La connaissance des structures tridimensionnelles des macromolécules biologiques est indispensable pour mieux comprendre leur rôle et pour la conception de nouvelles molécules thérapeutiques. Les techniques utilisées actuellement offrent une grande variété d'approches qui utilisent à la fois des informations spécifiques à la protéine étudiée et des informations génériques communes { l'ensemble des protéines. Il est possible de classer ces méthodes en fonction de la quantité d'information utilisée dans chacune de ces deux catégories avec d'un côté des méthodes utilisant le plus possible de données spécifiques { la protéine étudiée et de l'autre les méthodes utilisant le plus possibles de données génériques présentes dans les bases de données. Le travail présenté dans cette thèse aborde deux utilisations de techniques mixtes, présentant une autre combinaison entre données spécifiques et données génériques. En particulier nous avons cherché à obtenir la structure de protéines composée d'un ou deux domaines en ne disposant que d'un nombre restreint de données spécifiques. Pour déterminer la structure d'une protéine de grande taille composée de deux domaines { l'aide de données de diffusion des rayons X et de modèles obtenus par de la modélisation par homologie, nous avons adapté puis optimisé un programme récemment développé au laboratoire. Nous avons ensuite modélisé la structure d'un domaine d'une protéine de virus en incorporant un faible nombre de contraintes issues des données obtenues par RMN dans une méthode de prédiction de structure " ab initio ". Enfin, nous avons étudié l'intérêt d'intégrer les courants de cycle, une composante du déplacement chimique, dans un programme d'arrimage moléculaire pour la résolution de complexes protéine-ADN.

Equisetum spp. (horsetail / “Schachtelhalm”) is the only surviving genus of the primitive Sphenopsids vascular plants which reached their zenith during the Carboniferous era. It is an herbaceous plant and is distinguished by jointed stems with fused whorl of nodal leaves. The plant has been used for scouring kitchen utensils and polishing wood during the past time due to its high silica encrustations in the epidermis. Equisetum hyemale (scouring rush) can accumulate silica up to 16% dry weight in its tissue, which makes this plant an interesting candidate as a renewable resource of silica for the synthesis of biomorphous ceramics. The thesis comprises a comprehensive experimental study of silica accumulations in E.hyemale using different characterisation techniques at all hierarchical levels. The obtained results shed light on the local distribution, chemical form, crystallinity, and nanostructure of biogenic silica in E.hyemale which were quite unclear until now. Furthermore, isolation of biogenic silica from E.hyemale to obtain high grade mesoporous silica with high purity is investigated. Finally, syntheses of silicon carbide (b-SiC) by a direct thermoconversion process of E.hyemale is attempted, which is a promising material for high performance ceramics. It is found that silica is deposited continuously on the entire epidermal layer with the highest concentration on the knobs. The highest silicon content is at the knob tips (≈ 33%), followed by epidermal flank (≈ 17%), and inner lower knob (≈ 6%), whereas there is almost no silicon found in the interior parts. Raman spectroscopy reveals the presence of at least two silica modifications in E.hyemale. The first type is pure hydrated amorphous silica restricted to the knob tips. The second type is accumulated on the entire continuous outer layer adjacent to the epidermis cell walls. It is lacking silanol groups and is intimately associated with polysaccharides (cellulose, hemicellulose, pectin) and inorganic compounds. Silica deposited in E.hyemale is found to be mostly amorphous with almost negligible amounts of crystalline silica in the form of a-quartz (< 7%). The silica primary particles have a plate-like shape with a thickness of about 2 nm. Pure mesoporous amorphous silica with an open surface area up to 400 m2/g can be obtained from E.hyemale after leaching the plant with HCl to remove the inorganic impurities followed by a calcination treatment. The optimum calcination temperature appears to be around 500°C. Calcination of untreated E.hyemale causes a collapse of the biogenic silica structure which is mainly attributed to the detrimental action of alkali ions present in the native plant. Finally, pure b-SiC with a surface area of about 12 m2/g is obtained upon direct pyrolysis of HCl-treated E.hyemale samples in argon atmosphere. The original structure of native E.hyemale is substantially retained in the biomorphous b-SiC. The results of this thesis lead to a better understanding of the silicification process and allow to draw conclusions about the role of silica in E.hyemale. In particular, a templating role of the plant biopolymers for the synthesis of the nanostructured silica within the plant body can be deduced. Moreover, the high grade ultrafine amorphous silica isolated from E.hyemale promises applications as adsorbent and catalyst support and as silica source for the fabrication of silica-based composites. The synthesis of biomorphous b-SiC from sustainable and low-cost E.hyemale is still in its initial stage. The present thesis demonstrates the principal possibility of carbothermal synthesis of SiC from E.hyemale with the prospect of potential applications, for instance as refractory materials, catalyst supports, or high performance advanced ceramics. / Equisetum spp. (Schachtelhalm) ist die einzige überlebende Gattung der Schachtelhalmgewächse, die ihren Zenit während der Karbon Ära erreichten. Der Schachtelhalm ist eine krautartige Pflanze und wird durch verbundene Stämme mit fixiertem Wirtel der Knotenblätter unterschieden. Aufgrund seiner hohen Siliciumdioxid Bedeckung in der Epidermis sind Winterschachtelhalmen lange Zeit zur Reinigung von Küchegeräten und zum Polieren von Holz verwendet worden. Der Winterschachtelhalm (auch Scheuerkraut genannt) kann Siliciumdioxid bis zu 16% Trockengewicht in seinem Gewebe ansammeln. Dies macht aus dieser Pflanze einen interessanten Kandidaten als erneubare Ressource von Siliciumdioxid für die Synthese von biomorphen Keramiken. Die vorliegende Doktorarbeit beinhaltet eine ausführliche experimentelle Studie der Siliciumdioxidansammlungen in Winterschachtelhalmen mittels unterschiedlicher Charakterisierungstechniken auf allen hierarchischen Ebenen. Die Ergebnisse der Arbeit werfen neues Licht auf die lokale Verteilung, die chemischen Form, die Kristallinität und die Nanostruktur des biogenen Siliciumdioxids, die bisher ziemlich unklar waren. Außerdem werden Möglichkeiten zur Isolierung des biogenen Siliciumdioxids aus Winterschachtelhalmen untersucht, um hochgradig reines Siliciumdioxid zu erhalten. Auch wird die direkte carbothermale Synthese von Siliciumkarbid (b-SiC) aus Schachtelhalmen untersucht, mit dem Ziel einer kostengünstigen Herstellung von Hochleistungskeramiken aus nachwachsenden Rohstoffen Es wird gezeigt, dass das Siliciumdioxid in einer kontinuierlichen Schicht in der Epidermis vorliegt, mit der höchsten Siliciumkonzentration in den auffälligen knopfartigen Ausbuchtungen. Den höchsten Siliciumgehalt zeigen die Knopfspitzen (≈ 33%), gefolgt von der epidermalen Flanke (≈ 17%) und inneren unteren Teile der Knöpfe (≈ 6%), während es in den inneren Teilen der Pflanze praktisch kein Silicium gibt. Ramanspektroskopie beweist eindeutig, dass mindestens zwei Siliciumdioxid Modifikationen vorhanden sind. Der erste Typ ist reines hydratisiertes amorphes Siliciumdioxid, das auf den Bereich der Knopfspitzen beschränkt ist. Der zweite Typ wird in der gesamten kontinuierlichen äußeren Schicht angesammelt, weist keine Ramanbanden von Silanolgruppen auf, und ist örtlich eng verknüpft mit Banden von Polysacchariden (Zellulose, Hemizellulose, Pektin) sowie anorganischen Verbindungen. Der Großteil des Siliciumdioxids in Winterschachtelhalmen ist amorph mit unwesentlichen Mengen an kristallinem a-Quarz (< 7%). Die primären Siliciumdioxidpartikel haben eine plattenähnliche Form mit einer Dicke von ungefähr 2 nm. Hochreines mesoporöses amorphes Siliciumdioxid mit offener Porosität und innerer Oberfläche bis zu 400 m2/g kann aus Winterschachtelhalmen isoliert werden. Dies wird erreicht indem man die Pflanze mit Salzsäure behandelt um die anorganischen Verunreinigungen zu entfernen, gefolgt von einer Kalzinierung, wobei die optimale Temperatur bei etwa 500°C liegt. Im Gegensatz zu den chemisch vorbehandelten Schachtelhalmen, verursacht die Kalzinierung von unbehandelten Winterschachtelhalmen einen Kollaps der biogenen Siliciumdioxidstruktur, und es werden nur sehr kleine innere Oberflächen erzielt. Dies wird hauptsächlich dem Einfluss der Alkaliionen zugeschrieben die in der unbehandelten Pflanze vorhanden sind. Es wird schließlich gezeigt, dass durch direkte Pyrolyse der HCl-behandelten Winterschachtelhalme in Argonatmosphäre reines b-SiC mit einer Oberfläche von ungefähr 12 m2/g erzeugt werden kann. Die ursprüngliche Struktur von natürlichen Winterschachtelhalmen bleibt dabei im Wesentlichen im biomorphen b-SiC erhalten. Die Ergebnisse dieser Arbeit führen zu einem besseren Verständnis des Silicifizierungsprozesses und erlauben es auch, Aussagen über die mögliche Rolle von Siliciumdioxid in E.hyemale zu treffen. Insbesondere kann den Pflanzenpolymeren die Rolle eines Templates bei der Synthese des biogenen Siliciumdioxids im Pflanzengewebe zugeschrieben werden. Das aus den Pflanzen isolierte ultrafeine amorphe Siliciumdioxid mit hoher Reinheit verspricht potentielle Anwendungen, z.B. als Adsorbent oder Katalysatorsupport, und auch als Füllmaterial für die Herstellung von Komopositmaterialien. Die Synthese von biomorphem b-SiC aus erneubaren und preiswerten Winterschachtelhalmen steht zwar erst am Anfang, jedoch konnte die vorliegende Arbeit die prinzipielle Machbarkeit aufzeigen. Dieses Material scheint sehr vielversprechend für eine Reihe technischer Anwendung, zum Beispiel als Refraktärmaterial, Katalysatorsupport oder neuartige Hochleistungskeramik.

Le bactériophage T5 est un virus infectant E. Coli. L'assemblage et la maturation de sa capsidecomportent plusieurs étapes critiques pour la formation des virions lors du cycle infectieux.Parmi ces étapes, j'ai étudié les processus d'expansion et de décoration de la capside de T5.L'expansion implique d'importantes réorganisations conformationnelles des 775 sous-unités de laprotéine pb8 composant la capside, conduisant au doublement du volume de la capside qui peutalors contenir le génome du phage. J'ai déterminé des conditions physico-chimiques permettantd'induire l'expansion de la capside in vitro, puis j'ai effectué des expériences de SAXS résoluesdans le temps montrant que l'expansion est un processus hautement coopératif, qui conduit, en uneétape, à un état final remarquablement stable. D'autre part, j'ai réalisé une étude fonctionnelle de laprotéine de décoration pb10, montrant que sa fixation est un marqueur de l'expansion. Enfin l'étudestructurale de pb10 menée par SAXS a permis de déterminer un modèle à basse résolution de sonenveloppe moléculaire.

Streptococcus pneumoniae, pathogène majeur de la sphère oro-pharyngée, résiste fréquemment aux antibiotiques de la famille des ?-lactamines généralement administrés dans les infections associées à ce pathogène. Les cibles de ces antibiotiques sont des enzymes responsables de la biosynthèse du peptidoglycane bactérien, les Penicillin-Binding Proteins (PBP) dont la structure du site actif est modifiée dans le cas de souches résistantes aux antibiotiques. Dans un premier temps, la résolution de la structure à haute résolution par cristallographie des rayons X de PBP1b, une des trois PBP bifonctionnelles du pneumocoque, a mis en évidence un phénomène de réorganisation structurale du site actif de la molécule en fonction de son interaction avec un pseudo-substrat de la réaction. Ce résultat nous a permis de proposer que l'ouverture du site actif joue un rôle clef lors du processus de division cellulaire. Dans un deuxième temps, nous avons résolu les structures de complexes entre PBP1b et de nouvelles molécules inhibitrices, ce qui permet d'ouvrir la voie de la mise au point rationnelle de nouveaux médicaments. Pour finir, nous avons caractérisé le domaine glycosyltransférase de PBP1b ,qui représente une nouvelle cible moléculaire pour le développement de nouveaux antibactériens, notamment par diffusion de rayons X aux petits angles (SAXS). Cette approche originale nous a permis de proposer un modèle d'organisation et de repliement de ce domaine au sein de ces protéines.

A series of pyridinium cationic lipids was designed, synthesized and characterized. These lipids varied in the lipophilic part, bearing C9 to C20 saturated, unsaturated, straight and branched hydrocarbon chains. The lipid shape parameter was calculated from the molecular structure of these lipids based on the partial molar volumes of the atoms, and standard bond lengths and bond angles, using fragment additive methods. The shape parameter controls the lamellar/hexagonal phase balance in lipoplexes of the lipid with deoxyribonucleic acid (DNA). The lipid phase behaviour of the lipoplexes was derived from small-angle X-ray scattering experiments and was successfully correlated with the calculated lipid shape parameter. The synthesized pyridinium lipids were co-formulated (1:1) with 1,2-dimyristoyl-sn-glycero-3-ethylphosphocholine (EPC) as the co-cationic lipid in 1:1 ratio, and the mixed cationic lipids were co-formulated (3:2) with the neutral lipids 1,2-dioleoyl-sn-glycero-3-phosphatidylethanolamine (DOPE) or cholesterol. The effect of variation in cationic lipid structure and lipoplex formulation on the transfection of nucleic acid (β-galactosidase and green fluorescent protein (GFP)) into CHO-K1 cells and the cytotoxicity of these formulations was assessed. Initial studies on the synthesized lipids bearing saturated and terminally unsaturated C16 chains showed that a Transfection Index (TIPSV) which encompasses the variation in the lipid shape parameter, the phase packing in a hexagonal lipoplex and the partition of these lipids into the lipoplex successfully correlated with transfection efficiency. To further investigate the effect of the variation of the partition of these lipids to the lipoplex, transfection studies were performed on a series of pyridinium lipids with straight saturated and unsaturated chains of varied lengths, with similar shape parameters but varied partition coefficients (clogP). The correlation of these experimental transfection data with the initial TIPSV was unsuccessful, but the data suggested that chain length as it relates to chain mixing and chain melting behaviours of pure lipids played a role in transfection. A refined transfection index (TIPSVM) was proposed which contained terms for the lipid shape parameter, the phase packing into a hexagonal lipoplex, the partition of these lipids into the lipoplex and a chain melting term. TIPSVM gave an acceptable correlation with the experimental transfection efficiency for the range of compounds. Additional experimental transfection data were obtained for compounds with widely variable lipid shape parameters, either as pure compounds, blends of two pure compounds, or statistically produced mixtures of mixed-chain compounds. Although very short-chain compounds (C9) and very lipophilic compounds (C20) performed poorly, the results from the blends allow the assessment of the role of the shape parameter in the TI. Since the shape parameter and the volume filling term are both calculated with the same molecular parameter, the experimental work demonstrated that only one of these terms is required. Thus a three parameter transfection index (TIPVM) was proposed and found to correlate with the entire set of comparable data. A Quantitative structure–activity relationship (QSAR) study was done on the cytotoxicity of the transfection formulations utilized. The toxicity of the synthesized pyridinium lipids was shown to correlate with the shape parameter, the lipid mixture partition co-efficient (clogP) and the charge ratio of the lipoplex formulation. Taken together, the developed transfection index TIPVM and the cytotoxicity correlation uncovered can be used in the design of low-toxicity, high activity pyridinium lipids for transfection of DNA. / Graduate / pariapz@uvic.ca

Water is a complex liquid with many unusual properties. Our understanding of its physical, chemical and biological properties is greatly advanced after a century of dedicated research but there are still many unresolved questions. If answered, they could have important long-term consequences for practical applications ranging from drug design to water purification. This thesis presents results on the structure, dynamics and thermodynamics of liquid water. The focus is on theoretical simulations applied to interpret experimental data from mainly x-ray and neutron scattering and spectroscopy techniques. The structural sensitivity of x-ray and neutron diffraction is investigated using reverse Monte Carlo simulations and information on the pair-correlation functions of water is derived. A new method for structure modeling of computationally demanding data sets is presented and used to resolve an inconsistency between experimental extended x-ray absorption fine-structure and diffraction data regarding oxygen-oxygen pair-correlations. Small-angle x-ray scattering data are modeled using large-scale classical molecular dynamics simulations, and the observed enhanced scattering at supercooled temperatures is connected to the presence of a Widom line emanating from a liquid-liquid critical point in the deeply supercooled high pressure regime. An investigation of inherent structures reveals an underlying structural bimodality in the simulations connected to disordered high-density and ordered low-density molecules, providing a clearer interpretation of experimental small-angle scattering data. Dynamical anomalies in supercooled water observed in inelastic neutron scattering experiments, manifested by low-frequency collective excitations resembling a boson peak, are investigated and found to be connected to the thermodynamically defined Widom line. Finally, x-ray absorption spectra are calculated for simulated water structures using density functional theory. An approximation of intra-molecular zero-point vibrational effects is found to significantly improve the relative spectral intensities but a structural investigation indicates that the classical simulations underestimate the amount of broken hydrogen bonds. / Vatten är en komplex vätska med flera ovanliga egenskaper. Vår förståelse av dess fysiska, kemiska och biologiska egenskaper har utvecklats mycket sedan systematiska vetenskapliga studier började genomföras för mer än ett sekel sedan, men många viktiga frågor är fortfarande obesvarade. En ökad förståelse skulle på sikt kunna leda till framsteg inom viktiga områden så som medicinutveckling och vattenrening. Denna avhandling presenterar resultat kring vattnets struktur, dynamik och termodynamik. Fokusen ligger på teoretiska simuleringar som använts för att tolka experimentella data från huvudsakligen röntgen- och neutronspridning samt spektroskopier. Den strukturella känsligheten i röntgen- och neutrondiffraktionsdata undersöks via reverse Monte Carlo metoden och information om de partiella parkorrelationsfunktionerna erhålls. En ny metod för strukturmodellering av beräkningsintensiva data presenteras och används för att lösa en motsägelse mellan experimentell diffraktion och EXAFS angående syre- syre parkorrelationsfunktionen. Data från röntgensmåvinkelspridning modelleras med storskaliga klassiska molekyldynamiksimuleringar, och den observerade förhöjda småvinkelspridningen vid underkylda temperaturer kopplas till existensen av en Widomlinje härrörande från en vätske- vätske kritisk punkt i det djupt underkylda området vid höga tryck. En undersökning av inherenta strukturer i simuleringarna påvisar en underliggande strukturell bimodalitet mellan molekyler i oordnade högdensitetsregioner respektive ordnade lågdensitetsregioner, vilket ger en tydligare tolkning av den experimentella småvinkelspridningen. Dynamiska anomalier i underkylt vatten som har observerats i inelastisk neutronspridning, speciellt förekomsten av lågfrekventa excitationer som liknar en bosontopp, undersöks och kopplas till den termodynamiskt definierade Widomlinjen. Slutligen presenteras densitetsfunktionalberäkningar av röntgenabsorptionsspektra för simulerade vattenstrukturer. En approximation av intramolekylära nollpunktsvibrationseffekter förbättrar relativa intensiteteri spektrumen avsevärt, men en strukturanalys visar att klassiska simuleringar av vatten underskattar andelen brutna vätebindningar. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 6: Submitted. Paper 7: Submitted. Paper 8: Manuscript. Paper 9: Submitted.

No description available.

Myelin basic protein (MBP) has fascinated researchers and clinicians alike due to its major structural role in myelin and the central nervous system, and its potent auto-immunogenic properties that cause demyelination in animal models. The charge variants of MBP have been of particular interest. The C1 component, the least modified and most cationic of the variants, is the most abundant form of MBP in healthy adult myelin. The C8 component, the most modified and the least cationic variant, has been found in higher proportions in myelin of MS patients and children. Here, an investigation of the structural differences between C1 and C8 components of MBP was conducted. The spectral and hydrodynamic properties of these variants were monitored via a number of biophysical/biochemical techniques. The effect of zinc (Zn2+) on the conformational behaviour of MBP was examined. Zn2+ is an abundant metal in the brain, and had been previously shown to induce hydrodynamic compaction in MBP. Both variants have a loose tertiary arrangement with subtle differences. This arrangement is deficient in secondary structure and undergoes non-cooperative temperature-induced melting. Zn2+ stabilizes a molten globular-like state with enhanced ANS fluorescence, and promotes oligomerization.

No description available.

To achieve successful gene therapy, safe and efficient gene delivery vectors are needed. As an alternative to viral vectors, non-viral vectors, incorporating compounds such as cationic polymers and lipids have been widely studied. Much effort has been made to enhance transgene delivery efficiency, such as development of more effective cationic lipids or polymers, optimization of transfection formulations, and investigation on structural-activity of delivery vectors. Gemini surfactant, consisting of two surfactant monomers linked by a spacer group, is a thrust research area for gene therapy as non-viral vectors due to their high stability, longer storage on shelves, easiness to produce. A series of phytanyl substituted asymmetric gemini surfactants, phy-3-m (m = 12, 16, and 18) and phy-7NH-m (m = 12, 16, and 18), were rationally designed and synthesized. Due to the bulky nature and increased hydrophobicity of phytanyl branch, phy-3-m surfactants showed much lower values of critical micelle concentration (CMC) compared to their corresponding symmetric m-3-m. Particle size and transmission electron microscopy (TEM) imaging indicate that this type of gemini surfactants tends to form stacked bilayers rather than spherical or rod-like micelles which are typically observed in gemini surfactants with shorter spacers. Phy-3-m surfactants have higher degree of micelle ionization, indicating that the counter ions of the gemini surfactants can be easily replaced by other anionic ions, such as DNA, which is an advantage of phy-3-m used as transgene vectors. To evaluate transfection ability, transfection assays were carried out in OVCAR-3 cells. Transfection complexes formed by a plasmid pVGtelRL, coding enhanced green fluorescence protein (EGFP) gene, phy-3-m, and a neutral lipid, 1,2-Dioleyl-sn-glycerophosphatidylethanolamine (DOPE), at the charge ratios (+/-) of 2:1, 5:1, 10:1, and 20:1, were incubated with OVCAR-3 cells. Treated cells at all charge ratios except 20:1 showed EGFP signals under fluorescence microscopy. Meanwhile, EGFP expression and cell toxicity was quantified using fluorescence-activated cell sorting (FACS). For each gemini surfactant complex, the transfection efficiency and cytotoxicity go through a maximum, occurring at different values of the charge ratio. Considering both transfection efficiency and cytotoxicity, the optimal charge ratio to formulate the complexes containing phy-3-m was found to be 5:1 for in vitro transfection. Compared to a positive control, 16-3-16, phy-3-m showed higher transfection ability and lower cytotoxicity to OVCAR-3 cells. Initial characterization of transfection complexes was investigated by measuring particle size and zeta potential. At all charge ratios, transfection complexes were positively charged, and greater than +30 mV at 5:1 and 10:1, indicating that the complexes would be stable in solution at the ratio above 2:1. Transfection complexes were larger at lower charge ratio, but particle size dropped with increasing charge ratio (+/-). Comparing particle size and zeta potential with transfection efficiency, no correlation between size/zeta potential and transfection ability was observed. The larger particles may enter cells through caveolin-mediated pathway or phagocytosis, and smaller ones through a clathrin-mediated endocytosis. In addition, phase structures of the complexes were investigated using small angle X-ray scattering (SAXS). The complexes containing phy-3-m gemini surfactants were found to be able to adopt multiple phase structures, such as L, HII, and other highly ordered unidentified phase structures. By contrast, L structure was dominant in the transfection complexes formed by 16-3-16. The ability of phy-3-m system to adopt multiple phases appears correlated with their higher transfection efficiency in OVCAR-3 cells.