Movimentos coletivos prestam um papel fundamental na dinâmica e energética de biomoléculas em solução. Estes movimentos permitem o acoplamento de regiões significativamente distantes, apresentando considerável influência, por exemplo, no alosterismo para a formação de complexos macromoleculares e no funcionamento integrado de proteínas multidomínios como \"máquinas moleculares\". Neste trabalho de doutoramento, serão apresentados os resultados referentes à aplicação conjunta de técnicas experimentais biofísicas, de modelagem estrutural e de dinâmica molecular no estudo de dois sistemas para os quais estes movimentos coletivos demonstram considerável importância funcional. Para a interação do receptor nuclear do ácido 9-cis-retinóico com seu elemento responsivo específico no DNA (HRE), a comparação de estudos de dinâmica molecular com ensaios de afinidade por anisotropia de fluorescência sugere que a resistência inicial para a associação do monômero, seguida da acentuada colaboratividade na associação do dímero é regida por um impedimento da associação do domínio de ligação ao DNA (DBD) para o primeiro à sequência responsiva devido, em última análise, a uma não complementaridade dos modos coletivos mútuos. Este impedimento para a associação monomérica inicial é mais acentuado para o monômero 5\' (para o qual a menor especificidade de ligação à seqüência específica já é bem documentada), devido aos efeitos conjuntos de um \"defeito\" natural no empacotamento de bases da seqüência responsiva, que se manifesta mais significativamente na interface entre o meio-sítio 5\' e a seqüência espaçadora, e dos modos vibracionais entre os dois sítios decorrentes de seu faseamento relativo na topologia do DNA na seqüência responsiva, caracterizando um mecanismo \"chave e fechadura\" para a interação obrigatoriamente simultânea dos dois monômeros ao DNA. No segundo caso, um estudo integrado utilizando a técnica experimental de espalhamento de raios X a baixos ângulos e uma abordagem de modelagem estrutural baseada em dinâmica molecular foi realizado para a celobiohidrolase I de Trichoderma harziannum. Este estudo permitiu tanto a elaboração de um modelo estrutural de maior resolução para esta enzima de alto potencial biotecnológico como a constatação dos possíveis mecanismos moleculares a partir dos quais as glicosilações no peptídeo conector impõem restrições à orientação e modos vibracionais entre seus dois domínios de forma condizente com sua ação concertada na interação e no deslize da enzima sobre a superfície celulósica, ambos de fundamental importância para a processividade da enzima na hidrólise do substrato microcristalino. / Collective motions play a fundamental role in solution biomolecule dynamics and energetics. These movements can couple very distant regions in the protein structures affection, for instance, allosteric mechanisms, the establishment of macromolecular complexes, and on the integrated function of multidomain proteins as molecullar machines. In this thesis, we present results concerning to the joint use of experimental biophysical techniques, structural modeling and molecular dynamics simulations on the study of two systems for which these collective motions have substantial importance. First, we study the interaction of the nuclear retinoid X receptor with its specific DNA hormone response element (HRE) using a combination of molecular dynamics simulations and affinity assays performed by using fluorescence anisotropy. We find out that collective motions mediate the low binding affinity of monomers and the high cooperative binding of HRE dimers. The lower binding affinity of the monomer is more prominent for 5´ monomers. This occur due to an natural ineffective stacking of the last base pair step at the 5´-half-site and to the phasing of the two binding half-sites in the DNA topology, that impose a collective motions that tends to occlude the 5´ binding site. This behavior, in turn, is concurrent with the well known 3´ polarity and the decreased binding specificity to the 5´ half site for the hRXRα monomer. This same pattern impose a lock-and-key mechanisms dependent on the binding of the full dimer. Second, an integrated Small angle X ray scattering and molecular dynamics based structural modeling was used to comprehend the interdomain motions of cellobiohydrolase I of Trichoderma harziannum. We manage to build a refined model for this enzime, with important biotechnological potential. We also provide insights into molecular mechanisms of linker and glycosylation imposed restraints on the orientation and vibrational modes of the full-length enzyme, supporting a mechanism of sliding of on the cellulose surface. This mechanism is fundamental for the high processivity on the hydrolysis of microcrystalline cellulose.

This thesis deals with the preparation, characterization methods and in vitro imaging of nanoparticles with great potential for medical diagnostics. A key role in this work occupy nanoparticles comprising a core of calcium tungstate, CaWO4, covered by a natural polysaccharide together serve as a suitable model contrast agent for cell imaging techniques. CaWO4 natural properties such as the absorption of X-rays, natural fluorescence capabilities and capacities for doping fluorescently active lanthanides, makes from nanoparticles suitable candidates for the position of contrast agents for imaging in the diagnosis of oncological diseases. Moreover, by coverage of the inorganic core by natural polysaccharide nanoparticles reach the desired size and the possibility of active targeting to specific or nonspecific interactions with the cell membrane, which are key factors in in vitro cell studies. It was found the most suitable synthesis both doped and undoped core of this model reaching the formation of spherical particles of colloidal dimensions. Doping was realized by red fluorescent trivalent europium, Eu3+ , and green fluorescent trivalent terbium, Tb3+ , and neither of these dopants affected the original crystalline structure CaWO4. In the next stage, these fluorescent nuclei successfully dispersed...

Les phases concentrées de protéines sont au centre de nombreuses études visant à identifier et caractériser les interactions et transitions de phases mises en jeu, en utilisant le large corpus de connaissances acquis sur les phases concentrées de colloïdes. Ces phases concentrées de protéines possèdent en outre une grande importance dans des domaines aussi variés que l’industrie agroalimentaire, l’industrie pharmaceutique et la médecine. L’établissement d’équations d’état présentant la pression osmotique (Π) en fonction de la fraction volumique (Φ) est une méthode efficace de caractérisation des interactions entre les composants d’un système. Nous l’avons appliquée à des solutions de deux protéines globulaires, le lysozyme et l’ovalbumine, en balayant une gamme de fractions volumiques allant d’une phase diluée (Φ < 0,01) à une phase concentrée, solide (Φ > 0,62). Les équations d’état obtenues, couplées à d’autres techniques (SAXS, simulations numériques), ont permis de mettre en évidence un comportement très différent des deux protéines lors de la concentration et ont montré leur complexité en comparaison avec des colloïdes modèles. La mise en relation des équations d’état et du comportement interfacial de ces deux protéines a montré des points de convergence et permis de formuler une nouvelle hypothèse expliquant certaines observations portant sur l’adsorption des protéines à l’interface air-eau. / Concentrated phases of proteins are the subject of numerous studies aiming at identifying and characterizing the interactions and phase transitions at play, using the large corpus of knowledge in the field of concentrated colloids. Those concentrated phases of proteins have, in addition, a great importance in various fields, such as food industry, pharmaceutical industry and medicine. The establishment of equations of state relating osmotic pressure (Ð) and volume fraction (Φ) is an efficient way of characterization of the interactions between the components of a system. We applied this method to solutions of two globular proteins, lysozyme and ovalbumin, spanning volume fractions ranging from a dilute phase ( Φ < 0,01) to a concentrated, solid phase ( Φ > 0,62). The equations of state, coupled to other methods (SAXS, numerical simulations), enabled us to show that the two proteins carry a very different behavior when submitted to concentration and that their complexity is beyond that of colloids. Relating equations of state and interfacial behavior of these two proteins also showed points of convergence and enabled us to formulate a new hypothesis which explains some of the results obtained in the study of adsorption of proteins at the air-water interface.

Die heterogene Struktur von aus Rattenhirn isolierten Synaptischen Vesikeln wird untersucht mittels Daten aus Kleinwinkel-Röntgenstreuexperimenten unter Berücksichtigung von Daten erhalten durch cryogene Elektronenmikroskopie, dynamische Lichtstreuung und biochemische Analysen. Es werden niedrig aufgelöste Strukturmodelle des funktionellen Synaptischen Vesikels unter quasi-physiologischen Bedingungen vorgeschlagen. Details des Dichteprofils der Membran, einschließlich Beiträgen von Lipiden und Proteinen werden bestimmt. Die typische Konformation und die allgemeine laterale Organisation der Proteine in Mikrodomänen werden ermittelt. Entropische Beiträge zur freien Energie aufgrund möglicher Bildung und Auflösung der Proteinmikrodomänen auf dem Synaptischen Vesikel werden untersucht. Ferner werden zellfreie Fusionssysteme mittels dynamischer Lichtstreudaten charakterisiert und mögliche Anwendungen von Kleinwinkel-Röntgenstreuung für die Untersuchung von Membran-Fusionsprozessen erörtert.

The techniques of small-angle x-ray scattering (SAXS) and grazing-incidence small-angle x-ray scattering (GISAXS) have successfully been used for many years in the analysis of nanostructures in non-crystalline samples, e.g., polymers, metallic alloys, ceramics, and glasses. In many specimens, however, the nanostructure is not distributed homogeneously, but instead varies as a function of position in the sample. Conventional SAXS or GISAXS measurements on such heterogeneous samples merely yield an averaged scattering pattern of all the different structures present along the x-ray beam path. In this thesis, scanning tomography is combined with SAXS and GISAXS, revealing the individual local scattering cross section at each position on a virtual section through the sample. The technique thereby offers unique analytical possibilities in heterogeneous specimens. A brief review of the physics of x rays and x-ray scattering is given, before the methods of tomographic SAXS and GISAXS are introduced. Experimental requirements and limitations of both methods are discussed, including aspects of sampling, local rotational invariance and x-ray beam coherence. Experiments performed at the beamline BW4 at HASYLAB at DESY, Hamburg, Germany are described, illustrating the capabilities of the method. Finally, an outlook on possible future developments in tomographic small-angle x-ray scattering is given. / Die Methoden der Röntgenkleinwinkelstreuung (SAXS) und Röntgenkleinwinkelstreuung unter streifendem Einfall (GISAXS) werden seit vielen Jahren erfolgreich eingesetzt zur Analyse von Nanostrukturen in nicht-kristallinen Proben, z.B. Polymeren, metallischen Legierungen, Keramiken und Gläsern. In vielen Proben ist die Nanostruktur allerdings nicht homogen verteilt, sondern variiert als Funktion des Ortes in der Probe. Konventionelle SAXS- oder GISAXS-Messungen an solch heterogenen Proben liefern lediglich ein über alle unterschiedlichen Strukturen entlang des Röntgenstrahls gemitteltes Streubild. In dieser Arbeit wird Rastertomographie mit SAXS und GISAXS kombiniert und so der lokale Streuquerschnitt an jedem Ort auf einem virtuellen Schnitt durch die Probe gewonnen. Diese Technik bietet so einzigartige Analysemöglichkeiten von heterogenen Proben. Es wird zunächst ein kurzer Überblick über die Physik der Röntgenstrahlung und Röntgenstreuung gegeben, bevor die Methoden der SAXS- und GISAXS-Tomographie eingeführt werden. Die experimentellen Anforderungen und Grenzen beider Methoden werden besprochen, wobei Aspekte der Abtastung, der lokalen Rotationsinvarianz und der Kohärenz im Röntgenstrahl eine Rolle spielen. Experimente, die an der Messstrecke BW4 am HASYLAB bei DESY, Hamburg, durchgeführt wurden, werden beschrieben, um die Möglichkeiten der Methode zu illustrieren. Schließlich wird ein Ausblick auf mögliche zukünftige Entwicklungen der Kleinwinkelstreutomographie gegeben.

Nanopartikel auf Basis von NaYF4 erfreuen sich großer Beliebtheit durch ihre vielseitigen Einsatzmöglichkeiten. Durch die Dotierung mit Ytterbium und Erbium im Wirtsgitter ist es beispielsweise möglich, niedrigenergetisches Infrarotlicht in höher-ergetisches, sichtbares Licht umzuwandeln. Zudem lässt sich NaYF4 auch im Nanometermaßstab präparieren, sodass ein Einsatz in Zellen oder lebenden Organismen möglich ist, wo die zur Anregung verwendete infrarote Strahlung ohne Probleme das Gewebe durchdringen kann. Zu Beginn dieser Arbeit zeigten aufwärtskonvertierende Nanomaterialien wie NaYF4 :Yb,Er jedoch auch nach Umhüllen mit einer inaktiven Schale aus undotiertem NaYF4 nur sehr geringe Lumineszenz-Quantenausbeuten und kurze Energieniveau-Lebenszeiten. Im Rahmen dieser Arbeit wurde die Synthesemethode zur Herstellung von aufwärtskonvertierenden NaYF4 -Nanopartikeln durch den Einsatz neuer Eduktmaterialien modifiziert und die Auswirkung der Modifikationen auf die Partikeleigenschaften näher untersucht. So konnte gezeigt werden, dass durch den Einsatz einer alternativen Fluoridquelle (NaHF2) Partikel mit sehr engen Partikelgrößenverteilungen hergestellt werden können. Jedoch zeigte sich auch, dass die mit NaHF2 präparierten Partikel sich nicht mit einer Schale aus undotiertem NaYF4 umhüllen ließen. Im zweiten Teil dieser Arbeit wurde daher der Fokus auf die Verbesserung der optischen Eigenschaften gelegt. Durch die Verwendung von getrockneten Lösungsmitteln und wasserfreien Seltenerdacetaten, sowie NH4F als Fluoridquelle gelang es erstmals, aufwärtskonvertierende Kern/Schale-Nanopartikel (<50 nm) mit einer sehr hohen Lumineszenz-Quantenausbeute, ähnlich dem des makrokristallinen Referenzmaterials, herzustellen. Auch bei sehr kleinen Kern/Schale-Partikeln (≤15 nm) konnten Quantenausbeuten erzielt werden, die nur um einen Faktor 3-4 niedriger sind als beim Referenzmaterial. Dabei zeigte sich durch die Messung der Energieniveau-Lebenszeiten, dass die größten Verlustprozesse durch die Yb3+ Emission bei 940 nm auftraten und diese durch aufbringen einer Schale unterbunden werden konnten.

Lactobacillus kunkeei is one of the most abundant bacteria within the honey crop of the honey bee. Genome sequencing of L. kunkeei isolated from honey bees all over the world showed several genes unique for L. kunkeei. Among these orphan genes, an array of four to five highly conserved genes coding for giant extracellular proteins were found. Cryogenic electron microscopy imaging of a giant-protein preparation from L. kunkeei A00901 showed an overall structure similar to a long string with a knot at the end. Further analysis showed high similarity between the different giants at the N-terminus, and secondary structure predictions showed that the same region was rich in β-sheets.  These results, combined with the knowledge of other large extracellular proteins, led to the hypothesis that the “knot” domain is located at the N-terminus and that these proteins are used by the cell to latch on to the intestine lining or other cells in the honey crop. In this study, predictions were made to locate the N-terminal domains of two of these giant proteins. Four different constructs were made for each protein, where three constructs were designed for expression and purification of the N-terminal domain with different end-positions, and one construct was for a predicted β-solenoid domain located downstream from the N-terminal domain. The protein constructs were recombinantly produced in E. coli, and three of the N-terminal constructs from both proteins were purified. Thermal stability was tested using nano differential scanning fluorimetry (nanoDSF), Thermofluor, and circular dichroism (CD), which all showed characteristic melting curves at low melting temperatures, ranging from 33 °C to 44 °C, for all three constructs. During CD measurements, all three constructs showed refolding after thermal denaturation and a higher abundance of antiparallel β-sheets over α-helices. Looking at the protein structure, small angle X-ray scattering data indicated that all three proteins formed elongated structures. These results indicate that a folded domain has been found for both proteins. Although, further analysis will be required to determine the boundaries of the N-terminal domains, and to elucidate if these domains have anything to do with ligand binding and the L. kunkeei ability to latch onto the honey crop.

No description available.

The ability to quickly develop predictions of the time-to-failure under different loading levels allows designers to choose the best polymeric material for a specific application. Additionally, it helps material producers to design, manufacture, test, and modify a polymeric material more rapidly. In the case of polymeric pipes, previous studies have shown that there are two possible time-dependent failure mechanisms corresponding to ductile and brittle failure. The ductile mechanism is evident at shorter times-to-failure and results from the stretching of the amorphous region under loading and the subsequent plastic deformation. Empirical results show that many high-performance polyethylene (PE) materials do not exhibit the brittle failure mechanism. Hence, it is critical to understand the ductile mechanism and find an approach to predict the corresponding times-to-failure using accelerated means. The aim of this study is to develop an innovative rupture lifetime acceleration protocol for PE pipes which is sensitive to the structure, orientation, and morphology changes introduced by changing processing conditions. To accomplish this task, custom fixtures are developed to admit tensile and hoop burst tests on PE pipes. A pressure modified Eyring flow equation is used to predict the rupture lifetime of PE pipes using the measured mechanical properties under axial tensile and hydrostatic pressure loading in different temperatures and strain rates. In total, the experimental method takes approximately one week to be completed and allows the prediction of pipe lifetimes for service lifetime in excess of 50 years. / Master of Science / Steel, cast and galvanized iron, and asbestos cement (AC) pipelines have been historically used in water management services. However, they often experienced deterioration because of corrosion and encrustation, resulting in 23 to 27 bursts per 100 miles of pipeline in the US per year. Therefore, plastic pipes were developed to carry liquids (water and sewage), gases, etc. The Plastic Pipe Institute (PPI) requires a service life of at least 50-years for plastic pipes. Hence, pipe producers and material suppliers continuously attempt to improve the materials and manufacturing processes used for plastic pipes to increase their service lifetimes. However, there is still no plastic pipe that has been in service for 50 years. Therefore, a few techniques have been developed to accelerate the aging process and to predict if the plastic pipe is able to endure the 50-year lifetime without failure. In this work, a combined experimental and analytical framework is presented to develop accelerated lifetime estimates for plastic pipes. Custom axial tensile and internal pressurization fixtures are developed to measure the pipe response; the analytical method is used to extend the results to predict 50-year (and beyond) behavior.

No / The in-line development of crystalline morphology and orientation during melt extrusion of low density polyethylene (LDPE) tape at nil and low haul-off speeds has been investigated using Small-Angle X-Ray Scattering (SAXS). The processing parameters, namely haul-off speed and distance down the tape-line have been varied and the resulting crystalline morphology is described from detailed analysis of the SAXS data. Increasing haul-off speed increased orientation in the polymer tape and the resulting morphology could be described in terms of regular lamellar stacking perpendicular to the elongation direction. In contrast, under nil haul-off conditions the tape still showed some orientation down the tape-line, but a shish-kebab structure prevails. The final lamellae thickness (similar to 50 angstrom) and bulk crystallinity (similar to 20%), were low at, for all processing conditions investigated, which is attributed to the significant short-chain branching in the polymer acting as point defects limiting lamellae crystal growth. (C) 2013 Elsevier Ltd. All rights reserved.