This thesis is focused on determining the structures of two anti-carbohydrate antibodies to understand how they achieve their specificity toward antigen. First, the structure of the antigen-binding fragment from the monoclonal antibody S64-4 in complex with a pentasaccharide bisphosphate fragment from chlamydial lipopolysaccharide (LPS) has been determined by x-ray diffraction to 2.6 Å resolution. Like the well-characterized antibody S25-2, S64-4 displays a pocket formed by the residues of germline sequence corresponding to the heavy and light chain V gene segments that binds the terminal Kdo (3-deoxy-α-D-manno-oct-2-ulopyranosonic acid) residue of the antigen; however, although S64-4 shares the same heavy chain V gene segment as S25-2, it has a different light chain V gene segment. The new light chain V gene segment codes for a combining site that displays greater avidity, different specificity, and allows a novel antigen conformation that brings a greater number of antigen residues into the combining site than possible in S25-2. Further, while antibodies in the S25-2 family use complementarity determining region (CDR) H3 to discriminate among antigens, S64-4 achieves its specificity via the new light chain V gene segment and resulting change in antigen conformation. These structures reveal an intriguing parallel strategy where two different combinations of germline-coded V gene segments can act as starting points for the generation of germline antibodies against chlamydial antigens and show how anti-carbohydrate antibodies can exploit the conformational flexibility of this class of antigens to achieve high avidity and specificity independently of CDR H3. Second, the structure of a rabbit, single chain variable fragment against terminal mannose-6-phosphate (Man6P) residues, termed scFv M6P-1, has been determined by x-ray diffraction to 2.7 Å resolution with Man6P in the binding site. The Man6P pathway is the predominant pathway that transports acid hydrolases from the trans-Golgi to endosomes. Newly synthesized hydrolases first require the generation of Man6P markers before they can be transported. Maintaining a full complement of hydrolases within lysosomes is essential as failure to do so results in a number of different lysosomal storage diseases. Due to its specificity, scFv M6P-1 is able to diagnose lysosomal storage diseases mucolipidosis II and mucolipidosis III. scFv M6P-1 is also able to purify Man6P containing proteins which may be useful for enzyme replacement therapies. Additionally, scFv M6P-1 is one of the first structures of an antibody fragment that exhibits high specificity for a single carbohydrate residue and is one of the first structures of a rabbit antibody fragment. The specificity of scFv M6P-1, which gives it these unique attributes, is revealed in the structure where multiple hydrogen bonds are seen between the antibody’s heavy chain and the mannose ring while two salt bridges are observed between the antibody’s light chain and the phosphate moiety. Finally, scFv M6P-1 binds in such a way as to allow binding to proteins possessing terminal Man6P residues. Crystallographic challenges that arose during this research included poor crystal growth as well as twinning and these are explored while the structure of scFv M6P-1 complex with Man6P is analysed. / Graduate / 0487 / 0982 / 0307 / dyl.w.evans@gmail.com

With combination of the both ferroelectric and ferromagnetic and mutural coupling properties, multiferroics attracts a lot of researcher¡¦s attentions. Among these very popular materials, such as REMnO (113 series, 125 series), BiFeO3 etc¡K , the BiFeO3 interests us the most for it manifests multiferroic effects above the room temperature. However, the pure BiFeO3 phase is very difficult to form and a serious lost of Bi creates complex grain boundaries that produces enormous electric leaking. In this study, Pb is doped into BiFeO3 in Bi sites and we hope this doping effect may increase the stability and the ferroelectricity of Bi1-xPbxFeO3. It is found that the crystal structure is changed dramatically, because of the doping of Pb, from the rhombohedra structure of the parent pure BiFeO3 to the cubic structure of Bi0.85Pb0.15FeO3. By the Pb doping, the compounds exhibit free from impurity phases and the dielectric constants are enhanced qualitatively to the doping levels.

No description available.

This thesis is focused on determining the structures of two anti-carbohydrate antibodies to understand how they achieve their specificity toward antigen. First, the structure of the antigen-binding fragment from the monoclonal antibody S64-4 in complex with a pentasaccharide bisphosphate fragment from chlamydial lipopolysaccharide (LPS) has been determined by x-ray diffraction to 2.6 Å resolution. Like the well-characterized antibody S25-2, S64-4 displays a pocket formed by the residues of germline sequence corresponding to the heavy and light chain V gene segments that binds the terminal Kdo (3-deoxy-α-D-manno-oct-2-ulopyranosonic acid) residue of the antigen; however, although S64-4 shares the same heavy chain V gene segment as S25-2, it has a different light chain V gene segment. The new light chain V gene segment codes for a combining site that displays greater avidity, different specificity, and allows a novel antigen conformation that brings a greater number of antigen residues into the combining site than possible in S25-2. Further, while antibodies in the S25-2 family use complementarity determining region (CDR) H3 to discriminate among antigens, S64-4 achieves its specificity via the new light chain V gene segment and resulting change in antigen conformation. These structures reveal an intriguing parallel strategy where two different combinations of germline-coded V gene segments can act as starting points for the generation of germline antibodies against chlamydial antigens and show how anti-carbohydrate antibodies can exploit the conformational flexibility of this class of antigens to achieve high avidity and specificity independently of CDR H3. Second, the structure of a rabbit, single chain variable fragment against terminal mannose-6-phosphate (Man6P) residues, termed scFv M6P-1, has been determined by x-ray diffraction to 2.7 Å resolution with Man6P in the binding site. The Man6P pathway is the predominant pathway that transports acid hydrolases from the trans-Golgi to endosomes. Newly synthesized hydrolases first require the generation of Man6P markers before they can be transported. Maintaining a full complement of hydrolases within lysosomes is essential as failure to do so results in a number of different lysosomal storage diseases. Due to its specificity, scFv M6P-1 is able to diagnose lysosomal storage diseases mucolipidosis II and mucolipidosis III. scFv M6P-1 is also able to purify Man6P containing proteins which may be useful for enzyme replacement therapies. Additionally, scFv M6P-1 is one of the first structures of an antibody fragment that exhibits high specificity for a single carbohydrate residue and is one of the first structures of a rabbit antibody fragment. The specificity of scFv M6P-1, which gives it these unique attributes, is revealed in the structure where multiple hydrogen bonds are seen between the antibody’s heavy chain and the mannose ring while two salt bridges are observed between the antibody’s light chain and the phosphate moiety. Finally, scFv M6P-1 binds in such a way as to allow binding to proteins possessing terminal Man6P residues. Crystallographic challenges that arose during this research included poor crystal growth as well as twinning and these are explored while the structure of scFv M6P-1 complex with Man6P is analysed. / Graduate / 0487 / 0982 / 0307 / dyl.w.evans@gmail.com

The main objective of this research is to advance our understanding of the biochemical properties and the structure-function relationships of the chloroplast glycerol-3-phosphate acyltransferases in plants. De novo synthesised fatty acyl chains are diverted into the prokaryotic pathway of plant lipid biosynthesis by a soluble glycerol-3-phosphate acyltransferase (GPAT [EC. 2.3.1.15]) in the chloroplast. GPAT catalyses acylation at the sn- 1 position of sn-glycerol-3-phosphate to form lysophosphatidic acid. Recombinant GPAT from squash and Arabidopsis were overproduced in Escherichia coli, purified to about 23- fold and 90% pure enzyme using a procedure developed in this study. Antibodies were raised in rabbits against these denatured recombinant GPAT preparations and four peptide antigens, and preliminary experiments were performed to test their suitability for use in Western blotting. In collaboration with the University of Sheffield, squash GPAT was successfully crystallised, isomorphous heavy metal derivatives prepared and the complete 3-dimensional structure of the protein at 2.3 Angstrom resolution determined. The cloning, functional expression and characterisation of a novel GPAT from oil palm, 'domainswap' chimeric recombinant proteins of Arabidopsis and squash GPAT, and spinach and squash GPAT respectively, and the influence of the N-terminal domain and amino acid substitutions in the C-terminal domain of the squash GPAT, was described. By determining the apparent kinetic constants for acyl-ACP substrates of most of the enzymes and by in vitro assays using mixtures of two acyl-ACP substrates under physiologically relevant conditions, it was found that their substrate selectivities could be dramatically altered. The development of ribozyme- technology as a molecular tool to down-regulate the gene expression of one out of multiple GPATs, was initiated. The strategy would allow for a phenotypic indication of ribozyme- efficacy in vivo and may help further contribute to the role of glycerol-3-phosphate acyltransferase in processes determining the phenomenon of chilling-sensitivity of plants.

Pure intermetallic compounds Al3Fe, AlmFe, AlxFe, ac-AlFeSi, and Al6(Fe,Mn) have been extracted from Bridgman grown model aluminium alloys by dissolving the aluminium matrix in butanol. The resultant transmission Mdssbauer spectra for each intermetallic compound were interpreted according to their crystal structure. Variable temperature 57Fe Mdssbauer studies have enabled the Debye temperature thetaD of each compound to be determined. The crystal structure of Al3Fe contains five different Fe sites within the unit cell. Four of the iron, Fe(l)-Fe(4), sites are approximately identical and produced a thetaD = 434 +/- 5 K. The remaining Fe site, Fe(5), produced a thetaD = 488 +/- 5 K, and the combined spectral areas a 3D = 452 +/- 5 K. There is only one individual site within the crystal structures of AlmFe, AlxFe, and Al6(Fe,Mn), which produced a thetaD of 358 +/- 5 K, 360 +/- 5 K, and 352 +/- 5 K respectively. The ternary intermetallic compound, ac-AlFeSi, has two different Fe sites within the unit cell. Fe(l) had a thetaD - 291 +/- 5 K, and Fe(2) thetaD = 329 +/- 5 K. The combined spectral areas of these two sites produced a thetaD = 311 +/- 5 K. The variation in the OD values was attributed to changes in the Al-Fe shortest bond within the Fe centred A1 polyhedra. The Fe centred A1 polyhedra are a common feature of all the intermetallic compounds studied. The iron atom in all the intermetallic compounds may have existed in a Fe2+ oxidation state. A Direct Chill-cast ingot was grown and two samples, A and B, were taken from regions within the ingot containing a mixture of two intermetallic compounds. Alloy sample A was found to contain the intermetallic compound combination Al3Fe + Al6Fe. The intermetallic combination Al6Fe + ac- AlFeSi was found to exist in alloy sample B. Transmission Mdssbauer spectroscopy was performed on the extracted phases and the insitu phases to determine the relative proportions of the intermetallic compounds within the two alloy samples. Alloy sample A had 50:50 +/- 5 % Al3Fe + Al6Fe, whereas alloy sample B had 30:70 +/- 5 % Al6Fe + ac-AlFeSi. The surface of alloy sample B was investigated using several surface techniques, CEMS, SAAES, and SAXPS, to determine whether the same relative proportions existed in the surface, and near surface, regions of the sample. A region of very fine amorphous iron super-paramagnetic grains were to dominate the near surface region of the sample, which was present due to selective oxidation of the Al6Fe intermetallic compound. This was then removed when the surface of the alloy sample was KI electro-etched, which had the effect of leaving the intermetallic particles standing proud of the surface. The CEMS technique identified that the Al6Fe + ac-AlFeSi existed in a 80:20 +/- 5 %. This change in phase ratio after the KI electro-etch process was attributed to the preferential etching of the ac-AlFeSi aluminium intermetallic compound.

Following an introoduction on calixarene chemistry and their metal-ion complexes including some of their applications, the aims of the work are described. Thus, the first part of this thesis concerns the detemination of the standard enthalpies of solution, sH°, of new lithium and sodiimi 1:1 electrolytes based on eth p=tert-butycalix[4]arene tetraethanoate containing various anions in acetonitrile at 298.15 K. Using these data in conjunction with previously reported sH° values for the free metal-ion salts and the ligand and standard enthalpies of complexation, cH°H° of allcali-metal cations (Li+ and Na+) and the calix[4]arene ester in the same solvent, standard enthalpies of coordination, coordH° referred to the process in which the reactants and the product are in the solid stated were calculated. The anion effect on the coordination process was determined. The second part of this thesis is related to an investigation on the solution properties of pyridinocalix[4]arenes and their metal-ion complexes. Transfer Gibbs energies of geometrical isomers of pyridinocalix[4]arenes from acetonitrile to various solvents reflect that these ligands undergo selective solvation in the various solvents but these cannot be correlated with any single solvent property. The complexing ability of 5,11,17,23 - tetra - tert - butyl[25,26,27,28 - tetrakis (2-pyridyhnethyl) oxy]- calix[4]arene for metal cations was investigated by a variety of techniques. Thus 1H NMR studies were performed to obtain information about the active sites of the ligand in its interaction with metal cations. Conductance measurements were used to establish the composition of the metal-ion complexes in dipolar aprotic media. Potentiometric and calorimetric measurements were performed to derive the thermodynamics associated with the complexation process in acetonitrile and benzonitrile. Based on stability constant data, two metal-ion complexes were isolated. The crystal structure of the sodium and acetonitrile complex of 5,11,17,23- tetra- tert- butyl[25,26,27,28 - tetrakis (2-pyiidylmethyl)oxy] calix[4] arene solved by X-ray diffraction studies shows three different complexes in the lattice, two sited on a fourfold axis and a third one on a twofold axis where all ligands exhibit a 'cone' conformation and the sodium ion is encapsulated in their hydrophilic pockets with their hydrophobic cavities filled with an acetonitrile molecule. The crystal structure of the 1:1 monoacetonitrile and silver complex of the 2-pyridyl derivative with the perchlorate ion as the counter ion shows the macrocycle sited on a fourfold symmetry axis. The presence of acetonitrile in the hydrophobic cavity of the ligand is also found. The silver cation is encapsulated in the hydrophilic cavity through the ethereal oxygens and the pyridinic nitrogens. Conclusions and suggestions for furthur research in this area are given.

京都大学 / 新制・課程博士 / 博士(理学) / 甲第23026号 / 理博第4703号 / 新制||理||1674(附属図書館) / 京都大学大学院理学研究科化学専攻 / (主査)教授 北川 宏, 教授 吉村 一良, 教授 有賀 哲也 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

A series of new germanates was prepared and their structures were characterized with X-ray diffraction (XRD). We employed solid-state synthesis, flux growth, and crystallization from melts to obtain crystals of the new materials. The crystals were studied by means of single crystal XRD, providing the information on the structure and composition of the new materials. Germanates suitable to accommodate Mn4+ – a well-known activator ion for the preparation of the rare-earth-free red phosphors – were of a particular interest. The Ge4+ substitution for Mn4+ is possible if the crystal structure features octahedrally coordinated germanium atoms, and we indeed were able to prepare such germanates. The crystal structures of the following phases were characterized: Mg3Ge1-O4(1-)F2(1+2) ( ≈ 0.1), Mg14Ge4O20F4, Mg2Pb2Ge2O7F2, Sr3GeO4Cl2, Ba3GeO4Br2, Sr6Ge2O7Cl6, Ba5GeO4Br6, Na2BaGe8O18, Rb2BaGe8O18, Na0.36Sr0.82Ge4O9, Na2SrGe6O14, and K2SrGe8O18. Two phases, Mg3Ge1-O4(1-)F2(1+2) and Na0.36Sr0.82Ge4O9 demonstrate deficiency on certain crystallographic sites. We analyzed the connectivity of the GeO4 and GeO6 units in the new and reported tetra- and octagermanates. Despite the similar stoichiometry, the connectivity of GeOn polyhedra is different in RI2Ge4O9, RIIGe4O9 and RIRIIGe8O18 germanates (RI = alkali, RII = alkaline earth metal). The Ge4+ substitution for Mn4+ was successfully done for the Na2BaGe8O18, Rb2BaGe8O18, Na2SrGe6O14, and K2SrGe8O18 phases yielding new red phosphors. Based on the powder XRD data, the optimal synthetic strategies were developed yielding high purity (≈ 99 wt. %) samples. The photoluminescent excitation and emission spectra were collected for the new phosphors. Strong absorption of the UV light and emission in the far-red region of the visible spectra were confirmed, which is in a good agreement with the literature. The Mn4+ doping level was optimized to achieve the highest luminescence in the studied phases. Temperature-dependent luminescence spectra were collected for the Na2SrGe6O14 : Mn4+ and K2SrGe8O18: Mn4+, and the K2SrGe8O18: Mn4+ showed the highest resistance to temperature quenching. / Thesis / Doctor of Philosophy (PhD)

<p> The crystal structure of dioxotetrapyridine-rhenium(V) chloride dihydrate has been determined by single crystal x-ray diffraction methods. The structure has been found to belong to the trans-dioxo- group of compounds. The Re=O bond in the structure has been shown to have a bond-order of about 2, with the average Re=O bond length of 1.76(J) A. The probable structures of the monohydrate and anhydrous dioxotetrapyridine-rhenium(V) chloride have been discussed on the basis of the observed pseudo-symmetric structure for the dihydrate with a non-centrosymmetric space group. The nature and strength of the hydrogen bonds in the structure have also been discussed.</p> / Thesis / Master of Science (MSc)