This thesis describes the investigation of the coordination and supramolecular chemistry of three different types of pyridine-containing ligand with a selection of Ag(I), Cu(I), Cu(II) and Cd(II) salts. The ligand types are flexible and four-armed, rigid and four-armed and bent with two rigid arms. All the ligands also display the ability to form additional supramolecular interactions. Chapter one introduces supramolecular chemistry and crystal engineering and covers background on several areas of current interest in these fields. Network structures, both coordination polymers and hydrogen-bonded systems, are discussed and topological analysis as a method of describing and comparing network structures is introduced. An outline of the ligand design, choice of transition metals and anions is given. Chapter two provides a review of flexible four-armed pyridine-containing ligands and their use in coordination chemistry. The synthesis and characterisation of three flexible four-armed ligands 1,2,4,5-tetrakis(2-pyridylmethyl-sulfanylmethyl)benzene (2tet), 1,2,4,5-tetrakis(3-pyridylmethyl-sulfanylmethyl)benzene (3tet) and 1,2,4,5-tetrakis(4-pyridylmethyl-sulfanylmethyl)benzene (4tet) are given. The synthesis and characterisation of the Ag(I), Cu(II) and Cd(II) complexes formed with these three ligands are also given. The complex of [Cd(2tet)(NO₃)₄] was structurally characterised by X-ray diffraction and was found to be a discrete species. The complexes {[Ag₂(3tet)](ClO₄)₂}n̲, {[Ag₂(3tet)](PF₆)₂}n̲, {[Ag₂(3tet)](CF₃CO₂)₂}n̲, {[Ag₂(4tet)]-(ClO₄)₂�2MeCN�2CHCl₃}n̲, {[Ag₂(4tet)](PF₆)₂�6MeCN}n̲ and {[Ag₂(4tet)](ClO₄)₂-�3H₂O}n̲ were likewise structurally characterised by X-ray diffraction. All these complexes were three-dimensional coordination polymers. A comparison of the seven structures is given at the end of the chapter. Chapter three reviews rigid four-armed pyridine-containing ligands and their use in coordination chemistry. The preparation of the rigid four-armed ligand 2,3,4,5-tetrakis(4-pyridyl)thiophene (pyth) is given. The synthesis and characterisation of the Ag(I), Cu(I) and Cd(II) complexes formed with this ligand are also given. The complexes [Ag(pyth)](BF₄)�3MeCN�CH₂Cl₂}n̲, [Ag(pyth)](PF₆)�MeCN�CH₂Cl₂}n̲, [Ag(pyth)]-(CF₃SO₃)�2MeCN�CH₂Cl₂}n̲, [Cu(pyth)](PF₆)�MeCN�CH₂Cl₂}n̲ and [(Cu₂I₂)(pyth)]-(BF₄)�1/2CH₂Cl₂�H₂O}n̲ were structurally characterised by X-ray diffraction. The complex with CuI was a two-dimensional coordination polymer, and the other four complexes were three-dimensional coordination polymers. A comparison of the five structures is given at the end of the chapter. Chapter four begins with a review of rigid angular bridging ligands and their use in coordination and supramolecular chemistry. The preparation of the ligand bis(4-pyridyl)amine (bpa) is given. The structural arrangement of bpa in the solid state was determined by X-ray diffraction. Complexes of Ag(I), Cu(I), Cu(II) and Cd(II) formed with this ligand were synthesised and characterised. The complexes {[Ag(bpa)(MeCN)](CF₃SO₃)}n̲, {[Ag(bpa)](PF₆)�MeCN}n̲, {[Ag(bpa)](ClO₄)-�2MeCN}n̲, {[Ag(bpa)](ClO₄)}n̲, {[Ag(bpa)](NO₃)}n̲, [(Cu₂I₂)(bpa)₂]n̲, {[Cu(bpa)₂Cl₂]-�3DMF�3/2H₂O}n̲, {[Cd(bpa)₂(NO₃)(H₂O)](NO₃)}n̲, {[Cd(bpa)₂(SO₄)(H₂O)]�3H₂O}n̲, [Cd(bpaH)₂(SO₄)₂(H₂O)₂]�2MeCN and {[Cd(bpa)(SCN)₂]�1/5iPrOH}n̲ were structurally characterised by X-ray diffraction. All complexes with Ag(I) were one-dimensional coordination polymers, with two of them helical, the other three zigzag. Both complexes with Cu(I) and (II) were two-dimensional coordination polymers. One complex with CdSO₄ was discrete, with the bpa ligands mono-protonated, but all other three other Cd(II) complexes were three-dimensional coordination polymers. Seven of these complexes showed hydrogen-bonding interactions linking them together to form supramolecular structures of higher dimensionalities. A comparison of the twelve structures is given at the end of the chapter. Chapter five is a brief summary of the outcomes of this thesis.

The synthesis and coordination chemistry of eleven bridging ligands, eight of which are new compounds, are described. These ligands are all based on the tridentate terpyridyl system. The other metal ion binding sites of these ligands contain pyridine/bipyridine/pyrazole rings or amine/azamacrocycles domains. In these ligands, the two metal ion binding sites are differentiated by the number of atoms in each site, the configuration of the binding site or the types of donor atom that are present. This binding site differentiation allows to use the different coordination properties of the binding sites to control the regiochemistry of the complexation, ensuring that the correct metal ion is incorporated at the correct binding site in the ligand. Many of the complexes synthesised are mono-ruthenium(II) complexes where Ru(II) ions are situated in the terpyridyl sites of the ligands. These include heteroleptic Ru(II) complexes of the type [Ru(ttp)(L)]2+, where ttp is 4'-(p-tolyl)-2,2':6',2ʺ- terpyridine, and L is the bridging ligand. Reactions of the Ru(II) complexes with a range of metal ions including Co(III) ion have been investigated. The Ru(II) complexes can be classified into three main categories depending on the type of ligands that have been employed: (1) Ru(II) complexes which can react with Co(III) ions to form heterodinuclear Ru(II)-Co(III) complexes; (2) Ru(II) complexes which react only with Ag(I) ions and no other common metal ions that we have tried; (3) Ru(II) complexes with no detectable ability to coordinate other common metal ions. Following standard cobalt chemistry, some heterodinuclear Ru(II)-Co(III) complexes of the type [(ttp)Ru(cymt)Co(X)2]3+, where X = NO2 -, Cl-, and OH-, have been successfully prepared from the corresponding Ru(II) complexes. In these heterodinuclear complexes, anions such as NO2 -, Cl-, or OH- can be readily attached to the Co(III) ions. However, attachment of a neutral species such as en ligands to the Co(III) ions in the complexes proved to be more difficult. Reactions of heterodinuclear Ru(II)-Co(III) complexes with en ligands result in removal of the cobalt ions from the complexes. This is may be a result of a significant difference in the overall charges between the complexes with anionic and the complexes with neutral ligands (3+ vs 5+). Higher overall charge of the complexes when protonable ligands such as monodentate en are present, may destabilize the complexes even more. A combination of NMR spectroscopy, ESI-MS, UV-vis spectroscopy, elemental analysis, and X-ray crystallography has been used to characterise the ligands and their complexes. The crystal structures of one new ligand and sixteen complexes are described.

This thesis describes the preparation and characterisation of a number of homochiral coordination and metallosupramolecular assemblies. These species were formed from the reaction of chiral pyridine and quinoline containing ligands and metal ions. The combination of traditional coordination chemistry and supramolecular interactions led to a range of polymeric and network structures being formed. The ligands used in this thesis can be divided into two broad categories: alkaloids and ligands derived from them, and amino acid-based ligands. In the first category three new ligands were synthesized, and a variety of routes towards alkaloid-based homochiral ligands were investigated. The second category focused on three ligand motifs, and resulted in the preparation of 16 ligands. These two categories of ligands were reacted with a range of metal salts to investigate their coordination and supramolecular chemistry. The structure of twenty complexes was determined by single crystal X-ray crystallography. The complexes had a range of structures, with discrete and polymeric species being formed. Hydrogen bonding was an important feature in the supramolecular chemistry of the complexes, playing a different role in different series of complexes. Two chiral coordination polymers and one chiral coordination network were synthesized. All three of these structures possessed directionality to some degree: in the coordination network and one of the polymers the directionality is counterbalanced by the opposite directionality being present in the crystal, while the second coordination polymer is generated by the screw axis present and has a high degree of overall directionality.

Thesis (Ph. D.)--Ohio State University, 2007. / Title from first page of PDF file. Includes bibliographical references (p. 152-161).

Thesis (Ph. D.)--Michigan State University. Dept. of Chemistry, 2008. / Title from PDF t.p. (viewed on Aug. 20, 2009) Includes bibliographical references (p. 203-206). Also issued in print.

Thesis (Ph.D.)--McMaster University, 2004. / Advisor: G. J. Schrobilgen. Includes bibliographical references (leaves 333-352). Also available online.

Η μεταπτυχιακή εργασία αφορά στον δομικό χαρακτηρισμό πρωτεϊνών φαρμακευτικού ενδιαφέροντος. Στα πλαίσια της εργασίας πραγματοποιείται κρυστάλλωση και μετρήσεις περίθλασης ακτινών-Χ. Κρυσταλλογραφικές μέθοδοι εφαρμόζονται για την ανάλυση και την ερμηνεία των πειραματικών δεδομένων. Επιπλέον, σε συνεργασία με την φαρμακευτική εταιρεία Novo Nordisk A/S μελετάμε την ενδεχόμενη δημιουργία φαρμάκων υπό την μορφή μικροκρυσταλλικών ιζημάτων η οποία έχει εφαρμοστεί ήδη στην περίπτωση της ανθρώπινης ινσουλίνης. Τα πλεονεκτήματα των μικροκρυσταλλικών φαρμάκων έναντι των φαρμάκων υπό την μορφή διαλύματος περιλαμβάνουν την μεγαλύτερη σταθερότητα, υψηλότερη συγκέντρωση φαρμακευτικής ουσίας και τον ακριβή δομικό χαρακτηρισμό του μορίου . Η τεχνική περίθλασης ακτινοβολίας από πολυκρυσταλλικά υλικά (powder diffraction) αποτελεί ένα σημαντικό εργαλείο για τον χαρακτηρισμό των διάφορων πολυμόρφων πρωτεϊνικών μικροκρυσταλλικών ιζημάτων. Για αυτό τον σκοπό, πραγματοποιούμε πειράματα κρυστάλλωσης των υπό μελέτη βιομορίων κάτω από διαφορετικές συνθήκες (pH, προσδέτες) και στη συνέχεια, συλλέγουμε δεδομένα περίθλασης ακτινών-Χ από επιλεγμένα δείγματα, χρησιμοποιώντας όργανα υψηλής ευκρίνειας που βρίσκονται σε ερευνητικά ινστιτούτα μεγάλης κλίμακας (Ευρωπαϊκό σύγχροτρον, ESRF, Grenoble, France & Ελβετικό σύγχροτρον, SLS, Villigen, Switzerland). / The main subject of this master thesis is the structural characterization of pharmaceutically interesting proteins. For this purpose, protein crystallization experiments, as well as X-ray diffraction measurements were conducted. Crystallographic methods were employed for the analysis and interpretation of the experimental data. Furthermore, in collaboration with the pharmaceutical company Novo Nordisk A/S, we are investigating the possibility of developing polycrystalline drug formulations, as has already been done in the case of human insulin. The advantages of polycrystalline drugs, as opposed to drugs in solution, include higher stability and concentration of the pharmaceutical substance, as well as allowing for its accurate structural characterisation. The technique of X-ray powder diffraction is considered an important tool for the characterization of the various protein polymorphs that form polycrystalline precipitates. Protein crystallization experiments were performed under a variety of conditions (such as pH alteration, co-crystallization with ligands) and X-ray powder diffraction data were collected using high resolution instruments (European Synchrotron Radiation Facility, ESRF and Swiss Light Source, SLS).

No description available.

La transcription des gènes humains par la polymérase II (Pol II) commence avec l'assemblage du complexe de pré-initiation (PIC) au niveau du promoteur. L'assemblage du PIC est initié par le facteur de transcription général TFIID, un complexe de protéines faisant 1 mégadalton et contenant TBP et 13 facteurs TBP-associés (TAF). Des études structurales sur TFIID par cryo-EM ont révélé l'architecture globale de TFIID, donnant un aperçu de l'assemblage des sous-unités et la reconnaissance du promoteur à faible et moyenne résolution. Cependant, les structures à haute résolution de plusieurs TAF ne sont pas disponibles à ce jour, ce qui limite notre compréhension actuelle des interactions TAF-TAF et du mécanisme d'assemblage de TFIID.J'ai utilisé une stratégie de co-expression dans des cellules d'insectes sur la base de notre système MultiBac afin d'obtenir des sous-complexes recombinants TFIID de qualité sans précédent et de quantité suffisante pour des études structurales. J'ai cristallisé un complexe contenant les TAFs TAF5, TAF6 et TAF9 et déterminé sa structure à une résolution de 2.7 Å. Notre structure donne des aperçus détaillés sur les interactions de ces sous-unités essentiels de TFIID: La structure révèle des interactions serrés inattendues entre le domaine N-terminal et le domaine à répétition WD40 contenant 7 lames de TAF5 avec le domaines "histone fold" (HFDs) de TAF6/9. Les interactions entre ces domaines conservés inter-espèces expliquent en détail comment TAF5 sert de plate-forme de liaison pour les HFDs dans TFIID. Cette étude étend notre compréhension de l'échafaudage moléculaire au noyau central de la version humaine de TFIID, ce qui est essentiel pour la formation de holo-TFIID.De plus, j'ai pu isoler un domaine structural conservé de la version humaine de TAF6, le domaine à répétition HEAT de TAF6 en utilisant une approche de protéolyse limitée sur des core-complexes TAF5/6/9 prédéfinis. J'ai pu déterminer la structure du domaine à répétition HEAT de TAF6 jusqu'à 2,0 Å de résolution. La structure offre un éclairage supplémentaire sur l'architecture de la version humaine de TFIID et révèle la présence d'une grande zone chargée positivement sur sa surface, probablement impliqué dans la liaison à l'ADN du noyau promoteur liaison.Basé sur les structures résolues et les informations obtenues dans des expériences de protéolyse limitée, j'ai pu identifier les complexes minimaux de la base du complexe TFIID humain (TAF 4/5/6/9/12). J'ai identifié les HFDs de l'hétérodimère TAF4/12 comme étant essentielle à la formation d'un complexe avec TAF5/6/9. Ces résultats guideront la conception future de construction pour la cristallisation du complexe humain TFIID de base, améliorant ainsi nos connaissances sur le mécanisme d'assemblage de TFIID ainsi que sur l'architecture de ses principaux composants à une résolution atomique. / Human gene transcription by Polymerase II (PolII) begins with the assembly of the pre-initiation complex (PIC) at the promoter. PIC assembly is initiated by the general transcription factor TFIID, a megadalton sized protein complex containing TBP and 13 TBP associated Factors (TAFs).
Structural studies on TFIID by cryo-EM have revealed the overall architecture of TFIID, providing insights into subunit assembly and promoter recognition at low to medium resolution. However, high-resolution structures of several TAFs are not available to date, limiting our current understanding of TAF-TAF interactions and the assembly mechanism of TFIID.I used a co-expression strategy in insect cells based on our MultiBac system to obtain recombinant TFIID sub-complexes of unprecedented quality and quantity for structural studies. I crystallized a complex containing the TAFs TAF5, TAF6 and TAF9 and determined its structure up to a resolution of 2.7 Å. Our structure gives detailed insights into the interactions of these essential TFIID subunits: The structure reveals unexpected tight interactions between the N-terminal domain and the 7-bladed WD40 repeat domain of TAF5 with the TAF6/9 histone fold domains (HFDs). The interactions between these inter-species conserved domains explain in detail how TAF5 serves as a binding platform for HFDs in TFIID. This study extends our understanding of the molecular scaffold at the central core of human TFIID, which is essential for holo-TFIID formation.Additionally, I could isolate a conserved structural domain of human TAF6, the TAF6 HEAT repeat domain by using a limited proteolysis approach on predefined TAF5/6/9 core-complexes. I could determine the structure of the TAF6 HEAT repeat domain up to 2.0 Å resolution. The structure provides additional insights into the architecture of human TFIID and reveals the presence of a large positively charged patch on its surface, probably involved in core-promoter DNA binding.Based on the obtained structures and information gained in limited proteolysis experiments, I was able to identify minimal complexes of human core-TFIID (TAFs 4/5/6/9/12). I identified the HFDs of the TAF4/12 heterodimer to be essential for the complex formation with TAF5/6/9. These findings will guide future construct design for crystallization of human core-TFIID, enhancing our knowledge about the TFIID assembly mechanism and the architecture of its core-components at atomic resolution.

Orientador: Marcos Roberto de Mattos Fontes / Banca: Richard Charles Garrat / Banca: Antonio José da Costa Filho / Resumo: As serpentes do gênero Bothrops são de grande interesse científico, médico e social para o Brasil, visto que este gênero é responsável por cerca de 90% dos acidentes ofídicos que ocorrem em nosso país. Dois dos principais componentes do veneno desses animais são as fosfolipases A2 e as serino proteases. As fosfolipases A2 são enzimas responsáveis pela destruição da membrana celular através da hidrólise de fosfolipídios Ca2+ dependente. Uma classe destas fosfolipases, as fosfolipases homólogas (Lys49-PLA2s), que se caracteriza pela uma substituição natural na posição 49 de um resíduo de Asp para um resíduo de Lys, não apresenta atividade catalítica, mas é capaz de induzir mionecrose por um mecanismo Ca2+ independente devido, provavelmente, à resíduos da região C-terminal. Neste trabalho, através de estudos por cristalografia de raios-X de Lys49-PLA2s botrópicas nativas e quimicamente modificadas pelo brometo de p-bromofenacila (BPB), revisamos a posição da Lys122 - anteriormente apontado como um dos responsáveis ela ausência da atividade catalítica das Lys49-PLA2s por conta da hiperpolarização que causaria na ligação peptídica Cys29/Gly30 - e concluímos que, por conta de esta hiperpolarização ocorrer apenas em alguns monômeros de Lys49-PLA2s complexadas, a Lys122 não deve estar envolvida no "bloqueio" da atividade catalítica. Além disso, a comparação estrutural do loop de ligação de Ca2+ entre as Lys49 e Asp49-PLA2s nos mostra a importância da conservação da Tyr28 dentre as Asp49-PLA2s para a integridade do loop de ligação do Ca2+. Este resíduo estabiliza essa região através de uma ponte de hidrogênio com a Gly35. Nas Lys49-PLA2s, que possuem um resíduo de Asn na posição 28, não ocorre a formação dessa ponte, o que contribuiria para a desestabilização dessa região nessas proteínas ...(Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The snakes from Botrops genus are objects with great scientific, medical and social interesting since that these snakes are responsible of 90% of snakebites in our country. Two of the main components of the venom from these animals are the phospholipases A2 and the serine proteases. The phospholipases A2 are enzymes responsible of cellular membrane disruption through phospholipids hydrolysis Ca2+-dependent. A class of these phospholipases, the homolog phospholipases (Lys49-PLA2s) that underwent a natural substitution Lys to Asp substitution in 49 position, does not show catalytic activity. However, these proteins can perform myonecrosis by a Ca2+-independent mechanism probably, due to action of C-termini region residues. In this work, by x-ray crystallography studies with bothropic Lys49-PLA2s in native and chemically modified by p-bromophenacyl bromide (BPB) forms, we revised the position of Lys122, previously pointed as one of the responsibles of Lys49-PLA2s due to hiperpolarization of its side chain on Cys29/Cys30 peptide bond. Here, we conclude that this hiperpolarization are present only in a few monomers and thus, Lys122 may not be involved in the "blocking" of catalytic activity. Furthermore, structural comparisons of Ca2+ binding loop between Lys49 and Asp49-PLA2s revels the importance of the Tyr28 residue conservation to the integrity of this region. This residue stabilizes the Ca2+ binding loop by a hydrogen bond to Gly35. In Lys49-PLA2s that have an Asn residue in 28 position, does not occur the formation of this bond, contributing to unstabilization of this region and difficulting the binding of Ca2+ cofactor. Phylogenetic studies showed that Asp49- PLA2s with reduced catalytic inactivity and capable to induce myonecrosis are phylogenetic more related to Lys49-PLA2s than to others Asp49-PLA2s, forming a ...(Complete abstract click electronic access below) / Mestre