Rozprawy doktorskie: „X-ray crystallography”

1

Zora, J. A. "X-ray diffraction studies". Thesis, University of Sussex, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.374467.

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Wall, Clare. "Mathematical methods in protein x-ray crystallography". Thesis, University of York, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.403863.

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Mifsud, Richard William. "An exploration of some aspects of molecular replacement in macromolecular crystallography". Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/282871.

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This thesis reports work in three areas of X-ray crystallography. An initial chapter describes the structure of a protein, the methods based on the use of X-rays and computer analysis of diffraction patterns to determine crystal structure, and the subsequent derivation of the structure of part or all of a protein molecule. Work to determine the structure of the protein cytokine receptor-like factor 3 (CRLF3) leading to the successful generation of a structural model of a significant part of this molecule is then described in Chapter 2. A variety of techniques had to be deployed to complete this work, and the steps undertaken are described. Analysis was performed principally using phaser, using maximum likelihood methods. Areas for improvement in generating non-crystallographic symmetry (NCS) operators in existing programmes were identified and new and modified algorithms implemented and tested. Searches based on improved single sphere algorithms, and a new two-sphere approach, are reported. These methods showed improvements in many cases and are available for future use. In Chapter 4, work on determining the relative importance of low resolution and high intensity data in molecular replacement solutions is described. This work has shown that high intensity data are more important than the low resolution data, dispelling a common perception and helping in experimental design.

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4

Meng, Guoyu. "Structural study of levansucrase by x-ray crystallography". Thesis, University of Birmingham, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.403446.

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Geissbühler, Marc Phillip. "X-ray interfacial crystallography of water on calcite /". Thesis, Connect to this title online; UW restricted, 2000. http://hdl.handle.net/1773/9634.

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Nagpal, Akanksha. "Crystal Structures of Nitroalkane Oxidase: Insights into the Structural Basis for Substrate Specificity and the Catalytic Mechanism". Diss., Available online, Georgia Institute of Technology, 2005, 2005. http://etd.gatech.edu/theses/available/etd-07172005-152826/.

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Thesis (Ph. D.)--Chemistry and Biochemistry, Georgia Institute of Technology, 2006.
Dr. Allen M. Orville, Committee Chair ; Dr. Loren D. Williams, Committee Member ; Dr. Donald F. Doyle, Committee Member ; Dr. Dale E. Edmondson, Committee Member ; Dr. Giovanni Gadda, Committee Member.

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7

Oblezov, Alexandr Evgenievich. "Crystal structure determination at the Center for X-ray Crystallography a practical guide /". [Gainesville, Fla.] : University of Florida, 2003. http://purl.fcla.edu/fcla/etd/UFE0002700.

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8

Collins, Anna. "The X-ray crystallography of Z'>1 materials". Thesis, University of Oxford, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.437369.

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Lo, Victor Lai-Xin. "Iterative projection algorithms and applications in x-ray crystallography". Thesis, University of Canterbury. Electrical and Computer Engineering, 2011. http://hdl.handle.net/10092/5476.

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X-ray crystallography is a technique for determining the structure (positions of atoms in space) of molecules. It is a well developed technique, and is applied routinely to both small inorganic and large organic molecules. However, the determination of the structures of large biological molecules by x-ray crystallography can still be an experimentally and computationally expensive task. The data in an x-ray experiment are the amplitudes of the Fourier transform of the electron density in the crystalline specimen. The structure determination problem in x-ray crystallography is therefore identical to a phase retrieval problem in image reconstruction, for which iterative transform algorithms are a common solution method. This thesis is concerned with iterative projection algorithms, a generalized and more powerful version of iterative transform algorithms, and their application to macromolecular x-ray crystallography. A detailed study is made of iterative projection algorithms, including their properties, convergence, and implementations. Two applications to macromolecular crystallography are then investigated. The first concerns reconstruction of binary image and the application of iterative projection algorithms to determining molecular envelopes from x-ray solvent contrast variation data. An effective method for determining molecular envelopes is developed. The second concerns the use of symmetry constraints and the application of iterative projection algorithms to ab initio determination of macromolecular structures from crystal diffraction data. The algorithm is tested on an icosahedral virus and a protein tetramer. The results indicate that ab initio phasing is feasible for structures containing 4-fold or 5-fold non-crystallographic symmetry using these algorithms if an estimate of the molecular envelope is available.

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10

Alves-Areias, A. "Investigation of host-guest interactions by x-ray crystallography". Thesis, Queen's University Belfast, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.395365.

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11

Malle, Dominggus. "Structural studies of microbial pullulanases by X-ray crystallography". Kyoto University, 2007. http://hdl.handle.net/2433/136530.

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Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第13111号
農博第1616号
新制||農||940(附属図書館)
学位論文||H19||N4237(農学部図書室)
UT51-2007-H384
京都大学大学院農学研究科農学専攻
(主査)教授内海成, 教授三上文三, 教授松村康生
学位規則第4条第1項該当

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12

Kinna, David John. "Pattern recognition in chemical crystallography". Thesis, University of Oxford, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.318724.

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13

Derewenda, Urszula. "X-ray analysis of dimeric and hexameric insulins". Thesis, University of York, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.276517.

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14

Sadow, Jennifer Beth Hurley. "The X-ray crystal structure of wheat translation initiation factor eIF4E /". Thesis, Full text (PDF) from UMI/Dissertation Abstracts International, 2002. http://wwwlib.umi.com/cr/utexas/fullcit?p3085056.

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15

Sinangil, Mehmet Selcuk. "Estimation of crystal size and inhomogeneous strain in polymers using single peak analysis". Thesis, Georgia Institute of Technology, 1996. http://hdl.handle.net/1853/19096.

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16

Brooks-Bartlett, Jonathan C. "Quantifying radiation damage in X-ray diffraction experiments in structural biology". Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:2f311eea-82bc-4200-846c-068ae26599ea.

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Quantitative studies of global radiation damage are presented for two different types of experiments in structural biology: macromolecular crystallography (MX) and small angle X-ray scattering (SAXS) MX is the most common technique to elucidate the atomic resolution structures of biological macromolecules. However, these molecules undergo radiation induced changes during the experiment that undesirably affect the data. Global radiation damage, which is characterised by an overall loss in the diffracted intensity of Bragg reflections, limits the amount of useful data that can be collected from a single crystal in an experiment. Furthermore, for experimental phasing experiments, the radiation induced intensity changes can be so significant that the phasing signal becomes undetectable, thereby hindering successful structure determination. This thesis investigates methods to track and correct the diffraction data that are affected as a result of global radiation damage. First, extensions to the diffraction weighted dose (DWD) metric are investigated for the ability of DWD to track the overall intensity decay of reflections. This metric then is combined with a new mathematical model of intensity decay to perform zero-dose extrapolation. An additional probabilistic extrapolation approach is incorporated into the traditional regression based approach to allow extrapolation of low multiplicity reflections. As an alternative approach, a new hidden Markov model representation of the data collection experiment is developed that allows the time-resolved calculation of structure factor amplitudes, with error estimates calculated explicitly. This method gives comparable refinement statistics to that obtained from data processed with the current data reduction pipeline, and improvements to the algorithm are proposed. SAXS, on the other hand, is a complementary structural technique that results in low resolution information about macromolecules. However it still requires the probing of the macromolecules with ionising radiation, so radiation induced changes are still a problem. Unfortunately the tools for assessing radiation damage in SAXS experiments are not mature enough for them to be used routinely. This thesis presents extensions to RADDOSE-3D to perform dose calculations for SAXS samples. Additionally, a free, open source Python library has been developed to allow the exploration and visualisation of the results of a similarity analysis of frames within a dataset. These tools are then used to determine the efficacy of various radioprotectant compounds at different concentrations to mitigate radiation damage effects.

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17

Barnett, Stephanie Jayne. "X-ray powder diffraction studies of ettringite and related systems". Thesis, Staffordshire University, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.244708.

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18

Pearce, Nicholas M. "Multi-dataset electron density analysis methods for X-ray crystallography". Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:44fb5cf1-93a4-43c0-805c-c85dffd29101.

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X-ray crystallography is extensively deployed to determine the structure of proteins, both unbound and bound to different molecules. Crystallography has the power to visually reveal the binding of small molecules, assisting in their development in structure-based lead design. Currently, however, the methods used to detect binding, and the subjectivity of inexperienced modellers, are a weak-point in the field. Existing methods for ligand identification are fundamentally flawed when identifying partially-occupied states in crystallographic datasets; the ambiguity of conventional electron density maps, which present a superposition of multiple states, prevents robust ligand identification. In this thesis, I present novel methods to clearly identify bound ligands and other changed states in the case where multiple crystallographic datasets are available, such as in crystallographic fragment screening experiments. By applying statistical methods to signal identification, more crystallographic binders are detected than by state-of-the-art conventional approaches. Standard modelling practice is further challenged regarding the modelling of multiple chemical states in crystallography. The pervading modelling approach is to model only the bound state of the protein; I show that modelling an ensemble of bound and unbound states leads to better models. I conclude with a discussion of possible future applications of multi-datasets methods in X-ray crystallography, including the robust identification of conformational heterogeneity in protein structures.

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19

Mancuso, Adrian P. "Experimental phase retrieval using coherent x-ray diffraction /". Connect to thesis, 2005. http://eprints.unimelb.edu.au/archive/00001775.

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20

Bertrand, Jay Aaron. "X-ray crystal structures of inhibited bovine pancreatic trypsin". Diss., Georgia Institute of Technology, 1994. http://hdl.handle.net/1853/27321.

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21

Walker, Andrew W. "Synthesis and X-ray structure analysis of novel calixarene receptors". Thesis, Queen's University Belfast, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.318740.

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22

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

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23

Ko, Reamonn, i 高耀駿. "X-ray crystallographic studies of Plasmodium falciparum adenylate kinases". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/208020.

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Malaria is a global health concern accounting for approximately 219 million cases and an estimated 660 000 deaths in 2010. The most fatal strain of malarial parasite, Plasmodium falciparum is found to contain 3 Adenylate Kinases (PfAK1, PfAK2 and PfGAK). Adenylate Kinases are important enzymes that essentially catalyze and regulate energy metabolism processes. PfAK1 and PfAK2 catalyze the reversible MG2+ reaction ATP + AMP ←→ 2ADP whereas, the PfGAK catalyzes the Mg2+ dependent reaction GTP+AMP ←→ ADP+GDP. Of all malarial strains, only the Plasmodium falciparum Adenylate Kinase 2 (PfAK2) was found to contain a N-myristoylation sequence and subsequently formed a stable heterodimer with Plasmodium falciparum N-myristoyl transferase (PfNMT). The myristoylation of PfAK2 by PfNMT is believed to help transport PfAK2 to the parasitophorous vacuole membrane (PVM) so that the enzyme can perform its essential functions. With these enzymes being key components in the parasite’s survival, the structural study of these enzymes would provide a lot of insight into targeting these proteins for drug design that would effectively kill the parasite without affecting the human host. In this study, PfAK1 was able to be expressed, purified and crystallized with a dataset collected at 4.3Å. PfGAK was expressed and purified. A GTP analogue called GP5A was used to soak the purified PfGAKand the PfGAK bound to GP5A was crystallized and diffracted. Moreover, PfAK2 and PfNMT was successfully expressed and co-purified. The purified PfAK2-PfNMT heterodimer are undergoing crystal screening for possible crystallization conditions.
published_or_final_version
Physiology
Master
Master of Philosophy

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24

Andersson, Charlotta. "Structural studies of Erwinia carotovora L-Asparaginase by X-ray crystallography". Thesis, Linköping University, The Department of Physics, Chemistry and Biology, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-6188.

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Bacterial L-asparaginases (E.C.3.5.1.1) are enzymes that catalyze the hydrolysis of L-asparagine to aspartic acid. For the past 30 years these enzymes have been used as therapeutic agents in the treatment of acute childhood lymphoblastic leukemia. The presence of a low rate glutaminase activity however causes serious side-effects to patients in treatment, as glutamine depletion give rise to neurotoxicity, anaphylaxis, and other hypersensitivity reactions. The interest in the enzyme from Erwinia carotovora originates from the fact that it shows a decreased glutaminase activity, and therefore the enzyme is expected to exhibit fewer side effects when used in therapy.

The main focus of this thesis is the crystal structure determination of L-asparaginase from Erwinia carotovora in the presence of aspartic acid at 2.5 Å resolution. The structure was refined to an R/Rfree factor of 19.9/28.6 with good stereochemistry.

L-Asparaginases are homotetrameric enzymes with a known 222 symmetry and an identical fold. The Erwinia carotovora asparaginase consists of eight monomers of 330 amino acid residues each. In this case the enzyme is active as a dimer of tetramers. The two tetramers have an inner twofold non-crystallographic symmetry. Each monomer forms two identifiable domains a large N-domain and a small C-domain. The active sites are found at a topological switch-point between those domains.

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25

Cheung, Eugene. "Solid state photochemistry and x-ray crystallography of carbonyl-containing compounds". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape3/PQDD_0017/NQ56659.pdf.

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26

Lane, S. E. "Structure determination by X-ray crystallography of some Group IIIB compounds". Thesis, Lancaster University, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.355338.

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27

Tate, Graeme. "New methods in protein X-ray crystallography using maximum entropy techniques". Thesis, University of Glasgow, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.396507.

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28

Fothergill, Michael David. "Analysis of mutants of tyrosyl-tRNA synthetase by X-ray crystallography". Thesis, Imperial College London, 1989. http://hdl.handle.net/10044/1/47439.

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29

Petersson, Britt. "Structural studies of peptide nucleic acid (PNA) by X-ray crystallography /". Cph. : The Danish University of Pharmaceutical Sciences, Department of Medicinal Chemistry, 2004. http://www.dfh.dk/phd/defences/Brittpetersson.htm.

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30

Szell, Patrick. "The Halogen Bond: X-Ray Crystallography and Multinuclear Magnetic Resonance Investigation". Thesis, Université d'Ottawa / University of Ottawa, 2019. http://hdl.handle.net/10393/39233.

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The halogen bond has recently risen in prominence as a non-covalent interaction for use in supramolecular chemistry, allowing for the rational design of materials, pharmaceuticals, and functional molecules. The occurrence of the σ-hole opposite to the C-X covalent bond (X = F, Cl, Br, I) renders the halogen bond a highly directional and tuneable interaction, offering desirable features to crystal engineers. The halogen bond can be divided into its two components: the halogen bond donor bearing the halogen atom, and the electron-rich halogen bond acceptor. In this thesis, we investigate the nature of the halogen bond, its role in supramolecular assembly and impact on the local dynamics, along with developing synthetic methods to prepare this class of materials. We begin by fully characterizing the halogen bond donor by using 35Cl ultra-wideline solid-state nuclear magnetic resonance (NMR) spectroscopy on a series of single-component chloronitriles exhibiting the C-Cl···N halogen bond. We then perform the first modern nuclear quadrupole resonance (NQR) investigations of the halogen bond, observing the 79/81Br and 127I nuclei in a series of cocrystals exhibiting the C-Br···N and C-I···N halogen bond, respectively. Computational results attribute the observed increases in the quadrupolar coupling constants (CQ) to a reduction in the carbon-halogen σ-bonding contribution to V33 and an increase in the lone-pair and core orbital contributions, providing the first model of the electronic changes occurring on the halogen bond donor upon the formation of the halogen bond. Attention is then turned on characterizing the halogen bond acceptor and its surrounding environment, beginning by investigating a solid-state NMR approach relying on the 19F nucleus to characterize perfluorinated cocrystals. This strategy has reduced analysis times from hours to minutes while providing higher sensitivity and resolution, with the resulting chemical shifts permitting the unambiguous identification of the halogen bond and allowing for the refinement of X-ray crystal structures. The halogen bond acceptor is then investigated in a series of isomorphous dimers exhibiting both the halogen bond and hydrogen bond in the C≡C-I···X-···H-N+ motif, revealing the halogen bond’s relative contribution to the electric field gradient increasing in the order of Cl- > Br- > I-, contrasting the contributions of the hydrogen bond. We then explore the impact of the halogen bond on the surrounding environment, using the rotating methyl groups of 2,3,5,6-tetramethylpyrazine as a model. Upon the introduction of a halogen bond, we observe a reduction in the rotational energy barrier of 56% on average, overshadowing the 36% reduction observed in the hydrogen bonded cocrystals. This is the first instance of the halogen bond directly catalyzing the local dynamics, coining the term “dynamics catalyst”. These results provide an effective strategy of enhancing the dynamics in molecular systems, such as molecular machines, supramolecular catalyst, as well as correcting the faulty dynamics encountered in diseased proteins. The role of halogen bonding in crystal engineering is then explored, reporting the first supramolecular triangle, a series of discrete charged dimers, and supramolecular architectures built from 1,3,5-tri(iodoethynyl)-2,4,6-trifluorobenzene, with the potential of creating fully organic porous structures for gas absorption. Mechanochemistry is then investigated as a synthetic method, allowing for the preparation of cocrystals featuring 3-iodoethynylbenzoic acid as the donor, with the resulting structures exhibiting concurrent halogen and hydrogen bonding. Mechanochemical ball milling is shown to reduce preparation times of powdered cocrystals from days to a single hour, while using a fraction of the organic solvent. Lastly, we pioneer cosublimation as a solvent-free synthetic technique for rapidly preparing halogen bonded cocrystals, yielding quality single crystals within a few hours, and a microcrystalline product within 15 minutes. Among its advantages, cosublimation offers a significant acceleration of discovery, while eliminating the environmental footprint associated with conventional synthetic methods.

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31

Moloney, Janet M. "X-ray structural studies of lanthanide macrocycles and biological molecules". Thesis, Durham University, 1999. http://etheses.dur.ac.uk/4599/.

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The work described in this thesis is broadly divided into two sections. The structural study on the lanthanide macrocyclic complexes was afforded by means of X-ray crystallography In this chapter, the molecules dota, the cationic enantiopure tetraamide europium and dysprosium complexes, the sodium complexes of the tetranaphthylamide and quinoyl derivative, the enantiopure gadolinium and europium complexes of the tetraamide series with esteratic sidechains, the lanathanum and ytterbium complexes of the dota derivative with benzyl phosphinate sidechains, and the tetracarboxyethyl series both as three uncomplexed stereoisomer and complexes of the RRRR stereoisomer with europium, gadolinium and terbium. These complexes exhibit quite a lot of structural diversity. Chapter five deals with experiments carried out at ultra low temperatures. A phase transition that the molecule benzil undergoes is investigated on the Fddd diffractometer, a study of the interesting 1,12-dicarbonyl borane was undertaken to obtain precise values for the carbonyl bond lengths and the unprecedented structure of its hydrate was revealed to be a carbene diol and not the expected carboxylic acid complex The standard for macromolecular tests for diffraction, chicken egg white lysozyme, was crystallised and used to optimise conditions for low-temperature data acquisition from macromolecular samples The work described in this Thesis was carried out in the Department of Chemistry, Durham University from October 1995 to January 1999, under the supervision of Professor J.A.K. Howard. All of the work is my own, unless stated to the contrary, and it has not been submitted previously for a degree at this or any other university.

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32

Prince, Stephen Michael. "Synchrotron X-ray studies of ribonuclease A and other molecules". Thesis, Liverpool John Moores University, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.261490.

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33

Lerche, Michael. "Elucidating the activation mechanism of the transcription factor DntR using X-ray crystallography and small angle X- ray scattering". Thesis, Grenoble, 2014. http://www.theses.fr/2014GRENV013/document.

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Les protéines régulatrices de la transcription de type LysR (LTTR) appartient à la plus grande famille de facteur de transcription chez les procaryotes. Malgré l'importance de cette famille, les informations structurelles sur les protéines pleine-longueur sont très limitées car elles sont souvent insolubles et très difficiles à cristalliser. Les quelques structures existantes, couplés à d'autres analyses biophysiques ont pu montrer que ces protéines s'associent principalement sous forme d'homotétramère comprenant un dimère de dimères. Les dimères s'associent par un large domaine C-terminal dans une position " tête-bêche " et sont reliés en " tête-à-tête " par leurs domaines N-terminal et sont activées par la liaison de molécules inductrices. Le domaine dimèrique C-terminal qui contient la poche de liaison inductrice (Inducer Binding Cavity : IBC) est appelé domaine de liaison inductrice (Inducer Binding Domain : IBD), tandis que les dimères N-terminaux se lient chacun à une région de l'ADN par un motif hélice-tour-hélice ‘winged' (wHTH). Contrairement à d'autres facteurs de transcription, les protéines LTTR ne régulent pas l'expression par association/dissociation avec l'ADN. Ils se lient à l'ADN dans leur état actif et inactif. Le consensus actuel est qu'elles régulent l'expression des gènes par d'importants changements conformationnels qui relâchent la liaison avec l'ADN. À ce jour, aucune structure de LTTR pleine longueur homotétramérique dans une conformation active ou inactive n'a été résolu par cristallographie, et leur mécanisme d'action sur le gène reste structurellement non caractérisé.Le travail décrit dans cette thèse a utilisé DntR de la famille des LTTR. La première structure cristalline de l'apo-DntRis est présentée ici, ainsi que la structure du mutant H169TDntR, qui présente une activité en l'absence d'inducteur. L'analyse par fluorimétrie de différentiel thermique (TSA) montre que la température de dénaturation du mutant H169TDntR est similaire à DntR IBDs lié à une molécule inductrice. La comparaison de ces deux structures avec celle de DntR lié au salicylate révèle que la protéine dans son état apo adopte une conformation compacte de l'IBC, ce qui empêche la liaison d'une molécule inductrice. Dans l'IBC, les mouvements des résidus H169 et H206 permettent la liaison à l'inducteur. Pour éviter les limitations dues à l'empaquetage du cristal nous avons étudié la structure DntR en solution par diffusion des rayons X aux petits angles (SAXS).L'étude SAXS de DntR révèle que dans son état inactif, la conformation apo adopte un repliement plus compact par rapport à celle de la structure cristalline. Tout en maintenant un noyau compact de C-terminal, le repliement du dimère de wHTH est beaucoup plus fermé que dans la structure cristalline et adopte une conformation qui entrainerait une flexion beaucoup plus importante de l'ADN lié que postulé précédemment. Les études du mutant H169TDntR constitué actif ont confirmé comme l'analyse par TSA l'a suggéré que, la structure de cette protéine est nettement différente en solution que sous forme cristalline.En effet, la structure en solution de H169TDntR est très semblable à la forme ouverte de l'homotétramères observés dans la structure cristalline de TsaR. L'hypothèse de départ était que, lors de l'activation de LTTR, cet homotétramère subirait un changement de conformation d'une forme compact vers une forme ouverte, qui se traduirait par un relâchement de l'ADN lié. Cette hypothèse a été confirmée par des études de diffusion en solution de DntR activée par un inducteur.Le travail présenté dans cette thèse valide l'hypothèse précédemment, que lors de l'activation de DntR, et probablement tous les LTTRs homotétramériques, entraine un changement de conformation d'une forme compacte vers une forme beaucoup plus ouverte et permet l'accès aux régions promotrices par l'ARN polymerase et ainsi initier la transcription
LysR type transcriptional regulatory (LTTR) proteins are the largest family of transcription factors amongst prokaryotes. In spite of the size of the family, structural information on full-length constructs of these proteins is very limited as they are often insoluble and very difficult to crystallize. From the few existing crystal structures, coupled with other biophysical evidence, it is known that the proteins mainly associate as homotetramers comprising a dimer of dimers. The dimers associate through large C-terminal domains in a “head-to-tail” fashion and are connected “head-to-head” through their N-terminal domains and the resulting homotetramers are activated by the binding of inducer molecules. Each C-terminal domain contain an inducer binding cavity (IBC) and is denoted an inducer binding domain (IBD), while the N-terminal dimers each bind a region of DNA via a winged helix-turn-helix (wHTH) motif.Unlike other transcription factors, LTTR proteins do not regulate expression by associating or disassociating with DNA. They bind to DNA in both their active and inactive states and the current consensus is that they regulate gene expression through large conformational changes that relax the bending of bound DNA. However, to this date, no crystal structures of a full length homotetrameric LTTR in both an active and inactive conformation exists, and thus their mechanism of transcriptional regulation remains structurally uncharacterized.The work described in this thesis has used the LTTR DntR as a model protein to futher structurally characterizes the activation mechanism of LTTR proteins. The first crystal structure of apo-DntR is presented as is the crystal structure of H169TDntR, a mutant which shows activity in the absence of an inducer molecule. Thermofluor assays performed on this mutant, show that it has a melting temperature similar to that of inducer bound DntR. Comparison of these crystal structures with the crystal structure of salicylate-bound DntR reveals that the protein in its apo-state adopts a compact IBC, which precludes the binding of an inducer molecule. Despite the evidence of thermofluor assays, the crystal structure of H169TDntR is very similar to that of apo-DntR suggesting that crystal packing effects impose strong limitations on the use of crystallography to elucidate the active and inactive conformations of DntR. Small Angle X-ray Scattering (SAXS) was thus used to study the structure of DntR in solution.SAXS study reveals that in solution DntR in its inactive apo-state is found in a slightly different conformation compared to that seen in its crystal structure. While maintaining a compact tetrameric C-terminal core the DNA binding wHTH dimers pack much closer to this than seen in the crystal structure and adopt a conformation that would result in much higher bending of bound DNA than previously postulated.SAXS studies of the constitutively active H169TDntR mutant confirm, as thermofluor assays had suggested, that in solution the structure of this protein is markedly different from its crystal structure. Indeed the solution structure of H169TDntR appears very like that of open-form homotetramers seen in the crystal structure of TsaR. This same effect was observed in solution scattering studies of inducer bound-and thus activated, DntR.The work presented in this thesis thus appears to confirm, as previously hypothesized, that upon activation DntR, and presumably all homotetrameric LTTRs, undergo a conformational change from a compact, to a much more open form that allows the relaxation of the bound DNA promoter region, exposing it to solvent and allows RNA polymerase access and thus initiate transcription

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34

Fuller, Amy L. "Applications of X-ray crystallography : studies into the structural perturbations of peri-substituted naphthalene derivatives /". St Andrews, 2009. http://hdl.handle.net/10023/826.

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35

Strassner, Amanda M. "YZGD pyridoxal phosphatase from P. thiaminolyticus : subcloning, expression, and purification for x-ray crystallography structure determination /". Online version of thesis, 2008. http://hdl.handle.net/1850/6894.

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36

Zhang, Kam Yong Jian. "On phase refinement and extension of macromolecular structures using both real and reciprocal space approaches". Thesis, University of York, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.329753.

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37

Phetmung, Hirihattaya. "Structural studies of phospholes and phosphines". Thesis, University of Bristol, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.324324.

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38

Liang, Shutian. "Structural basis of porcine RNase 4 recognition". Thesis, University of Bath, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.665403.

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Bovine pancreatic ribonuclease (RNase A) and its homologues are pyrimidine-specific ribonucleases widely present in mammals, birds, amphibians, reptiles, and fish. RNases recognise a specific sequence – an adenosine 3' to a pyrimidine – on RNA, and cleave the molecule on the 3' side of the 3'-phosphate of the pyrimidine base. Extensive studies have been carried out on the RNase A homologues, including eosinophil-derived neurotoxin (EDN; RNase 2), eosinophil cationic protein (ECP; RNase 3), and angiogenin (ANG; RNase 5), and revealed distinct biological functions: EDN and ECP are involved in neurotoxicity, and ANG possesses angiogenic activity. RNase 4, although being discovered for a long time, is not as well characterised as much as other RNases. RNase 4 has been found in several mammalian species including a few primates, porcine, bovine, and rodents. The mature protein of RNase 4 consists of 119 amino acids, making it the shortest amongst all RNase A homologues. It has a higher inter-species similarity than its homologues, and such high evolutionary conservation suggests that RNase 4 has a more specialised function than RNA degradation. While RNase A, EDN, ECP, and ANG show cytidine preference, RNase 4 has a strong preference for uridine, which can be reversed back to cytidine by a single amino acid substitution of Asp-80, as shown by studies performed with porcine RNase 4 (also known as PL3). In this study, we used PL3 as a model to study the substrate specificity of RNase 4, and have solved four structures, including PL3, PL3 D80A mutant, and these two proteins in complex with dUMP and dCMP respectively. PL3 adopts the classic kidney-shaped RNase A fold, and residues forming the substrate binding subsites occupy similar positions as those in human RNase 4 and the prototypic RNase A. The structure of PL3 D80A mutant resembles that of the wild type iii PL3, and only hydrogen bond interactions between the side chains of Asp-80 and Arg-101 are lost. The structure of PL3·dUMP complex revealed interactions between the dUMP and residues Arg-7, His-12, Thr-44 and Phe-117 of PL3, which were also observed in the structure of human RNase 4 in complex with dUp. The additional hydrogen bonds identified between dUMP and residues Gln-11, Lys-40, Asn-43, and Lys-119 of PL3, as well as the absence of the interactions between Arg-101 of PL3 and the ligand that were present in the hRNase 4·dUp structure, could be due to the flexibility of the mononucleotide ligand. The crystal structure of PL3 D80A·dCMP complex presents a small number of hydrogen bond interactions between the protein and the dCMP ligand, which might be sufficient to stabilise the ligand in the B1 subsite, as the repulsion force on the dCMP ligand from the side chain of Arg-101 is absent in the PL3 D80A mutant. This is because in the D80A mutant, Ala-80 cannot provide hydrogen bonding that would hold the side chain of Arg-101 towards the B1 subsite. The activities of RNases can be inhibited by a 50 kDa cytosolic protein, the natural ribonuclease inhibitor (RI). RI binds to all the members of the RNase A superfamily, thus regulating the cytoplasmic RNA levels and protecting cells from inappropriately secreted RNases. The interactions between RNase and RI are tight, reversible, and in a 1:1 ratio. Several complex structures of RNase·RI from various species have been determined, and the residues in the interfaces between RNase and RI are conserved in all of the complexes. Studies revealed a 17-fold tighter interaction between PL3 and human RI than RNase A, making it very interesting to study the structure of the PL3·RI complex and characterise the interactions between PL3 and RI proteins. iv To date, we have established purification protocols for both proteins, and the next step towards the structure of PL3·RI would be to prepare and purify the protein complex, subject the protein complex to crystallisation experiments, and eventually lead us to the structural determination of PL3·RI complex.

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39

Erskine, Peter Thomas. "X-ray crystallographic studies of 5-aminolaevulinic acid dehydratase". Thesis, Birkbeck (University of London), 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.299090.

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40

Wilson, Claire. "Structure-reactivity relationships through X-ray and neutron diffraction studies". Thesis, Durham University, 1995. http://etheses.dur.ac.uk/5314/.

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This thesis is primarily concerned with the investigation of a structure-reactivity relationship in a series of pentacyclic Isodrin derivatives. These compounds undergo a two-hydrogen atom dyotropic rearrangement at vastly differing rates when apparently small structural changes are made. Two pairs of these isomers (with the formulas C(_16)H(_8)Cl(_10) and C(_16)H(_9)Cl(_9) ) have been investigated using both X-ray and neutron single crystal diffraction studies, at ambient and low temperatures. The experimental details of these studies are given for five experiments and the results of the least-squares refinements made using the data from these experiments are reported herein. In addition to conventional crystallographic studies, an experimental charge density study of one of these compounds, C(_16)H(_9)Cl(_9), has been made at 123K. The electron density was modelled using a multipole model which allows explicitly for the aspherical nature of the electron density. The results of this study, including a topological analysis of the charge density are reported in this thesis. The structures of six organometallic, four molybdenum bis(imido) and two half-sandwich niobium imido complexes, are also reported herein. Their structures were determined from single crystal diffraction data. These compounds show the expected structures predicted using the pseudo-isolobal relationship to the Group 4 bent metallocenes of which they may be considered analogues.

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41

Sutton, Karim J. "Determining structure and atomic properties of materials using resonant X-ray diffraction". Thesis, University of Oxford, 2015. http://ora.ox.ac.uk/objects/uuid:3944a985-9339-4c8c-970b-4b460848f200.

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X-ray crystallography is a widely used analytical technique for the structure solution of small molecules. Since the determination of the rock salt structure in 1913 by Henry and Lawrence Bragg the technique has developed allowing the solution of larger and more complex structures. The information that can be determined about these structures has increased as X-ray sources, detectors, and computational methods have improved. However, certain properties of molecules cannot always be directly determined from single wavelength X-ray diffraction. These include, inter alia: the site specific oxidation or spin state of an element in compounds where more than one state of the same element exist; discrimination between consecutive heavy elements in the periodic table. As the size of molecules being studied increases, reduced data resolution also becomes a problem. The aim of this research was to determine whether these problems can be addressed by measuring the changing anomalous scattering contribution of heavy atoms within structure through careful selection of the X-ray energy. Firstly, I report an investigation into the problemof discriminating oxidation state, spin state and elements of near identical scattering by exploiting their anomalous signal. I first present DetOx, a program written during the course of the project to deconvolute the fluorescence signal from materials containing more than one state of the same element into their respective spectra. This allows the calculation of anomalous scattering factors for both atomic states of an atom, which can subsequently be used to refine the occupancy of the different states at ambiguous sites within the crystal structure. The approach taken here, to determine differences due to relatively small anomalous signals, is analogous to the refinement of the Flack parameter whereby small changes in many hundreds or thousands of observations can be used to fit a parameter with a high degree of precision and accuracy. I show the application of this technique to the mixed oxidation state compound, GaCl₂, and the two-step spin crossover material, Fe(btr)₃(ClO₄)₂. Refinement of the occupancy of charged ions on multiple sites using data at a single, carefully selected wavelength proved successful for these compounds, although upon extension to materials containing a larger number of anomalous scatterers, the absorption became a major issue in the data along with problems associated with simultaneously refining occupancies at more sites in the structure. We have demonstrated that calculations can be made to select specific experimental data to collect in order to improve the measured signal. However, due to limitation of the current collision model on the diffractometer used we have not yet been able to construct data collection strategies to take advantage of this. I next present a new ratio refinement technique to overcome this absorption problem due to the increased number of scatterers. By using ratios between datasets close in energy, but below the absorption edge, we were able to exploit small changes in f' without encountering absorption problems associated with the increase in f''. These ratio values were then refined against a lab structure using a modified version of CRYSTALS to reveal the site specific occupancies of different atomic species within a given structure. For mixed-valence compounds, e.g. Mn₃ and Mn₆ clusters, the difference in anomalous signal between the different states proved too small for a stable least-squares refinement solution. However, we have shown that using a simulated annealing algorithm (to refine only occupancies), we can consistently obtain the expected structure. For mixed-metal structures e.g. the Mn₅Co₄ cluster, there was enough contrast in the data to refine occupancies with a least-squares approach, and these results were supported using simulated annealing. Lastly, I describe the application of structure solution techniques based on methods used in macromolecular crystallography to 'large' small molecules. Traditionally these have been reserved for non-centrosymmetric protein structures, however with the trend of synthesising larger and larger small molecules, problems encountered in macromolecular crystallography leading to low resolution datasets are becoming increasingly common. I have shown that it is possible to solve the structure of centrosymmetric structures by exploiting the anomalous signal in multiple wavelength diffraction experiments. The technique is applied successfully to two relatively small molecules, however the results are promising for moving to larger structures in the future.

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42

Du, Junyi. "X-ray crystallographic studies of sulfur/selenium heteroatom compounds". Thesis, University of St Andrews, 2016. http://hdl.handle.net/10023/8984.

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The major aim of research reported on this thesis uses X-ray crystallography to investigate the structural features of a series of pentafluorosulfuranyl (SF₅) containing aromatic compounds, chalcogen amides, 2,4-diaryl-1,3-selenazoles and 2,4-diaryl-1,3-chalcogen azoles bearing SF₅ group and organo phosphorus-chalcogen macrocycles incorporationg double OP(S)SC[sub]n or OP(Se)SeC[sub]n scaffolds. The basic theory of crystallography is introduced in Chapter 1, followed by a general discussion on pentafluorosulfuranyl (SF₅) containing heteroatom compounds and sulfur/selenium heterocycles in Chapter 2. Ten pentafluorosulfuranyl (SF₅)-containing aromatic compounds have been studied crystallographically in Chapter 3. All S-F bond lengths in these compounds are very similar [1.571(3) to 1.618(3) Å and 178.5(3) to 180.0° for the C-S-F(ax) bond] and the angles of two adjacent F(eq) is approximate to 90°. The intramolecular C[sub](aryl)-H···F(eq) and intermolecular C[sub](aryl)-H···O/N/F/Cl interactions, and π-stacking interactions are observed in the packing frameworks. X-ray crystal structure analysis reveals that in the structures of 2,4-diaryl-1,3-selenazoles in Chapter 4, the five-membered N-C-Se-C-C rings have either planar or near-planar conformations, and exhibit a series of the intramolecular and intermolecular C-H∙∙∙O/N/Se/Br/Cl) interactions and π-stacking interactions. The crystal structures of 2,4-diaryl-1,3-chalcogen azoles with both a pentafluorosulfuranyl (SF₅) group and a five-membered N-C-Se-C-C ring have been investigated in Chapter 5. A diverse picture of molecular configuration and intramolecular/intermolecular C-H∙∙∙N/Se/S and π-stacking interactions information are disclosed in selenamide, thiamides, 1,3-selenazoles and 1,3-thiazoles. Nine organo phosphorus-chalcogen macrocycles with nine- to fifteen-membered ring incorporating double OP(S)SC[sub]n or OP(Se)SeC[sub]n scaffolds have been discussed crystallographically in Chapter 6. The similar intramolecular and intermolecular C-H∙∙∙O, C-H∙∙∙S or C-H∙∙∙Se interactions are observed to lead to the similar packing networks.

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43

Lamont, R. Brian. "Studies of ring-chain tautomerism and molecular conformation by X-ray crystallography". Thesis, Queen's University Belfast, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.335988.

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44

Wong, S. F. "Synthesis, X-ray crystallography and '9'5Mo NMR spectroscopy of some molybdenum complexes". Thesis, University of Hertfordshire, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.377905.

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45

Ali, Rashid Majid Yousif. "Fragment-screening by X-ray crystallography of human vaccinia related kinase 1". Thesis, Linköpings universitet, Institutionen för fysik, kemi och biologi, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-166811.

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Fragment-screening by X-ray crystallography (XFS) is an expensive and low throughput fragment drug discovery screening method, and it requires a lot of optimization for each protein target. The advantages with this screening method are that it is very sensitive, it directly gives the three-dimensional structure of the protein-fragment complexes, and false positives are rarely obtained. The aim of this project was to help Sprint Bioscience assess if the advantages with XFS outweigh the disadvantages, and if this method should be used as a complement to their differential scanning fluorimetry (DSF) screening method. An XFS campaign was run using the oncoprotein vaccinia related kinase 1 (VRK1) as a target protein to evaluate this screening method. During the development of the XFS campaign, a diverse fragment library was created which consisted of 298 fragments that were all soluble in DMSO at 1 M concentration. The crystallization of the protein VRK1 was also optimized in this project to get a robust, high throughput crystallization set up which generated crystals that diffracted at higher resolution than 2.0 Å when they were not soaked with fragments. The soaking protocol was also optimized in order to reduce both the steps during the screening procedure and mechanical stress caused to the crystals during handling. Lastly, the created fragment library was used in screening VRK1 at 87.5 mM concentration with XFS. 23 fragment hits could be obtained from the X-ray crystallography screening campaign, and the mean resolution of the crystal structures of the protein-fragment complexes was 1.87Å. 11 of the 23 fragment hits were not identified as hits when they were screened against VRK1 using DSF. XFS was deemed as a suitable and efficient screening method to complement DSF since the hit rate was high and fragments hits could be obtained with this method that could not be obtained with DSF. However, in order to use this screening method a lot of time needs to be spent in optimizing the crystal system so it becomes suitable for fragment screening. Sprint Bioscience would therefore need to evaluate the cost/benefit ratio of using this screening method for each new project.

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46

Voss, James. "Chikungunya envelope glycoprotein structure at neutral PH determined by X-ray crystallography". Paris 7, 2011. http://www.theses.fr/2011PA077021.

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Le virus de Chikungunya (CHIKV) est un alphavirus émergent, transmis par les moustiques, qui a provoqué des épidémies de maladies débilitantes chez homme pendant les dernières cinq années. L'invasion de CHIKV dans les cellules sensibles est médiée par deux glycoprotéines virales, E1 et E2, qui portent respectivement les boucles de fusion à la membrane et les déterminants antigéniques principaux, et forment une couche protéinique icosaédrique à la surface du virion. La glycoprotéine E2, provenant du clivage par la furine du précurseur p62 (en E3 et E2), est responsable de la liaison au récepteur, tandis que E1 est impliqué dans la fusion membranaire. Dans le cadre d'un effort multidisciplinaire pour comprendre la biologie de CHIKV, nous avons déterminé les structures cristallines de l'hétérodimère précurseur immature (p62-E1; 2. 17 A de résolution) et du complexe mature (E3-E2-E1; 2. 6 A de résolution). Les structures atomiques nous ont permis de faire la synthèse d'une multitude de données génétiques, biochimiques, immunologiques et de microscopie électronique accumulées pendant plusieurs années sur les arbovirus en général. Cette analyse donne une image détaillée de l'architecture fonctionnelle de la couche de surface (25 MDa) des alphavirus. Les structures des complexes matures et immatures de CHIKV a aussi permis de décrire les causes et les mécanismes du changement de conformation des protéines d'enveloppe du virion lors du passage de celui-ci dans l'endosome à pH acide et précédant la fusion membranaire
Chikungunya is an emerging mosquito-bome alphavirus that has caused widespread outbreaks of debilitating human disease in the past five years. CHIKV invasion of susceptible cells is mediated by two viral glycoproteins, E1 and E2, which carry the main antigenic determinants and form an icosahedral shell at the virion surface. Glycoprotein E2, derived from furin cleavage of the p62 precursor to E3 and E2 is responsible for receptor binding and is the major viral antigen. The E1 protein is responsible for inducing the fusion of viral and cellular membranes in the target cell endosome which is required for release of the viral nucleocapsid into the cytoplasm to initiale infection of a cell. While the structure of E1 has been determined, the structure of E2"has remained elusive over the years. This thesis reports the atomic structures of the mature (E3/E2/E1) and immature (P62/E1) envelope glycoprotein complexes from Chikungunya virus determined by X-ray crystallography using a recombinant protein construct. This construct contained the covalently linked ectodomains of p62 and E1. Diffracting crystals of the purified complexes were obtained at neutral pH when the linker joining the ectodomains was cleaved. The glycoprotein structures were fit into reconstructions of the alphavirus virion obtained from cryo-electron microscopy (cryoEM). This analysis resulted in an inferred atomic model of the entire 25MDa surface of the highly conserved alphavirus virion and allowed for the synthesis of a wealth of genetic, biochemical, immunological and electron microscopy data accumulated over the years on alphaviruses in general

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47

Flood, Kelly-Jayne. "Comparative X-ray Structure Analyses of Multidentate Transition Metal Complexes". Thesis, University of Canterbury. Chemistry, 2006. http://hdl.handle.net/10092/1390.

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The biological significance of macrocyclic complexes has been recognized since they were first synthesized by Neil Curtis. They have the potential to play a critical role in mimicking metalloprotein active sites. Nine Curtis macrocyclic complexes have been studied using X-ray crystallographic techniques. Their structures have been solved and comparisons of the results have been made. Biological importance is also true of the macrocyclic counterpart; side-off and end-off compartmental ligands. In some circumstances these types of ligands are more appropriate because they have extra flexibility due to their pendant arms not being fixed in place by another head-unit, like a traditional macrocycle. The synthesis of a proposed compartmental ligand; 2,2-(N,Nʼ-bis(benzimidazole-2-ylmethyl)methylamine-5,5ʼ-di-tert-butyl-3,3ʼmethanediyl-dibenzyl alcohol (Ligand 1(L1)), has been proposed and outlined. The pendant arms: bis(benzimidazole-2-ylmethyl)amine (BBIM), were successfully synthesized and characterized with 1H NMR, IR and X-ray crystallography. The head-unit: 5,5ʼ-Di-tert-butyl-2,2ʼ-dihydroxy-3,3ʼ-methanediyl-dibenzene methanol (DHTMBA), of L1 was synthesized and characterized using 1H NMR, IR and mass spectrometry. A similar head-unit; 5,5ʼ-Di-methyl-2,2ʼ-dihydroxy-3,3ʼ-methanediyl-dibenzene methanol (DHMMBA), was synthesized in an effort to shorten the synthetic time of the head-unit. This was consequently converted to the chlorine analogue; 3,3ʼ-Bis(chloromethyl)-5,5ʼ-dimethyl-2,2ʼ-methane-diyldiphenol (Cl-DHMMB), and characterized with 1H NMR, IR and X-ray crystallography. Efforts were made to synthesize Ligand 1, but due to synthetic difficulties and time restraints this proved unsuccessful. Suggestions have been made to develop this synthesis.

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48

Zhang, Weizhe, i 张蔚哲. "Development of crystallographic phasing method and structural study ofDscam". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B46940996.

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49

Butterworth, Susanna. "Single crystal X-ray diffraction studies on small, medium and large molecules". Thesis, Durham University, 1996. http://etheses.dur.ac.uk/5352/.

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Chapter 1. Production of crystals for diffraction analysis would be assisted by the devising of a set of rules which, given molecular formula, could predict crystal formation conditions. By studying trends in structural properties of a group of closely related simple molecules, deductions could be drawn which could then be applied more generally. Chalcone derivatives with minor substituent differences were recrystallised. X-ray diffraction data collected and the structures solved and refined. Additionally, NMR and UV studies were performed, investigating an observed dimerisation reaction. Chapter 2. Discovery of peptide hormones and neurotransmitters has stimulated the study of structure-activity relationships, although the structure of these molecules is often poorly defined. Proctolin, a linear pentapeptide, is a neurotransmitter in insects. Crystallisation was attempted, with the aim of deducing the active conformation structure, thereby assisting in design of small molecule analogues for use as non-cholinergic pesticides. No diffraction was observed from the crystals produced. Chapter 3. Glucosamine 6-phosphate synthase is an N-terminal nucleophile amidotransferase catalysing the first step in the hexosamine pathway, from which all amino-sugar containing macromolecules are derived. Structure determination of each of two subdomains was attempted. In one case, pseudo-symmetry appeared to obstruct structure solution. The symmetry has subsequently been understood and the structure obtained. Crystals of the second domain are rotationally disordered. Chapters 4 and 5. Recent advances in macromolecular crystallographic techniques have facilitated the collection of an increasing number of high quality, atomic resolution data sets. Methods for refinement, previously limited to small molecule structures, have increasing relevance for proteins. Atomic resolution refinements using these evolving protocols have been performed on two small proteins, rubredoxin from Desulfovibrio vulgaris and the protein G immunoglobulin-binding domain. Appropriate treatment of the solvent structure in a protein crystal and the benefit to be gained by using sharpened density maps during refinement were investigated.

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Vandenakker, Focco. "X-ray crystallographic studies of heat-labile enterotoxins from Escherichia coli /". Thesis, Connect to this title online; UW restricted, 1997. http://hdl.handle.net/1773/9252.

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