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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
1

Sample preparation of membrane proteins suitable for solid-state MAS NMR and development of assignment strategies

Hiller, Matthias January 2009 (has links)
Although the basic structure of biological membranes is provided by the lipid bilayer, most of the specific functions are carried out by membrane proteins (MPs) such as channels, ion-pumps and receptors. Additionally, it is known, that mutations in MPs are directly or indirectly involved in many diseases. Thus, structure determination of MPs is of major interest not only in structural biology but also in pharmacology, especially for drug development. Advances in structural biology of membrane proteins (MPs) have been strongly supported by the success of three leading techniques: X-ray crystallography, electron microscopy and solution NMR spectroscopy. However, X-ray crystallography and electron microscopy, require highly diffracting 3D or 2D crystals, respectively. Today, structure determination of non-crystalline solid protein preparations has been made possible through rapid progress of solid-state MAS NMR methodology for biological systems. Castellani et. al. solved and refined the first structure of a microcrystalline protein using only solid-state MAS NMR spectroscopy. These successful application open up perspectives to access systems that are difficult to crystallise or that form large heterogeneous complexes and insoluble aggregates, for example ligands bound to a MP-receptor, protein fibrils and heterogeneous proteins aggregates. Solid-state MAS NMR spectroscopy is in principle well suited to study MP at atomic resolution. In this thesis, different types of MP preparations were tested for their suitability to be studied by solid-state MAS NMR. Proteoliposomes, poorly diffracting 2D crystals and a PEG precipitate of the outer membrane protein G (OmpG) were prepared as a model system for large MPs. Results from this work, combined with data found in the literature, show that highly diffracting crystalline material is not a prerequirement for structural analysis of MPs by solid-state MAS NMR. Instead, it is possible to use non-diffracting 3D crystals, MP precipitates, poorly diffracting 2D crystals and proteoliposomes. For the latter two types of preparations, the MP is reconstituted into a lipid bilayer, which thus allows the structural investigation in a quasi-native environment. In addition, to prepare a MP sample for solid-state MAS NMR it is possible to use screening methods, that are well established for 3D and 2D crystallisation of MPs. Hopefully, these findings will open a fourth method for structural investigation of MP. The prerequisite for structural studies by NMR in general, and the most time consuming step, is always the assignment of resonances to specific nuclei within the protein. Since the last few years an ever-increasing number of assignments from solid-state MAS NMR of uniformly carbon and nitrogen labelled samples is being reported, mostly for small proteins of up to around 150 amino acids in length. However, the complexity of the spectra increases with increasing molecular weight of the protein. Thus the conventional assignment strategies developed for small proteins do not yield a sufficiently high degree of assignment for the large MP OmpG (281 amino acids). Therefore, a new assignment strategy to find starting points for large MPs was devised. The assignment procedure is based on a sample with [2,3-13C, 15N]-labelled Tyr and Phe and uniformly labelled alanine and glycine. This labelling pattern reduces the spectral overlap as well as the number of assignment possibilities. In order to extend the assignment, four other specifically labelled OmpG samples were used. The assignment procedure starts with the identification of the spin systems of each labelled amino acid using 2D 13C-13C and 3D NCACX correlation experiments. In a second step, 2D and 3D NCOCX type experiments are used for the sequential assignment of the observed resonances to specific nuclei in the OmpG amino acid sequence. Additionally, it was shown in this work, that biosynthetically site directed labelled samples, which are normally used to observe long-range correlations, were helpful to confirm the assignment. Another approach to find assignment starting points in large protein systems, is the use of spectroscopic filtering techniques. A filtering block that selects methyl resonances was used to find further assignment starting points for OmpG. Combining all these techniques, it was possible to assign nearly 50 % of the observed signals to the OmpG sequence. Using this information, a prediction of the secondary structure elements of OmpG was possible. Most of the calculated motifs were in good aggreement with the crystal structures of OmpG. The approaches presented here should be applicable to a wide variety of MPs and MP-complexes and should thus open a new avenue for the structural biology of MPs. / Biologische Membranen bestehen hauptsächlich aus Lipiden, ihre Funktion wird jedoch vor allem durch die eingebetteten Membranproteine (z.B. Kanäle, Ionenpumpen und Rezeptoren) bestimmt. Mutationen in dieser Proteinklasse können zum Auftreten verschiedener Krankheitsbilder führen, weshalb die Untersuchung der dreidimensionalen Struktur von Membranproteinen nicht nur von strukturbiologischem, sondern auch von pharmakologischem Interesse ist. In den letzten Jahren wurde eine Methode, die Festkörper NMR Spektroskopie, für Strukturuntersuchungen an Proteinproben im festen Aggregatzustand entwickelt. Diese Arbeit beschäftigt sich mit drei verschiedenen Präparationsarten von Membranproteinen, die eine Aufnahme von hochaufgelösten Festkörper NMR Spektren erlauben. Als Modelsystem wurde das Protein G der äußeren Membrane (outer membrane protein G, OmpG) von Escherichia coli gewählt. Eine wichtige Vorraussetzung zur Berechnung der Proteinstruktur aus den NMR-Spektren, ist die Zuordnung der einzelnen Signale zur jeweiligen Aminosäure in der Proteinsequenz. In dieser Arbeit wurde eine Methode entwickelt, die das Auffinden von Startpunkten für die sequentielle Zuordnung in großen Membranproteinen, wie zum Bsp. OmpG (281 Aminosäuren), erlaubt. Multidimensionale NMR Experimente mit verschieden spezifisch markierten Proben wurden durchgeführt und ermöglichten die Zuordnung von 50 % der NMR Signale der OmpG Proteinsequenz. Zur Überprüfung der gewonnenen Daten wurden diese zur Vorhersage von Sekundärstrukturelementen genutzt. Es konnte gezeigt werden, dass die berechneten Strukturmotive in guter Übereinstimmung zu den bisher veröffentlichten OmpG Strukturen liegen. Die in dieser Arbeit angewendeten Methoden sollten auf eine Vielzahl anderer Membranprotein anwendbar und somit einen neuen Weg zur Strukturbiologischen Untersuchung von Membranproteinen eröffnen.
2

Mechanochemical Synthesis of low F-Doped Aluminium Hydroxide Fluorides

Scalise, Valentina 21 January 2019 (has links)
Die Mechanochemie ist eine effekive und überzeugende Methode zur Herstellung von Alumniumhydroxidfluoriden (Al(OH)3-xFx) mit einem sehr geringen Fluorgehalt. Durch den Prozess des Mahlens werden strukturelle Defekte in den Kristalliten erzeugt, die zu einer zunehmenden Amorphisierung des Kristallsystems führen. Die partielle Fluorierung von Alumniumhydroxid während des Mahlprozesses führt dabei zu einer noch stärkeren Amorphisierung und zur Bildung von Alumniumhydroxyfluoriden. Eine wichtige Rolle bei der resultierenden Produktzusammensetzung spielt die Variation der Synthesebedingungen, wie der Grad der Fluorierung, der Dauer des Mahlprozesses und des Wassergehalt der Edukte. Folglich wurde zuerst der Einfluss von Wasser und dessen Bedeutung durch die verschiedenen Kombinationen von Oxid- und Hydroxid- (Al(OH)3, Al2O3), sowie Fluorid-Quellen mit oder ohne Kristallwasser (β-AlF3.3H2O, α-AlF3) bei der mechanochemischen Synthese von hochgestörten Alumniumhydroxidfluoriden untersucht. Um den optimalen Fluorierungsgrad zu ermitteln, wurden verschiedene Aluminiumhydroxidfluoride mit Al/F-Molverhältnissen von 1:1.5 bis 1:0.05 über die mechanochemische Syntheseroute hergestellt. Eine tiefergehende Charakterisierung der Struktur- und Oberflächeneigenschaften der entsprechenden Produkte erfolgte mittels XRD, 27Al- und 19F-Festkörper-NMR, thermischer Analyse, Stickstoffabsorptions- und Zeta Potentialmessungen. Mit γ-Al(OH)3 und β-AlF3•3H2O als Hydroxid- und Fluorid-Quellen wurden dabei ab einem Verhältnis Al:F von 1:0.25 und hin zu höheren Fluoridanteilen besonders ungeordnete Strukturen erzeugt. Der Fluorierungsgrad betrifft dabei besonders die Ausbildung von 4- und 5-fach koordinierten Al-Zentren, die sonst nicht in den Edukten vorkommen. Diese Spezies beeinflussen die Bildung von Alumniumoxid und ermöglichen den Phasenübergang zu α-Al2O3 schon bei tieferen Temperaturen. Der Einfluss der Mahldauer auf die Struktur und Oberfläche wurde am Beispiel von γ-Al2O3 im Detail untersucht. Die mechanochemische Synthese beeinflusst dabei die Absorption von Fluor an der Grenzschicht von γ-Al2O3 zu Wasser stark. Die Dauer des Mahlprozesses gewinnt daher einen großen Einfluss auf die entstehenden Produkte. Da Fluor nicht im Bulk von γ-Al2O3 vorkommt, kann mit der 19F-Festkörper-NMR eine Zuordnung der unterschiedlichen an der Oberfläche adsorbierten F-Spezies getroffen werden. / The mechanochemical approach opens a reliable and effective strategy for the formation of aluminium hydroxide fluorides with a very low F-content. Milling has the effect of introducing structural defects, causing amorphisation. The fluorination by milling creates a further and drastic increase of this degree of amorphisation. Synthesis conditions (milling time, fluorination degree, water content) play a crucial role in the product composition. Firstly, the significant role played by water in the mechanochemical synthesis of highly distorted aluminium hydroxide fluorides was evaluated. The importance of water in the synthesis was considered by a separated combination of O/OH sources (Al(OH)3, Al2O3) and fluorine sources with or without structural water (β-AlF3.3H2O, α-AlF3). Concerning the degree of fluorination, different aluminium hydroxide fluorides with varying Al/F molar ratios from 1:1.5 up to 1:0.05 were successfully synthesized by mechanochemical reactions. The characterization of the products by XRD, 27Al and 19F MAS NMR, thermal analysis, nitrogen adsorption and zeta potential techniques allows a detailed understanding of the structure and surface properties of the products. Using γ-Al(OH)3 and β-AlF3•3H2O as OH- and F-sources, respectively, strongly disordered products were obtained with an Al: F molar ratio higher than 1:0.25. The degree of fluorination affects the amount of 4- and 5-fold coordinated Al sites, not present in the reactants. Obviously, these species affect the phase transition to alumina, by decreasing the transition temperature of the formation of α-Al2O3. The influence of the milling time was considered by studying the power of a high energy ball milling process on the structure and at the surface of γ-Al2O3. The mechanochemical treatment strongly influences the adsorption of fluorine at the γ-Al2O3/ water interface. The time of the treatment has relevant importance on these processes. Since fluorine is not originally present in the bulk of γ-Al2O3, 19F MAS NMR studies allow the discrimination of different F-species adsorbed at the surface or present as metal fluoride particles in γ-Al2O3 powders after adsorption experiments.

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