To Hing-lun. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references. / Abstracts in English and Chinese. / ABSTRACT --- p.i / 摘要 --- p.ii / ACKNOWLEDGMENT --- p.iii / CONTENTS --- p.iv / ABBREVIATIONS --- p.vi / Chapter CHAPTER 1 --- Synthesis and Reactivity Studies of Copper Complexes Supported by a Pyridine-Containing Ligand / Chapter 1.A. --- General Introduction / Chapter 1.A.I. --- Introduction --- p.1 / Chapter 1.A.II. --- Dioxygen Activation by Copper-Containing Species --- p.2 / Chapter 1 A.III. --- Reactivity of Copper(I) Complexes Towards Dioxygen Binding --- p.11 / Chapter 1.A.IV. --- Synthetic Models for Copper-Containing Proteins --- p.12 / Chapter 1.A.V. --- Objective of This Work --- p.27 / Results and Discussion / Chapter 1.B. --- Synthesis and Characterization / Chapter 1.B.I. --- Synthesis / Chapter 1.B.I.a. --- Ligand Synthesis --- p.28 / Chapter 1.B.I.b. --- Synthesis of Copper(I) Complexes --- p.31 / Chapter 1.B.II. --- Characterization / Chapter 1.B.II.a. --- Physical Characterization of Complex25 --- p.33 / Chapter 1.B.II.b. --- Structural Studies / Chapter 1.B.II.b.i. --- Molecular Structure of Complex25 --- p.34 / Chapter 1.B.II.b.ii. --- Comparisons of The Structural Parameters of 25 with Those of 24 and Other [Cu1(u-Br)]2 Complexes --- p.37 / Chapter 1.B.II.c. --- Electrochemical Studies --- p.38 / Chapter 1.C. --- Reactivity Studies --- p.40 / Chapter 1.D. --- Summary --- p.44 / Chapter 1.E. --- Experimental Procedures --- p.45 / Chapter 1.F. --- References --- p.54 / Chapter CHAPTER 2 --- Synthesis and Reactivity Studies of Nickel Complexes With a N3O-Donor Ligand / Chapter 2.A. --- General Introduction / Chapter 2.A.I. --- Introduction --- p.61 / Chapter 2.A.II. --- Studies of Metal-Phenoxyl Radical Arrays --- p.67 / Chapter 2.A.III. --- Objective of This Work --- p.72 / Results and Discussion / Chapter 2.B. --- Synthesis and Characterization / Chapter 2.B.I. --- Synthesis of Nickel(II) Complexes --- p.73 / Chapter 2.B.II. --- Characterization / Chapter 2.B.II.a. --- Physical Characterization of Complexes 34 and 35 --- p.75 / Chapter 2.B.II.b. --- Structural Studies / Chapter 2.B.II.b.i. --- Molecular Structure of Complex 34 --- p.75 / Chapter 2.B.II.b.ii. --- Molecular Structure of Complex 35 --- p.78 / Chapter 2.B.II.b.iii. --- Structural Comparisons --- p.81 / Chapter 2.B.II.c. --- Electrochemical Studies --- p.82 / Chapter 2.C. --- Reactivity Studies --- p.84 / Chapter 2.D. --- Summary --- p.90 / Chapter 2.E. --- Experimental Procedures --- p.91 / Chapter 2.F. --- References --- p.94 / APPENDIX A General Procedure and Physical Measurements / Chapter A.I. --- General Procedures --- p.99 / Chapter A.II. --- Physical Measurements --- p.100 / APPENDIX B Crystallographic Data / Chapter B.I. --- Selected Crystallographic Data for Compounds 25，34 and 35 --- p.102

by Chan Sau Han. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2001. / Includes bibliographical references. / Abstracts in English and Chinese. / ABSTRACT --- p.i / 摘要 --- p.ii / ACKNOWLEDGMENT --- p.iii / CONTENTS --- p.iv / ABBREVIATIONS --- p.vi / Chapter CHAPTER 1 --- General Introduction / Chapter 1-A. --- Role of Copper in Biology --- p.1 / Chapter 1-B. --- A Brief Review on Radical Copper Proteins --- p.4 / Chapter 1-C. --- Objectives of This Work --- p.12 / Chapter 1-D. --- References --- p.13 / Chapter CHAPTER 2 --- Copper(II) and Zinc(II) Complexes containing N3O Tetradentate Ligands / Chapter 2-A. --- Introduction Results and Discussion --- p.14 / Chapter 2-B. --- Preparation of Tetradentate Ligands and Complexes --- p.27 / Chapter 2-C. --- Characterization --- p.36 / Chapter 2-D. --- Generation of Metal Phenoxyl Radical Species --- p.51 / Chapter 2-E. --- Summary --- p.57 / Chapter 2-F. --- References --- p.59 / Chapter CHAPTER 3 --- Copper(I) Complexes with N30 Tetradentate Ligands / Chapter 3-A. --- Introduction Results and Discussion --- p.62 / Chapter 3-B. --- Preparation of Copper(I) Complexes with N30 Tetradentate Ligands --- p.75 / Chapter 3-C. --- Characterization --- p.79 / Chapter 3-D. --- Reactivities of 86，87 and 88 toward Dioxygen --- p.88 / Chapter 3-E. --- Summary --- p.93 / Chapter 3-F. --- References --- p.94 / Chapter CHAPTER 4 --- Experimental Sections / Chapter 4-A. --- General Preparations and Physical Measurements --- p.97 / Chapter 4-B. --- Compounds Described in Chapter2 --- p.99 / Chapter 4-C. --- Compounds Described in Chapter3 --- p.113 / Chapter 4-D. --- Oxo-Transfer to Triphenylphosphine as Described in Chapter3 --- p.117 / Chapter 4-E. --- References --- p.119 / Chapter APPENDIX A --- 1H and13 C̐ưث1H ̐ưحNMR Spectra / Chapter A-1. --- Compounds Described in Chapter2 --- p.120 / Chapter A-2. --- Compounds Described in Chapter3 --- p.127 / Chapter APPENDIX B --- Crystallographic Data / Chapter B-1. --- X-ray Crystal Structure Data for Complexes in Chapter2 --- p.131 / Chapter B-2. --- X-ray Crystal Structure Data for Complexes in Chapter3 --- p.133 / Chapter APPENDIX C --- GC-MS Spectra / Chapter C-1. --- GC-MS Spectra for Standard Samples --- p.134 / Chapter C-2. --- GC-MS Spectra for the Reactions with Triphenylphosphine Described in Chapter3 --- p.136

Devant la nécessité de préservation de l’environnement, la chimie devra de plus en plus devenir « verte ». Le développement de catalyseurs bio-hybrides est une voie prometteuse vers une chimie verte. En effet, ces catalyseurs combinent à la fois les avantages de la catalyse homogène (large gamme de réactivité) et ceux de la catalyse enzymatique (réaction en milieux aqueux, optimisation possible par génie biotechnologique). Ces nouveaux types de catalyseurs éco-compatibles semblent être à ce jour une alternative intéressante à la catalyse chimique classique.Cette thèse s’inscrit dans le cadre du développement de nouveaux catalyseurs bio-hybrides appelés Hémozymes, basés sur l’insertion non covalente de complexes métalliques hydrosolubles (responsables de l’activité catalytique), au sein d’une protéine hôte : la Xylanase A (pouvant induire une régio/stéréo/chimio-sélectivité).Pour cette étude, nous avons synthétisé différents complexes métalliques de taille variable (porphyrines, salens et salophens) métallés soit par du fer soit par du manganèse. L’étude de leur association avec la Xln A ainsi que les essais de leur activité catalytique nous ont permis d’aboutir à des résultats intéressants, d’une part pour la réaction d’oxydation du thionanisole par le peroxyde d’hydrogène, d’autre part pour l’oxydation d’alcènes aromatiques par l’oxone (KHSO5). Nous avons ainsi obtenu deux métalloenzymes artificielles remarquables, l’une capable de catalyser l’oxydation énantiosélective du thioanisole par le peroxyde d’hydrogène (84% de rendement, 40% d’excès énantiomérique en faveur de l’isomère S), l’autre capable de catalyser l’époxydation asymétrique du paraméthoxy-styrène par KHSO5 (17% de rendement, 80% d’excès énantiomérique en faveur de l’isomère R). Enfin, de nouvelles stratégies pour concevoir des catalyseurs bio-hybrides ont également été envisagée comme le greffage covalent de complexes métalliques au sein d’une protéine hôte, ou encore l’utilisation d’une forte affinité ligand-protéine (comme les interactions de type inhibiteur) pour enfouir un cofacteur métallique au sein d’une protéine. / In those days, the preservation of the environment is a huge challenge, so chemistry has to become more "Green". The development of bio-hybrid catalysts is a promising way towards a green chemistry. Indeed, these catalysts both combine the benefits of homogeneous Catalysis (wide range of reactivity) and those of enzyme catalysis (reaction in aqueous media, possible optimization by biotechnological engineering). These new kind of eco-compatible catalyst seem to be an interesting alternative to classical chemical catalysis to this day.For this study, we have synthesized various complexes with various size (porphyrins, salens and salophens) metalled by iron or manganese. The study of their association with Xln A and the catalytic activity assays allowed us to achieve interesting results, on the one hand to the oxidation of the thionanisole by hydrogen peroxide, on the other hand for the oxidation of aromatic alkenes by the oxone (KHSO5).This thesis is about the development of new bio-hybrid catalysts called Hemozymes, based on the non-covalent insertion of water-soluble metal complexes (responsible for the catalytic activity), inside a host protein: Xylanase A (which can induce a regio/stereo/chemo-selectivity).We have thus obtained two remarkable artificial metalloenzymes, one able to catalyze the enantioselective oxidation of thioanisole by hydrogen peroxide (84% yield, 40% of enantiomeric excess for the S isomer), the other able to catalyze the asymmetric epoxidation of paramethoxy-styrene by KHSO5 (17% yield, 80% enantiomeric excess for the R isomerFinally, new strategies to develop bio-hybrid catalysts have also been considered, such as covalent linkage of metal complexes within a host protein or the use of a high ligand-protein affinity (such as the interactions of inhibitor with proteins) to introduce the metal cofactor inside the protein pocket.

There are approximately 20,000 genes in the human genome. Around 2% of these genes code for transcriptional repressors known as KRAB-ZFPs. It is already known that Zinc-Finger Proteins contain two main functional domains at either end of the polypeptide. In today's database, you will find a KRAB (Kruppell-associated Box) domain at one end and a tandem array of Zinc-finger repeats at the other end. The carboxyl terminal tandem Zinc-finger repeats function as sequence-specific DNA-binding domains. The amino terminal KRAB domain serves as a repressor domain, which will recruit a co-repressor termed KAP-1 (KRAB Associated Protein-1). Located in between these two domains is a region of uncharacterized DNA referred to as the "Linker Region". This thesis will explore the DNA-binding domains of 6 known KRAB-ZFPs, as well as utilize the linker regions to derive an evolutionary history for this superfamily. / by Alain Chamoun. / Thesis (M.S.)--Florida Atlantic University, 2010. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2010. Mode of access: World Wide Web.

O objetivo desse trabalho foi demonstrar a viabilidade do acoplamento entre as técnicas de cromatografia líquida de alta eficiência com a espectrometria de emissão óptica com plasma indutivamente acoplado (HPLC - ICP OES) em um equipamento da Thermo Fisher Scientific, visando análise de especiação elementar de espécies com maiores concentrações na amostra. A identificação de espécies moleculares associadas aos elementos Cu, Fe, Mg, e Zn em amostras de castanha de caju foi adotada como modelo para comprovar tal acoplamento. Para que o ICP OES pudesse adquirir sinais de emissão ao longo de um tempo determinado, ou seja, para que o equipamento pudesse coletar um sinal transiente, fundamental para o acoplamento HPLC - ICP OES, foi necessário executar algumas modificações. Para isso, foram feitas alterações na placa eletrônica principal do equipamento, e trocada sua caixa controladora de gases. Os parâmetros instrumentais do ICP OES foram otimizados em uma série de ensaios com o intuito de estabelecer e avaliar desempenho do instrumento e a robustez do método empregado nas análises de castanha de caju. Determinações das concentrações totais de Ca, Cu, Fe, Mg, Mn, Ni, e Zn foram feitas em amostras de castanha de caju e nos materiais de referência NIST 1515 e NIST 1547, apresentando uma exatidão do método aceitável, levando-se em consideração o preparo de amostra e a medida no ICP OES. As determinações totais elementares nas amostras de castanha de caju indicaram que os teores de Ca foram de (0,04 ± 0,01) % ; Cu (26,3 ± 5,0) mg kg-1; Fe (47,9 ± 8,8) mg kg-1; Mg (0,31 ± 0,04) %; Mn (25,6 ± 3,9) mg kg-1; Ni (24,8 ± 1,9) mg kg-1; Zn (66,3 ± 2,4) mg kg-1. Para identificação de espécies moleculares associadas aos elementos Cu, Fe, Mg, e Zn, foi feita nas amostras de castanha de caju uma extração de metais e proteínas utilizando-se de uma solução extrato de NaOH 1 mol L-1. O extrato ainda foi submetido à uma etapa de clean-up, com precipitação das proteínas com acetona e ressupenção das mesmas com tampão Tris-HCl, pH 7,4. As proteínas e metais ressupensos em tampão foram analisados no sistema HPLC ICP OES, em que a separação cromatográfica ocorreu através de uma coluna de exclusão por tamanho (SEC), a detecção molecular através do detector UV-Vis do HPLC, e a detecção elementar através do ICP OES. As espécies moleculares identificadas estão no intervalo de massa molecular compreendido entre 2 e 177 kDa, sendo que Cu, Fe e Zn apresentam associação com essas espécies moleculares. Foram monitorados ainda, no ICP OES, os sinais de intensidade de emissão de P e S. Esses elementos também apresentaram associação com espécies moleculares com peso molecular entre 2 e 177 kDa, sugerindo que essas espécies se tratam de metaloproteínas. / The aim of this study was to demonstrate the capability of coupling between liquid chromatography techniques of high efficiency with the optical emission spectrometry with inductively coupled plasma (HPLC - ICP OES) in an equipment of Thermo Fisher Scientific, aiming elemental speciation analysis of species with higher concentrations in the sample. The identification of molecular species associated with elements Cu, Fe, Mg and Zn in cashew nuts samples was adopted as a model to prove such coupling. For ICP OES could get emission signal through a certain time, so that the equipment could collect a transient signal, critical to the HPLC coupling - ICP OES, it was necessary to perform some modifications in the instrument. For this, changes were made to the main electronic board of the equipment and also changed their gas controller box. The instrumental parameters of the ICP OES were optimized in a series of tests in order to establish and evaluate performance of the instrument and the robustness of the method employed in cashew nut analysis. Determination of the total concentration of Ca, Cu, Fe, Mg, Mn, Ni and Zn were made in cashew sample and reference materials NIST 1515 and NIST in 1547, with an accuracy acceptable method, taking into account the sample preparation and measurement by ICP OES. The elemental total determinations in cashew nut samples indicated that Ca were (0.04 ± 0.01)%; Cu (26.3 ± 5.0) mg kg-1; Fe (47.9 ± 8.8) mg kg-1; Mg (0.31 ± 0.04)%; Mn (25.6 ± 3.9) mg kg-1; Ni (24.8 ± 1.9) mg kg-1; Zn (66.3 ± 2.4) mg kg-1. For the identification of molecular species associated with the elements Cu, Fe, Mg, and Zn was performed on samples of cashew nuts an extract of metals and proteins using an extract solution of NaOH 1 mol L-1. The extract was further subjected to one-step of clean-up with protein precipitation with acetone following by a resuspension with Tris-HCl buffer, pH 7.4. Proteins and metals resuspended in buffer, were analyzed in the HPLC - ICP OES system, wherein the chromatographic separation took place by a size exclusion column (SEC), the molecular detection by UV-Vis detector of HPLC, and elemental detection by ICP OES. The molecular species were identified in the molecular weight range between 2 and 177 kDa, and Cu, Fe and Zn are associated with these molecular species. Were also monitored in the ICP OES, P and S emission intensity signals. These elements also associated with molecular species having a molecular weight between 2 and 177 kDa, suggesting that this species are metalloproteins.

Jusqu’à 40% des protéines sont connues pour fixer des métaux, ces hétéroatomes jouant un rôle capital dans la régulation, la catalyse ou le maintien de la structure de ces protéines. Ces métalloprotéines sont ubiquitaires et d’une importance primordiale dans les trois domaines du vivant. Cependant, les méthodes actuelles dédiées à l’identification des membres de cette grande famille dans les protéomes bactériens sont soit inadaptées pour des approches à grande échelle, soit présentent des performances relativement limitées en l’absence d’une structure tridimensionnelle résolue. Dans ce contexte, différents outils d’analyse de séquence ont été testés, en recherchant des descripteurs de ces protéines (e.g. motifs, domaines conservés, empreintes phylogénétiques). Pour pallier le relatif manque de sensibilité de ceux-ci, de nouveaux descripteurs ont été construits, dédiés spécifiquement à l’identification des protéines à centre fer-soufre : (i) des profils de co-conservation des ligands du métal et (ii) des profile-HMMs adaptés à la détection d’homologues distants. Les pouvoirs prédictifs respectifs de ces catégories de descripteurs ont été évalués sur un jeu de protéines fer-soufre expertisé, en les considérant soit séparément soit en combinaison. L’ensemble de ces descripteurs a finalement été intégré dans un modèle linéaire généralisé en utilisant la technique d’elastic-net. Le modèle prédictif obtenu a été évalué sur le protéome complet d’Escherichia coli, sur lequel il atteint une précision de 89% et une sensibilité de 83%. Enfin, il a été appliqué à environ 300 protéomes pour explorer différentes relations biologiques comme l’abondance relative des protéines Fe-S et la tolérance à l’oxygène des organismes auxquelles elles appartiennent. / Up to 40% of all proteins are known to bind metals, the intrinsic metal atoms providing catalytic, regulatory and/or structural roles critical to their functions. These metalloproteins are ubiquitous and of major importance within the three domains of life. However, current methods dedicated to identifying members of this large family within bacterial proteomes are either not suitable for large-scale approach or are of relatively limited performance when no 3D structural template is available. Within this context, different sequence analysis tools relying on different category of protein descriptors (e.g. patterns, conserved domains, phylogenetic prints) were assessed. To overcome their relative lack of sensibility, new descriptors, specific towards iron-sulfur proteins identification were built: (i) co-conservation profiles of the metal ligands and (ii) tailored profile-HMMs for remote homologs detection. Their respective predictive power towards the identification of a manually curated iron-sulfur proteins dataset were assessed, either separately or in combination. All relevant descriptors were finally gathered into a generalized linear model by using the elastic-net method. The predictive model has been evaluated on Escherichia coli whole proteome resulting in a precision of 89% and a recall of 83%. Eventually, it has been applied to 300 proteomes allowing investigating different biological relationships, such as iron-sulfur proteins relative abundances and the oxygen dependency of bacterial organisms.

Le contrôle fin de la structure et de la chimie de surface en milieu confiné a été développé dans des silices poreuses mésostucturées de type MCM-41 pour synthétiser des catalyseurs hétérogènes combinant confinement moléculaire, hydrophobicité et spécificité de sites à l'instar des métalloprotéines. La surface considérée comme lisse a en fait une rugosité de type alvéolaire due à l'empreinte de la tête ammonium du tensioactif de synthèse. Pour des températures croissantes du traitement hydrothermal, la taille des mésopores augmente par érosion de cette rugosité puis diminue par épaississement des parois. On a aussi trouvé des conditions de synthèse de zéolihes mésoporeuses avec une micro- et mésoporosité hiérarchisée. Ces surfaces sont polyfonctionnalisées grâce à la technique de pochoir moléculaire pour isoler des fonctions bidentatés aminoéthylaminopropyles par des groupements hydrophobes triméthylsimyles. Les ions cuivriques sont alors retenus dans le matériau par complexation à ces fonctions diamino.

It is hypothesized that exposing endothelial cells to steady or non-reversing pulsatile shear stress produces a healthy, anti-atherogenic endothelium, whereas a reversing pulsatile shear stress promotes an unhealthy, pro-atherogenic endothelium. To further investigate this hypothesis, a novel parallel plate flow chamber system was used to expose human endothelial cells to a pro-atherogenic reversing shear stress waveform designed to simulate the wall shear stress at the carotid sinus, a region prone to atherosclerosis. Cells exposed to this reversing shear stress were compared to cells exposed to high levels of steady shear stress (15 dynes/cm²), low steady shear stress (1 dyne/cm², the time-average of the carotid shear stress), and static culture conditions. Functional analysis confirmed previous findings that reversing shear stress increases cell proliferation and monocyte adhesion. Microarray results indicate that although there are unique sets of genes controlled by both low average shear stress and by reversing flow, more genes were controlled by low average shear stress. We propose that low-time average shear stress, and not fluid reversal/oscillation, may be the more significant mechanical force. The reversing shear stress system was also used to investigate two shear stress-responsive genes, CYP1A1 and CYP1B1. Both were maximally up-regulated at arterial steady shear stresses of at least 15 dynes/cm² and reversing pulsatile shear stress attenuated expression of both genes. Furthermore, AhR nuclear localization and CYP1A1 protein expression correlate with the flow patterns in the mouse aortic arch. The data strongly suggest that the AhR/CYP1 pathway promotes an anti-atherogenic phenotype in the endothelium. Changes in free zinc were measured under different shear stresses. High steady shear stress dramatically increases the levels of free zinc in endothelial cells as compared to cells grown in static culture. This increase in free zinc is attenuated under reversing shear stress and low steady shear stress, which correlates with an increase in zinc-binding metallothinein proteins and zinc exporter Znt-1. Overall, the findings provide further insight into endothelial responses to mechanical forces and may be important in understanding mechanisms of atherosclerotic development and localization to regions of disturbed flow.

Diss. (sammanfattning). Uppsala : Sveriges lantbruksuniv., 2003. / Härtill 4 uppsatser.

Thesis (Ph. D. in Biochemistry)--Vanderbilt University, Dec. 2005. / Title from title screen. Includes bibliographical references.