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Dissertations / Theses on the topic 'Cryo-EM structures'

Author: Grafiati

Published: 6 September 2023

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1

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.

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2

Preis, 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.

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3

Zhou, 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.

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In eukaryotic translation initiation, eIF2B, a 295 kDa multisubunit (from α to ε) complex,is the guanine nucleotide exchange factor (GEF) of eIF2, a GTP binding protein, and hasmultiple roles in regulating the level of active eIF2-GTP-Met-tRNAi ternary complexes inthe cytoplasm. Mutations in eIF2B subunits affect global protein synthesis and, in human,are responsible to cause a genetically inherited lethal childhood brain disease calledLeukoencephalopathy with Vanishing White Matter (VWM). Although the genetic aspectseIF2B have been widely studied over decades, detailed structural knowledge on

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4

Abdelkareem, Moamen. "Structural basis of transcription : RNA polymerase backtracking and its reactivation." Thesis, Strasbourg, 2019. http://www.theses.fr/2019STRAJ062.

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Ma thèse se focalise sur la compréhension d’un phénomène de transcription, appelé backtracking, qui inactive la RNAP et arrête la transcription. La réactivation des complexes RNAP arrêtés et la reprise de la transcription nécessitent un facteur protéique appelé GreB. L’objectif du projet était d’obtenir des informations structurelles sur: i) la façon dont le retour en arrière inactive la RNAP dans E. coli; et ii) comment GreB sauve la RNAP en marche arrière pour continuer la transcription. À l'aide de SP cryo-EM, j’ai capturé quatre instantanés de RNAP dans différents états. Mes résultats mont

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Brito, Querido Jailson Fernando. "Structural study of mRNA translation in kinetoplastids by Cryo-electron microscopy." Thesis, Strasbourg, 2017. http://www.theses.fr/2017STRAJ108.

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Les kinétoplastides sont un groupe de protozoaires, et qui menace plus de 400 millions de personnes dans le monde entier. Ils possèdent des segments d'expansion d'ARNr (SE) inhabituellement plus larges dans les sous-unités 40S. Ici, nous avons purifié à partir de lysats de cellules de T. cruzi des complexes d'initiation natifs (48S IC) et des sous-unités de 40S natives que nous avons ensuite analysées par cryo-ME. La structure des 48S IC révèle certains des aspects spécifiques de la traduction aux kinétoplastides, tels qu'un réseau d’interaction complexe entre eIF3 et SEs. En outre,

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6

Spikes, Tobias Edward. "Structural studies of the mitochondrial F-ATPase." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/274349.

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The mitochondrial F-ATPases make about 90% of cellular ATP. They are multi-protein assemblies with a membrane extrinsic catalytic domain attached to a membrane embedded sector. They operate by a mechanical rotary mechanism powered by an electro-chemical gradient, generated across the inner mitochondrial membrane by respiration. A detailed molecular description has been provided by X-ray crystallographic studies and "single molecule" observations of the mechanism of the F1 catalytic domain. Details are known also of the architecture of the peripheral stalk of part of the stator and the membrane

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He, Shaoda. "Helical reconstruction in RELION." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/284086.

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Helical assemblies of proteins are ubiquitous in nature and they perform vital functions in a wide range of organisms. The recent development of direct electron detectors and other imaging techniques in cryo-electron microscopy (cryo-EM) has opened new possibilities in solving helical structures at atomic resolution. Existing software packages for helical processing often require experience in tuning many ad hoc parameters to achieve optimal reconstruction results. REgularised LIkelihood OptimisatioN (RELION), an open-source single-particle analysis package, reduces the need for user expertise

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8

Nojima, 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.

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9

Torchy, Morgan. "Etude structure-fonction du complexe de remodelage de la chromatine NuRD." Thesis, Strasbourg, 2014. http://www.theses.fr/2014STRAJ113/document.

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Une approche de biologie structurale intégrative a été mise à profit pour l'étude de l’organisation structurale du complexe NuRD. Mon travail s'est focalisé essentiellement sur trois sous-unités du complexe: MBD3, RbAp46 et RbAp48. J'ai mis en place les protocoles de production et de purification de ces différentes sous-unités, et les ai caractérisé biophysiquement par diverses méthodes. Nous avons ensuite entrepris des études de liaisons sur des nucléosomes reconstitués au laboratoire. Pour MBD3, l'optimisation du complexe nous a permis d'obtenir des cristaux diffractant jusqu'à 7 A de résolu

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10

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.

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La pause transcriptionnelle marquée par les ARN polymérases (RNAP) est un mécanisme clé pour réguler l'expression des gènes dans tous les règnes de la vie et est une condition préalable à la terminaison de la transcription. Le facteur de transcription bactérien essentiel NusA stimule à la fois la pause et la terminaison de la transcription, jouant ainsi un rôle central. Ici, je présente des reconstructions par cryo-microscopie électronique (cryo-EM) à une seule particule de NusA lié à des complexes d'élongation en présence et en absence d’ARN en épingle à cheveux dans le canal de sortie de l'A

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11

Busselez, Johan. "Structure et oligomérisation de complexes membranaires photosynthétique bactériens : une analyse par cryo-microscopie électronique." Paris 6, 2007. http://www.theses.fr/2007PA066094.

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Le travail de cette thèse a été consacré à l'analyse structurale par microscopie électronique du « core complexe » de l'appareil photosynthétique bactérien. Ce multicomplexe membranaire est le dernier composant de l'appareil photosynthétique bactérien dont on ne dispose pas de structure atomique. L'enjeu de la détermination de la structure de ce complexe est la compréhension de la transformation de l'énergie lumineuse en séparation de charges et du couplage entre le centre réactionnel et le cytochrome bc1. Pour répondre à ces questions, la démarche a consisté en une analyse structurale compara

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Thonghin, 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.

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P-glycoprotein (P-gp or ABCB1) is a membrane-bound active transporter belonging to the ABC protein superfamily. It is responsible for xenobioIc efflux and also contributes to multidrug resistance in diverse diseases including cancer and epilepsy. P-gp has been increasingly recognised as a potential target for future therapeutics. Although the protein has been studied for decades, understanding of the P-gp transport mechanism is still incomplete. Two P-gp orthologues, mouse (m) and human (h), were therefore expressed in yeasts and purified in the presence of the detergent, n-Dodecyl-Î²-D- Malt

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13

Polovinkin, Lucie. "Etudes structurales du récepteur 5-HT3." Thesis, Université Grenoble Alpes (ComUE), 2019. http://www.theses.fr/2019GREAV028.

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Les récepteurs Cys-loop sont des canaux ioniques pentamériques activés par un ligand (pLGIC), qui jouent un rôle essentiel dans la neurotransmission rapide. Ils sont la cible de nombreuses familles de médicaments (antiémétiques, anesthésiques généraux, benzodiazépines, médicaments pour arrêter de fumer, etc.) et leurs propriétés physiologiques sont, en conséquent, très étudiées. Lorsque les pLGIC lient des neurotransmetteurs, ils subissent des modifications conformationnelles, d’un état au repos où le pore est fermé vers un état transitoire ouvert. La liaison de ligand peut également provoquer

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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.

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Ryanodine receptors (RyR) are intracellular channels that are intricately involved in Ca2+ release. These channels large membrane proteins~2.26MDa in size. In this multi-goal project firstly we successfully studied the gating mechanics of the RyR1 in the presence of Mg2+. We used single particle reconstruction and image processing techniques to obtain the 3D structure of the RyR1 with Mg2+. The 3D structure in the presence of Mg2+ and an ATP analog is the closest representation of human physiological conditions. The open and closed state structures of RyR1 are known. However, the physiological

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15

Ramsay, 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.

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X-Linked Retinoschisis (XLRS) is a currently incurable, progressive retinal degeneration that affects approximately 1:20,000 males. Sufferers have a loss of retinal structure and visual acuity, leading to blindness. The condition is caused by mutation of the RS1 gene encoding the retinal-specific protein retinoschisin. Retinoschisin is critical in maintaining the normal, ordered retinal architecture, with deletion in mice models leading to loss of both structure and visual processing, analogous to XLRS sufferers. However, re-introduction of retinoschisin using adeno-associated viral vectors le

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16

Gomez, de Segura Jesus. "Caractérisation structurale et fonctionnelle des NuRD Complexes." Thesis, Université Grenoble Alpes (ComUE), 2019. https://thares.univ-grenoble-alpes.fr/2019GREAV063.pdf.

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Le complexe de remodelage des nucléosomes et de désacétylation des histones (NuRD) est l'un des principaux régulateurs épigénétiques du génome. Il contribue à la formation et au maintien de l'hétérochromatine, une structure très dense d'ADN et de protéines réprimant la transcription. La NuRD joue un rôle central dans les processus biologiques pertinents tels que la régulation de la pluripotence ou la tumorigenèse. Malgré cela, sa structure et son mécanisme d'action restent largement inconnus. Cela est dû en grande partie à l'hétérogénéité inhérente de composition et de conformation de NuRD. Da

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17

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.

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18

Khusainov, Iskander. "Structural studies of the Staphylococcus aureus ribosome." Thesis, Strasbourg, 2015. http://www.theses.fr/2015STRAJ071/document.

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Le ribosome est une machinerie cellulaire importante impliquée dans la synthèse protéique de toute cellule vivante. Par conséquent, le ribosome est l'une des principales cibles des antibiotiques naturels, qui sont capables de tuer les cellules bactériennes en bloquant la synthèse protéique. Toutefois, certaines bactéries sont résistantes à ces antibiotiques en raison de petites modifications au niveau de leurs ribosomes. Entre autres, Staphylococcus aureus (S. aureus) est un agent pathogène responsable de nombreuses infections graves chez l’Homme. Les structures cristallines d'antibiotiques en

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19

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.

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Photosynthesis is indisputably the primary biological process to introduce chemical energy and biomass into ecosystems by oxidizing water and reducing carbon dioxide into organic compounds. Photosystem II (PSII) is a unique protein complex, present in thylakoid membranes of all oxygenic photosynthetic organisms, able to catalyze the water-splitting reaction using sunlight as driving force, thus being responsible for the generation of all the molecular oxygen accumulated in the atmosphere for over three billion years. Although its catalytic core has been extremely conserved throughout evolution

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20

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.

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21

Chen, Ichia. "Structural basis for the dual transport-channel functions of SLC1A transporters." Thesis, The University of Sydney, 2021. https://hdl.handle.net/2123/26804.

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The excitatory amino acid transporters (EAATs) play a vital role in the maintenance of glutamatergic neurotransmission within the synapse, involved in fundamental brain functions such as learning and memory. These secondary active transporters enable rapid glutamate reuptake into the surrounding glial cells and neurons by coupling to pre-existing electrochemical gradients of sodium ions, potassium ions and protons. In addition to this conventional transporter function, the EAATs also possess a unique ability to conduct chloride ions in a channel-like process that is thermodynamically uncoupled

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22

Santosh, Vishaka. "Rep-DNA complexes and their role in AAV DNA transactions." VCU Scholars Compass, 2018. https://scholarscompass.vcu.edu/etd/5648.

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Adeno-associated Virus (AAV) Rep proteins are multifunctional proteins that carry out various DNA transactions required for the life cycle of AAV. The Rep proteins have been found to be important for genome replication, gene regulation, site-specific integration and play an essential role in genome packaging. There are two main groups of Rep proteins: large and small Reps; both groups are SF3 helicase family members. During DNA packaging, studies have shown that the small Rep proteins are critical to produce fully packed particles. Using stopped-flow kinetic analysis, we show a significant dif

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23

Guyomar, Charlotte. "Études structurales de la trans-traduction, cible privilégiée pour le développement de nouveaux antibiotiques." Thesis, Rennes 1, 2018. http://www.theses.fr/2018REN1B039.

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Le travail retranscrit dans cette thèse porte sur un processus biologique impliqué dans le contrôle qualité de la synthèse protéique bactérienne : la trans-traduction. Ce processus permet de libérer les ribosomes bloqués sur des ARNm défectueux tout en détruisant les peptides et ARNm problématiques impliqués dans le blocage. Il nécessite deux acteurs principaux qui interagissent avec le ribosome: l’ARN transfert-messager (ARNtm) et la protéine SmpB. Dans un premier chapitre, une étude en cryo-microscopie électronique à transmission (cryo-MET) a permis d’obtenir deux structures à l’échelle atom

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24

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.

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25

Schenk, 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.

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Abdelshahid, 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.

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27

Johnson, 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.

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Electron crystallography of two-dimensional crystals is a structure-determination method well suited to the study of membrane protein structure-function. Two-dimensional crystals consist of ordered arrays of protein within reconstituted lipid bilayers, an arrangement that mimics the natural membrane environment. In this work we describe our recent progress in the use of this method with three different proteins, each providing a window into a separate paradigm in the electron crystallographic pipeline. Specific crystallization conditions for human leukotriene C₄ synthase (LTC₄S) have previousl

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Clinton, 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.

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29

James, Nathan Rhys. "Structural insights into noncanonical mechanisms of translation." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/267783.

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Translation is the process by which proteins are synthesized from the instructions in the genetic code. Translation is mediated by the ribosome, a large ribonucleoprotein complex, in concert with messenger RNA (mRNA), transfer RNA (tRNA), and a variety of proteins. The canonical mechanism of translation, introduced in Part I of my thesis, is divided into four distinct phases: initiation, elongation, termination, and recycling. Under unusual circumstances, each phase of translation can also proceed via a number of noncanonical mechanisms, many of which are vitally important for cellular growth

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30

Sousa, 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.

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Pochopień-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.

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Sousa, 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.

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Righetto, 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.

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Orientadores: Fernando José Von Zuben, Rodrigo Villares Portugal<br>Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Elétrica e de Computação<br>Made available in DSpace on 2018-08-25T22:36:38Z (GMT). No. of bitstreams: 1 Righetto_RicardoDiogo_M.pdf: 5898819 bytes, checksum: c98b9e2b61390aa847a4a6040d3f550b (MD5) Previous issue date: 2014<br>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

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34

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.

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Macé, 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.

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Le travail retranscrit dans cette thèse regroupe l'étude de différents processus biologiques impliqués dans la synthèse protéique bactérienne. Dans un premier chapitre, les origines de la synthèse protéique au temps du monde ARN sont traitées en guise d'introduction. Ce travail théorique se poursuit par la présentation d'une structure à haute résolution du facteur d'élongation G (EF-G) en complexe avec le ribosome par cryo-microscopie électronique à transmission (cryo-MET). Grâce aux avancées techniques de la cryo-MET, nous avons observé pour la première fois EF-G lié au ribosome en l'absence

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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.

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Chen, 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.

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Weyers, 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.

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Lambrecht, 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.

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Singh, Kashish [Verfasser], Holger [Akademischer Betreuer] Stark, Holger [Gutachter] Stark, et al. "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.

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Ayranci, 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.

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Viruses are entities which are made of a few genes and are reliant on obligate parasitism to propagate. Due to the obligate connection to their hosts, virus evolution is constrained to the type of host. Viruses however do transmit to evolutionary distinct hosts; in these cases, the phylogenetic relationship of the hosts usually are close. In some instances, RNA-viruses have made host jumps between evolutionary distant hosts, such as the host jump from invertebrates to vertebrates, and fungi to arthropod. Partitiviruses are double stranded RNA viruses which mainly infect fungi and plants. The d

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Ravikumar, Ashraya. "Stereochemical studies on peptide and protein structures: Implications for validation, flexibility, and dynamics." Thesis, 2020. https://etd.iisc.ac.in/handle/2005/5049.

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Accuracy of 3-D structures of proteins is crucial, both in terms of its agreement with the experimental data used to determine the structure and stereochemistry, especially when they are utilized for applications like drug design. Hence, stereochemical validation of 3-D structures is of fundamental importance. In this thesis, we have performed stereochemical studies on various systems, starting from peptide structures to high-resolution protein structures and large multi-protein assemblies. In peptide structures, we noted that subtle deviations in backbone bond lengths and angles from ideal bo

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Rakesh, Ramachandran. "Structural and Mechanistic Features of Protein Assemblies with Special Reference to Spliceosome." Thesis, 2016. http://etd.iisc.ac.in/handle/2005/2871.

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Macromolecular assemblies such as the ribosome, spliceosome, polymerases are imperative for cellular functions. The current understanding of these important machineries and many other assemblies at the molecular level is poor. The lack of structural data for many macromolecular assemblies further causes a bottleneck in understanding the cellular processes and the various disease manifestations. Hence, it is essential to characterize the structures and molecular architectures of these macromolecular assemblies. Though the number of 3-D structures for individual proteins structures or domains in

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Rakesh, Ramachandran. "Structural and Mechanistic Features of Protein Assemblies with Special Reference to Spliceosome." Thesis, 2016. http://hdl.handle.net/2005/2871.

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Abstract:

Macromolecular assemblies such as the ribosome, spliceosome, polymerases are imperative for cellular functions. The current understanding of these important machineries and many other assemblies at the molecular level is poor. The lack of structural data for many macromolecular assemblies further causes a bottleneck in understanding the cellular processes and the various disease manifestations. Hence, it is essential to characterize the structures and molecular architectures of these macromolecular assemblies. Though the number of 3-D structures for individual proteins structures or domains in

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Sheng-ZheFu and 傅晟哲. "The cryo-EM structure of Zika virus-like particle." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/8msrj5.

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Tuhman-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.

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Vacuolar-type ATPases (V-ATPases) are ubiquitous membrane-bound protein complexes present in the endo-membrane system of all eukaryotic cells. In eukaryotic cells, the reversible dissociation of the V1 and Vo regions is an essential mechanism for regulating V-ATPase activity. Therefore, knowledge of the structure of the dissociated V1-ATPase is necessary for understanding the regulation of V-ATPase activity. In this thesis, I showed that by introducing a 3xFLAG tag at the C terminus of different V1-ATPase subunits, highly purified V1-ATPase complex could be isolated. Electron cryomicroscopy (

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(6589034), Matthew D. Therkelsen. "Structural Asymmetry of Flaviviruses." Thesis, 2019.

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<p>Flaviviruses 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 tran

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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.

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Ouch, 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.

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Legionella pneumophila (Lp) is a gram-negative, intracellular parasite. These bacteria evade the host response with the help of a Type IVb secretion system (T4bSS), composed of Defective in organelle trafficking (Dot) and Intracellular multiplication (Icm) proteins. This secretion system delivers over 300 effectors into the host, and a large number of these molecules are dependent on IcmS and IcmW. These effectors are essential for the bacterium’s survival in the host. This work and previous studies have shown that IcmS and IcmW interact to stabilize each other and the C-terminal "tail" of Dot

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FREDA, IDA. "Cryo-EM structure of PdxR from Bacillus clausii in complex with its target DNA." Doctoral thesis, 2021. http://hdl.handle.net/11573/1607611.

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PdxR is a bacterial transcription factor belonging to the MocR family, which is involved in the regulation of the de novo biosynthesis of pyridoxal 5’-phosphate (PLP). PdxR has been extensively studied at the functional level and its target regulon has been characterized. However, a structural characterization of this transcription factor, and of MocRs in general, is missing. In fact, to date no structure of MocRs in complex with DNA is available, and a mechanism of their regulatory activity has been hypothesised on the basis of functional and computational data. In this thesis I report th

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