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Dissertations / Theses on the topic 'Serial crystallographie'

Author: Grafiati

Published: 31 May 2025

Last updated: 31 July 2025

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1

Delaunay, Quentin. "Exploration des limites de la micro-diffraction et de la nanocristallographie in vivo par implémentation d'une approche de collecte de données en série." Electronic Thesis or Diss., Université Grenoble Alpes, 2025. http://www.theses.fr/2025GRALV001.

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Alors qu’il fallait jusqu’en 2011 utiliser des cristaux de taille submillimétrique (~50-100 µm) pour espérer résoudre une structure macromoléculaire à résolution atomique, des échantillons nanométriques peuvent désormais être utilisés. Ce changement de paradigme a été permis par l’avènement des méthodes de diffraction en série tel que la cristallographie sérielle à l’échelle de la femtoseconde (SFX) implémentée dans des XFEL, mais aussi grâce à l’exploitation de l’interaction des électrons avec la matière, permettant d’obtenir des données de diffraction utiles à partir de nanocristaux présenté

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2

Ginn, Helen. "Improved methods for serial femtosecond crystallography reduction." Thesis, University of Oxford, 2017. http://ora.ox.ac.uk/objects/uuid:a69f65b8-84d9-4c3a-84b9-155ded0e5dee.

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X-ray free electron lasers (XFELs) are a young technology which alleviates a number of issues, including radiation damage, which remain problematic in conventional macromolecular X-ray crystallography. As it turned out, existing methods had been optimised for synchrotron-based rotation data and coped poorly with snapshot XFEL diffraction images. In the first four results chapters, I present algorithms developed in my efforts to contribute to improved data reduction for XFEL analysis. In order of execution, these are: detector geometry refinement, indexing, initial orientation matrix refinement

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3

Shilova, Anastasiia. "Development of serial protein crystallography with synchrotron radiation." Thesis, Université Grenoble Alpes (ComUE), 2016. http://www.theses.fr/2016GREAY034/document.

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Le rayonnement synchrotron est l'un des facteurs clés du grand succès de la cristallographie macromoléculaire au cours des dernières décennies. Plus de 90% de toutes les structures de protéines de la base de données PDB a été résolu par cristallographie en utilisant des sources de rayonnement synchrotron et environ 95% d'entre elles a été déterminé à partir de cristaux congelés.Cependant, les structures déterminées par des techniques de congélation sont limitées par la nature statique des cristaux congelés. Avec le développement récent des sources de RX produites par lasers à électrons libres

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4

Nakane, Takanori. "Data processing pipeline for serial femtosecond crystallography at SACLA." Kyoto University, 2017. http://hdl.handle.net/2433/217997.

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5

Halsted, T. "Femtosecond serial crystallography of two classes of copper nitrite reductase." Thesis, University of Liverpool, 2018. http://livrepository.liverpool.ac.uk/3026895/.

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Copper-containing nitrite reductases (CuNiR) catalyse the reduction of nitrite to the gaseous product nitric oxide. The enzyme forms part of the denitrification pathway which, in some bacteria, forms part of their respiratory network where nitrogen reduction is coupled to the synthesis of adenosine triphosphate. Denitrifying bacteria, through the production of nitrous oxide, have a large greenhouse gas impact and are also opportunist pathogens often found infecting immunocompromised patients. The structure and biochemical properties of CuNiRs have been extensively studied revealing a common fu

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6

Gevorkov, Yaroslav [Verfasser]. "Indexing algorithms for current and upcoming challenges in serial crystallography / Yaroslav Gevorkov." Hamburg : Universitätsbibliothek der Technischen Universität Hamburg-Harburg, 2020. http://d-nb.info/121575633X/34.

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7

Tolstikova, Aleksandra [Verfasser], and Henry N. [Akademischer Betreuer] Chapman. "Development of diffraction analysis methods for serial crystallography / Aleksandra Tolstikova ; Betreuer: Henry N. Chapman." Hamburg : Staats- und Universitätsbibliothek Hamburg, 2020. http://d-nb.info/1211480054/34.

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8

Chen, Joe. "Image Reconstruction in Serial Femtosecond Nanocrystallography." Thesis, University of Canterbury. Electrical and Computer Engineering, 2015. http://hdl.handle.net/10092/10661.

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X-ray crystallography is a form of microscopy that allows the three-dimensional arrangement of atoms belonging to molecules within crystals to be determined. In this method, a crystal is illuminated with a beam of X-rays and the diffracted amplitudes resulting from the illumination are measured and computationally processed to enable the electron density of the unit molecule, or the unit cell, constituting the crystal to be calculated. The recent development of the X-ray free-electron laser (XFEL) provides new routes for determining molecular structures via its ability to generate intense but

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9

Gati, Cornelius [Verfasser], and Christian [Akademischer Betreuer] Betzel. "Data processing and analysis in serial crystallography at advanced X-ray sources / Cornelius Gati. Betreuer: Christian Betzel." Hamburg : Staats- und Universitätsbibliothek Hamburg, 2015. http://d-nb.info/1079002235/34.

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10

Gati, Cornelius Verfasser], and Christian [Akademischer Betreuer] [Betzel. "Data processing and analysis in serial crystallography at advanced X-ray sources / Cornelius Gati. Betreuer: Christian Betzel." Hamburg : Staats- und Universitätsbibliothek Hamburg, 2015. http://nbn-resolving.de/urn:nbn:de:gbv:18-76091.

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11

Nass, Kovacs Gabriela [Verfasser], and Ilme [Akademischer Betreuer] Schlichting. "Light-energy conversion in rhodopsins studied by time-resolved serial femtosecond crystallography / Gabriela Nass Kovacs ; Betreuer: Ilme Schlichting." Heidelberg : Universitätsbibliothek Heidelberg, 2019. http://d-nb.info/1196207631/34.

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12

Seine, Thomas [Verfasser], and Henry [Akademischer Betreuer] Chapman. "Novel Approaches to the Production & Analysis of Biological Nanomaterials for Serial-Femtosecond X-ray Crystallography / Thomas Seine ; Betreuer: Henry Chapman." Hamburg : Staats- und Universitätsbibliothek Hamburg, 2019. http://d-nb.info/1186892242/34.

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13

Seine, Thomas Verfasser], and Henry N. [Akademischer Betreuer] [Chapman. "Novel Approaches to the Production & Analysis of Biological Nanomaterials for Serial-Femtosecond X-ray Crystallography / Thomas Seine ; Betreuer: Henry Chapman." Hamburg : Staats- und Universitätsbibliothek Hamburg, 2019. http://nbn-resolving.de/urn:nbn:de:gbv:18-97364.

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14

Baitan, Daniela-Paraschiva [Verfasser], and Christian [Akademischer Betreuer] Betzel. "Analyzing Crystal Growth Phenomena and Mechanisms for the Production and Optimization of Protein Crystals for Serial Crystallography / Daniela-Paraschiva Baitan ; Betreuer: Christian Betzel." Hamburg : Staats- und Universitätsbibliothek Hamburg, 2018. http://d-nb.info/1170872999/34.

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15

Aumonier, Sylvain. "Cristallographie monochromatique résolue en temps au synchrotron d'un domaine de photorécepteur de plante Specific radiation damage is a lesser concern at room temperature Room temperature crystallography visualisation of LOV domain : photoadduct relaxation on the second to minute time scale Millisecond time-resolved serial oscillation crystallography at synchrotrons Tailing miniSOG: structural bases of the complex photophysics of a flavin-binding singlet oxygen photosensitizing protein." Thesis, Université Grenoble Alpes (ComUE), 2019. http://www.theses.fr/2019GREAV046.

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La cristallographie résolue dans le temps (TRX) permet l’identification à l’échelle quasi atomique des changements structuraux progressifs au sein d’une protéine lorsqu’elle réalise sa fonction, permettant la constitution de véritables films moléculaires. La diffraction Laue (polychromatique) dans les synchrotrons de 3ème génération a d’abord permis d’obtenir de tels films à une échelle de temps de 100 ps, et plus récemment les sources de rayons X de 4ème génération, les lasers à électrons libres (XFELs, pour X-Ray Free Electron Lasers), ont permis d’atteindre une résolution temporelle de 100

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16

Jönsson, Olof. "Ultrafast Structural and Electron Dynamics in Soft Matter Exposed to Intense X-ray Pulses." Doctoral thesis, Uppsala universitet, Molekyl- och kondenserade materiens fysik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-331936.

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Investigations of soft matter using ultrashort high intensity pulses have been made possible through the advent of X-ray free-electrons lasers. The last decade has seen the development of a new type of protein crystallography where femtosecond dynamics can be studied, and single particle imaging with atomic resolution is on the horizon. The pulses are so intense that any sample quickly turns into a plasma. This thesis studies the ultrafast transition from soft matter to warm dense matter, and the implications for structural determination of proteins. We use non-thermal plasm

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17

De, Wijn Raphaël. "Application des nouvelles approches de cristallisation et de cristallographie sérielle à l’étude structurale de complexes enzymes : ARNt." Thesis, Strasbourg, 2018. http://www.theses.fr/2018STRAJ095/document.

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Cette thèse porte sur deux aspects complémentaires, le développement et l’implémentation de nouvelles approches de cristallisation et de cristallographie sérielle ainsi que leur mise en œuvre dans l’étude structurale de complexes enzymes : ARNt. La cristallographie est la méthode la plus employée en biologie structurale, mais elle présente encore des points délicats. Plusieurs méthodes avancées ont été déployées dans ce travail pour y pallier qui ont conduit à la résolution de la structure de l’ARNt nucléotidyltransférase du psychrophile Planococcus halocryophilus et à l’étude de son adaptatio

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18

Kölsch, Adrian. "Kinetische, theoretische und strukturelle Charakterisierung des Cytochrom c-Photosystem I-Komplexes." Doctoral thesis, Humboldt-Universität zu Berlin, 2020. http://dx.doi.org/10.18452/21735.

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Photosystem I (PSI) aus dem thermophilen Cyanobakterium Thermosynechococcus elongatus ist ein transmembraner Protein-Pigment-Superkomplex der photosynthetischen Elektronentransportkette. Er wandelt die Energie des Lichts in elektrische Energie mit einer Quanteneffizienz von nahezu 100 % um. Dazu uberträgt PSI Elektronen von Plastocyanin bzw. Cytochrom c6 (Cyt c6) auf Ferredoxin. Die Struktur des PSI wurde bereits 2001 mit einer Auflösung von 2,5 Å beschrieben (Jordan et al. 2001). Es lässt sich zur Generierung von Photoströmen auf Elektrodenoberflächen assemblieren und zur Produktion von Biokr

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19

"Serial Crystallography: Beyond Monte Carlo Data Analysis." Doctoral diss., 2016. http://hdl.handle.net/2286/R.I.40701.

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abstract: The superior brightness and ultra short pulse duration of X-ray free electron laser (XFEL) allows it to outrun radiation damage in coherent diffractive imaging since elastic scattering terminates before photoelectron cascades commences. This “diffract-before-destroy” feature of XFEL opened up new opportunities for biological macromolecule imaging and structure studies by breaking the limit to spatial resolution imposed by the maximum dose that is allowed before radiation damage. However, data collection in serial femto-second crystallography (SFX) using XFEL is affected by a bunch o

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20

"Serial Femtosecond Crystallography Data Analysis of Photosystem II." Doctoral diss., 2019. http://hdl.handle.net/2286/R.I.55497.

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abstract: Serial femtosecond crystallography (SFX) uses diffraction patterns from crystals delivered in a serial fashion to an X-Ray Free Electron Laser (XFEL) for structure determination. Typically, each diffraction pattern is a snapshot from a different crystal. SFX limits the effect of radiation damage and enables the use of nano/micro crystals for structure determination. However, analysis of SFX data is challenging since each snapshot is processed individually. Many photosystem II (PSII) dataset have been collected at XFELs, several of which are time-resolved (containing both dark and la

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21

"Serial Femtosecond Crystallography of Proteins in Proteins and Cancer." Master's thesis, 2020. http://hdl.handle.net/2286/R.I.57193.

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abstract: This thesis focuses on serial crystallography studies with X-ray free electron lasers (XFEL) with a special emphasis on data analysis to investigate important processes in bioenergy conversion and medicinal applications. First, the work on photosynthesis focuses on time-resolved femtosecond crystallography studies of Photosystem II (PSII). The structural-dynamic studies of the water splitting reaction centering on PSII is a current hot topic of interest in the field, the goal of which is to capture snapshots of the structural changes during the Kok cycle. This thesis presents

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22

"Overcoming Barriers in Structural Biology Through Method Development of Serial Crystallography." Doctoral diss., 2016. http://hdl.handle.net/2286/R.I.41245.

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abstract: Serial crystallography (SX) is a relatively new structural biology technique that collects X-ray diffraction data from microcrystals via femtosecond pulses produced by an X-ray free electron laser (X-FEL) or by synchrotron radiation, allowing for challenging protein structures to be solved from microcrystals at room temperature. Because of the youth of this technique, method development is necessary for it to achieve its full potential. Most serial crystallography experiments have relied on delivering sample in the mother liquor focused into a stream by compr

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23

"Life In Motion: Visualizing Biomacromolecules By Time-Resolved Serial Femtosecond Crystallography." Doctoral diss., 2018. http://hdl.handle.net/2286/R.I.49407.

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abstract: Time-resolved serial femtosecond crystallography is an emerging method that allows for structural discovery to be performed on biomacromolecules during their dynamic trajectory through a reaction pathway after activation. This is performed by triggering a reaction on an ensemble of molecules in nano- or microcrystals and then using femtosecond X-ray laser pulses produced by an X-ray free electron laser to collect near-instantaneous data on the crystal. A full data set can be collected by merging a sufficient number of these patterns together and multiple data sets can be collected

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24

"Sample Injector Fabrication and Delivery Method Development for Serial Crystallography using Synchrotrons and X-ray Free Electron Lasers." Doctoral diss., 2015. http://hdl.handle.net/2286/R.I.36010.

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abstract: Sample delivery is an essential component in biological imaging using serial diffraction from X-ray Free Electron Lasers (XFEL) and synchrotrons. Recent developments have made possible the near-atomic resolution structure determination of several important proteins, including one G protein-coupled receptor (GPCR) drug target, whose structure could not easily have been determined otherwise (Appendix A). In this thesis I describe new sample delivery developments that are paramount to advancing this field beyond what has been accomplished to date. Soft Lithography was used to impleme

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25

"Injection Methods and Instrumentation for Serial X-ray Free Electron Laser Experiments." Doctoral diss., 2015. http://hdl.handle.net/2286/R.I.30049.

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abstract: Scientists have used X-rays to study biological molecules for nearly a century. Now with the X-ray free electron laser (XFEL), new methods have been developed to advance structural biology. These new methods include serial femtosecond crystallography, single particle imaging, solution scattering, and time resolved techniques. The XFEL is characterized by high intensity pulses, which are only about 50 femtoseconds in duration. The intensity allows for scattering from microscopic particles, while the short pulses offer a way to outrun radiation damage. XFELs are powerful enough to obl

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26

"Sample Delivery Enabled by 3D Printing for Reduced Sample Consumption and Mix-and-Inject Serial Crystallography at X-ray Free Electron Lasers." Doctoral diss., 2019. http://hdl.handle.net/2286/R.I.55665.

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abstract: Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) has enabled the determination of damage-free protein structures at ambient temperatures and of reaction intermediate species with time resolution on the order of hundreds of femtoseconds. However, currently available XFEL facility X-ray pulse structures waste the majority of continuously injected crystal sample, requiring a large quantity (up to grams) of crystal sample to solve a protein structure. Furthermore, mix-and-inject serial crystallography (MISC) at XFEL facilities requires fast mixing for shor

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27

"Structural Elucidation of Membrane Proteins Involved in Photosynthesis." Doctoral diss., 2018. http://hdl.handle.net/2286/R.I.50617.

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abstract: Over the last century, X-ray crystallography has been established as the most successful technique for unravelling the structure-function relationship in molecules. For integral membrane proteins, growing well-ordered large crystals is a challenge and hence, there is room for improving current methods of macromolecular crystallography and for exploring complimentary techniques. Since protein function is deeply associated with its structural dynamics, static position of atoms in a macromolecule are insufficient to unlock the mechanism. The availability of X-ray free electron lasers

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28

Klymanska, Kateryna. "Structural studies of a W-Formate dehydrogenase by X-ray crystallography – a bacterial enzyme that catalyze greenhouse gas (CO2) fixation." Master's thesis, 2022. http://hdl.handle.net/10362/134441.

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Mo/W-Formate dehydrogenases (Fdhs) are unique bacterial enzymes that catalyze the reversible reduction of CO2 to formate. This capability is not just a possible route for greenhouse gas sequestration, but also a possibility to create a compound that is currently used as a fuel. Only five different Fdhs have their structure solved and the two recent structures of FdhAB from Desulfovibrio vulgaris (oxidized and formate-reduced forms) showed conformational changes that may bring new insights about the catalytic mechanism. So, the main goals of this work are to attain new structures of reduced for

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29

"Electric Field Driven Migration and Separation in the Microenvironment." Doctoral diss., 2020. http://hdl.handle.net/2286/R.I.62691.

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abstract: Novel electric field-assisted microfluidic platforms were developed to exploit unique migration phenomena, particle manipulation, and enhanced droplet control. The platforms can facilitate various analytical challenges such as size-based separations, and delivery of protein crystals for structural discovery with both high selectivity and sensitivity. The vast complexity of biological analytes requires efficient transport and fractionation approaches to understand variations of biomolecular processes and signatures. Size heterogeneity is one characteristic that is especially important

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