterized by mass spectrometry. EVs may play a significant role in flavivirus infection, as they have been shown to transport both viral proteins and infectious RNA. EVs likely represent alternative modes of virus transmission and aid in immune evasion. However, previous studies on EVs are controversial because EVs are potential contaminated during assays by co-purifying virions and other particulates. The identification of EV biomarkers would greatly reduce contamination because biomarkers would enable isolation of pure EVs by affinity purification. Therefore, a strategy was developed to isolate EVs and profile them with proteomics. The four proteins cystatin-A, filamin B, fibrinogen beta chain, and endothelin converting enzyme 1 were found to be statistically enriched in the DENV sample and represent potential EV biomarkers.
Bertram, Karl. "High-resolution structure determination of human spliceosome complexes by cryo-EM." Thesis, 2018. http://hdl.handle.net/11858/00-1735-0000-002E-E592-2.
Повний текст джерелаOuch, Christna. "Cryo-EM structure of IcmS-IcmW-DotL(655-783) from the type IVB secretion system of legionella pneumophila." Thesis, 2018. https://hdl.handle.net/2144/29959.
Повний текст джерелаFREDA, IDA. "Cryo-EM structure of PdxR from Bacillus clausii in complex with its target DNA." Doctoral thesis, 2021. http://hdl.handle.net/11573/1607611.
Повний текст джерела