Macromolecular transitions such as conformational changes and protein-protein association underlie many biological processes. Conformational changes in the N-terminal domain of the transmembrane protein DsbD (nDsbD) were studied by NMR and molecular dynamics (MD) simulations. nDsbD supplies reductant to biosynthetic pathways in the oxidising periplasm of Gram-negative bacteria after receiving reductant from the C-terminal domain of DsbD (cDsbD). Reductant transfer in the DsbD pathway happens via protein-protein association and subsequent thiol-disulphide exchange reactions. The cap loop shields the active-site cysteines in nDsbD from non-cognate oxidation, but needs to open when nDsbD bind its interaction partners. The loop was rigid in MD simulations of reduced nDsbD. More complicated dynamics were observed for oxidised nDsbD, as the disulphide bond introduces frustration which led to loop opening in some trajectories. The simulations of oxidised and reduced nDsbD agreed well with previous NMR spin-relaxation and residual dipolar coupling measurements as well as chemical shift-based torsion angle predictions. NMR relaxation dispersion experiments revealed that the cap loop of oxidised nDsbD exchanges between a major and a minor conformation. The differences in their conformational dynamics may explain why oxidised nDsbD binds its physiological partner cDsbD much tighter than reduced nDsbD. The redox-state dependent interaction between cDsbD and nDsbD is thought to enhance turnover. NMR relaxation dispersion experiments gave insight into the kinetics of the redox-state dependent interaction. MD simulations identified dynamic encounter complexes in the association of nDsbD with cDsbD. The mechanism of the conformational changes in the transport cycle of LacY were also investigated. LacY switches between periplasmic open and cytoplasmic open conformations to transport sugars across the cell membrane. Two mechanisms have been proposed for the conformational change, a rocker-switch mechanism based on rigid body motions and an “airlock” like mechanism in which the transporter would switch conformation via a fully occluded structure. In MD simulations using the novel dynamics importance sampling approach such a fully occluded structure was found. The simulations argued against a strict “rocker-switch” mechanism.

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This thesis combines solid-state nuclear magnetic resonance (NMR) spectroscopy, X-ray diffraction (XRD), chemical synthesis, isotopic enrichment and density-functional theory (DFT) calculations to provide insight into a number of microporous materials. The first class of materials studied is metal-organic frameworks (MOFs), where the presence of paramagnetic ions has a range of effects on the ¹³C NMR spectra, depending on the nature of the ligand-metal interactions. For the Cu²⁺-based MOFs, HKUST-1 and STAM-1, the assignment of the NMR spectra is non-intuitive, and unambiguous assignment requires specific ¹³C labelling of the organic linker species. It is shown that ¹³C NMR spectra of these two MOFs could act as a sensitive probe of the nature of “guest” molecules bound to the Cu²⁺. The second class of materials is aluminophosphates (AlPOs). It is shown that, using a series of relatively simple linear relationships with the crystal structure, the NMR parameters calculated by DFT (with calculation times of several hours) can be predicted, often with experimentally-useful accuracy, in a matter of seconds using the DIStortion analysis COde (DISCO), which is introduced here. The ambient hydration of the AlPO, JDF-2, to AlPO-53(A) is shown to occur slowly, with incomplete hydration after ~3 months. The resulting AlPO-53(A) is disordered and some possible models for this disorder are investigated by DFT. The final class of materials is gallophosphates (GaPOs), particularly GaPO-34 and related materials. The two as-prepared forms of GaPO-34 are characterised by solid-state NMR, and their calcination investigated by TGA and in-situ powder XRD. An unusual dehydrofluorinated intermediate phase is isolated and characterised for the first time by solid-state NMR. The fully calcined material is shown to be stable under anhydrous conditions, but hydrates rapidly in air. The hydrated material is stable under ambient conditions, but collapses upon heating. Partial dehydration without collapse is achieved by gentle heating or room-temperature evacuation. The impurity phases, GaPO₄ berlinite and GaPO-X are investigated by solid-state NMR and, while the structure of GaPO-X remains unknown, much structural information is obtained.

Mass spectrometry coupled with liquid chromatography and gel electrophoresis enables separation and detection of components in a complex mixture. During the last two decades, its applications were dramatically extended and remarkable progress has been made in many fields, in particular, environmental and biological analyses. This dissertation focuses on identification and characterization of biologically active compounds and comparative analysis of protein expression changes. The first two projects (Chapters 2 and 3) focus on the application of LC/MS approach to profile the bioactivated intermediates of 4, 4'-methylenedianiline (DAPM) from rat vascular smooth muscle cells (VSMCs) and bile. In our study, several DAPM metabolites were detected and characterized in detail by liquid chromatography-electrospray tandem mass spectrometry. The structural assignments of these metabolites from VSMCs and rat bile significantly improve our understanding of DAPM biotransformations and toxicity. The third project described in Chapter 4 focuses on using electrospray tandem mass spectrometry (ES-MS/MS) and theoretical calculation (GAUSSIAN 03 program) to investigate the unusual methyl radical loss and consecutive fragment ions that dominate the low-energy collision induced dissociation (CID) mass spectra of prodiginine compounds. Structures of the fragment ions are proposed and explanations are given to rationalize the observed competition between the formation of even-electron ions and radical ions. Our study shows that the lower apparent threshold associated with methyl radical loss points to a lower kinetic barrier. In Chapter 5, hypoxia-induced changes of zebrafish skeletal muscle were studied using two-dimensional difference in-gel electrophoresis (2D-DIGE) in vivo after 48 h in hypoxia vs. normoxia. The results showed that proteins involved in mitochondrial oxidative metabolism are down-regulated, whereas glycolytic enzymes are up-regulated to compensate for the loss of ATP synthesis in aerobic metabolism. The up-regulation of two spots identified as hemoglobin variants was also observed. These protein expression changes are consistent with a hypoxic response that enhances anaerobic metabolism or O2 transport to tissues.

Les silices pyrogéniques sont très utilisées comme charge pour les polysiloxanes mais elles sont l’un des principaux constituants des superisolants thermiques. Cependant, l’échelle nanométrique de ces silices et leur chimie de surface (groupes silanol) est également responsable de leur aptitude à adsorber la vapeur d’eau, ce qui a pour conséquence d’altérer leurs propriétés d’isolant thermique au cours du temps, notamment lors de leur stockage dans des conditions non contrôlées. Malgré son importance industrielle ce phénomène n’a fait l’objet dans la littérature que d’une seule étude assez limitée.En effet, initialement la surface de ces silices ne sont que partiellement hydroxylées et la présence de ponts siloxanes tendus, susceptibles de réagir avec l’eau va mener à une évolution de leurs propriétés de surface en présence d’humidité.Une première étude a porté sur les silices N20, T30 et T40 (Wacker Chemie AG) sont obtenues par combustion de SiCl4 dans un mélange air/H2, de surfaces spécifiques égales respectivement à 200, 300 et 400 m2/g. Elles ont été vieillies à température constante 22,5 ± 0,1 °C, dans une enceinte fermée, sous humidité relative (HR) contrôlée : 62, 75, 84, 92 et 100%.L'adsorption d'eau a été suivie par gravimétrie. La masse d’eau adsorbée, par unité de surface augmente à la fois avec HR et la surface spécifique. Cette augmentation qui peut atteindre près de 60% de la masse initiale pour une HR de 100%, est liée à l’augmentation de l’hydrophilie de la surface de la silice liée à la formation de nouveaux groupes silanol. Nous avons démontré que cette augmentation suit une cinétique du 1er ordre et que la constante cinétique passe par un maximum pour une RH égale à 84%.L’augmentation du nombre de silanol superficiels a été confirmée par leur dosage chimique. Leur densité superficielle augmente d’environ 50%, passant de 2,4 SiOH/nm2 à 3,6 SiOH/nm2 pour l’HR égale à 100%.La spectroscopie IR atteste clairement d’une diminution nette des silanol isolés au profit de silanol fortement liés par pont hydrogène. Les spectroscopies RMN du proton et du silicium confirment l’augmentation de la densité locale en groupes silanols.L’évolution des propriétés superficielles des silices vieillies environ 1000 h a été suivie par chromatographie inverse à dilution infinie (CGI-DI) et concentration finie (CGI-CF).La CGI-DI pratiquée avec des sondes alcanes linéaires et cycliques démontre que le vieillissement n’affecte que très faiblement tant la composante dispersive de l’énergie de surface que leur rugosité à l’échelle moléculaire, autrement dit qu’il ne modifie pas la morphologie de la surface. Notamment la rugosité superficielle des silices T30 et T40 n’est pas affectée.La variation de l’hétérogénéité superficielle avec le vieillissement a été déterminée, en termes de fonctions de distribution des énergies d’adsorption de l’isopropanol, par CGI-CF.Le processus de vieillissement conduit, comme attendu, à une augmentation de la composante de haute énergie liée à l'apparition de nouveaux groupes silanol par ouverture nucléophile des ponts siloxane. Le glissement du maximum de cette composante vers les hautes énergies montre la formation d’un nouveau type de silanol plus interactif par liaison hydrogène.Ces résultats confirment la réactivité des silices de combustion vis-à-vis de l'eau lorsqu’elles sont exposées à une humidité relative élevée. L'eau est chimisorbée sur la surface de la silice par une réaction d'ouverture des ponts siloxane. L'étude de l'influence de la variation de l'humidité relative, montre qu’il existe un seuil (HR50%) au-dessous duquel ces silices restent stables par rapport à la vapeur d'eau. [...] / Pyrogenic silicas , produced by combustion of SiCl4 into a mixture hydrogene/air, are widely used as filler for polysiloxanes, but also as one of the main components of super-thermal insulating. However, the nanoscale of these silicas and surface chemistry (silanol groups) is also responsible for their ability to adsorb water vapour, which alters their insulation and reinforcement properties, especially when stored in uncontrolled conditions. Initially the surface of pyrogenic silicas is partially hydroxylated, silanol groups, but presents also strained siloxane bridges, which can react with adsorbed water, leading to a change in their surface properties when exposed to the atmospheric moisture. Despite its industrial importance, this phenomenon has been rarely studied in the literature, except a single study, which was rather limited.Our study was focused on a set of six pyrogenic silicas, having specific surface areas comprised between 150 to 400 m2 / g. They were aged at constant temperature 22.5 ± 0.1 ° C in a closed chamber under controlled relative humidity (RH): 62, 75, 84, 92 and 100%.The water adsorption was followed gravimetrically. The mass of water adsorbed per unit area increases with both HR and the specific surface area. This increase, which can reach nearly 60% of the initial mass at 100% RH, is induced by the increase of their surface hydrophilicity due to the formation of new silanol groups. But, the study of the influence of the variation in RH, indicates that a threshold exists around HR50%, below which these silicas are stable.Finally, fitting the gravimetric curves, it was evidenced that the water sorption follows a first order kinetics and that the kinetic constant goes through a maximum for an HR equal to 84%. This increase of silanol density was testified by chemical titration. It increases by about 50%, from 2.4 to 3.6 SiOH/nm2 for ageing under 100% RH, but is dependent of the specific surface area and surface roughness. IR spectroscopy clearly indicates a net decrease of isolated silanol band correlated with an increase of H-bounded silanol. Proton and silicon NMR spectroscopies confirm the increase of the local density silanol groups on the aged silca surface.Finally, the evolution of the surface properties of these silica samples, aged during about 1000 h, was followed by inverse gas chromatography in infinite dilution (IGC-ID) and at finite concentration (CGI-FC) conditions.The CGI-ID was performed using linear and cyclic alkane probes. It shows that the ageing process affects only very slightly both the dispersive component of surface energy and the nano-roughness at the molecular level of all studied, indicating that the surface morphology is quite unchanged. Then; the variation of their surface heterogeneities with ageing time, in terms of the distribution functions of the probe adsorption energies, was assessed by CGI-CF, using isopropanol as probe.The aging process leads, as expected, to an increase of the high energy component related to the appearance of new silanol groups by nucleophilic opening of siloxane bridges by water confirming the reactivity of fumed silicas toward water when exposed to a high RH. All our observations, existence of a threshold, maximum for the kinetic constant and decrease of the chemisorbed of water amount with both specific surface area and surface roughness is supported by a model for the ageing process. [...]

Made available in DSpace on 2017-07-24T19:38:06Z (GMT). No. of bitstreams: 1 CAROLYNE BRUSTOLIN BRAGA.pdf: 3440444 bytes, checksum: b267696c3988d456840fac4ec2aeded0 (MD5) Previous issue date: 2012-03-07 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / In this study was approached the conformational study of dopamine, L-dopa and L-dopaquinone, in their neutral and protonated forms, by theoretical calculations and NMR and IR spectroscopies. The interest in evaluate the conformational equilibrium of these compounds was obtained by the fact that there are no reports in the literature about them at this level of theory, considering that are compounds with high biological importance. The theoretical calculations were performed at HF/6-311++G(d,p) level of theory, available in the programs package GAUSSIAN 03. These calculations determined the energies and geometries of most stable conformers in the isolated phase and in aqueous solution. For some compounds, the analysis of hyperconjugatives effects by NBO calculations also showed that some orbital interactions stabilize the system. For protonated dopamine, by 1H NMR, it was not possible to associate the solvent or temperature effects with possible changes in populations of conformers. In the case of two forms of L-dopa, the behavior of the couplings constants 3JHH in different solvents and temperatures could not tell us if there was variation in the populations with change of polarity of the medium. However, their values allowed affirm that the predominant form at equilibrium in solution is the trans, in agreement with theoretical data obtained. The carbonyl stretching bands, in IR spectrum, in fundamental region, could not determine the variations in the populational equilibrium, but a significant asymmetry and width of these bands showed that the equilibrium is composed of multiple conformations, such as this case. Finally, electrostatic potential maps were used to demonstrate in the most stable conformers which regions of higher and lower electron density. Keywords: Conformational analysis. Theoretical calculations. NMR Spectroscopy. / Abordamos neste trabalho um estudo conformacional da dopamina, L-dopa e L-dopaquinona, nas suas formas neutras e protonadas, por meio de cálculos teóricos e das espectroscopias de RMN e IV. O que despertou o interesse em avaliar o equilíbrio conformacional desses compostos foi o fato de não existirem relatos na literatura sobre os mesmos com este tipo de nível de teoria, visto que são compostos com grande importância biológica. Os cálculos teóricos foram efetuados com o nível de teoria HF/6-311++G(d,p), disponíveis no pacote de programas GAUSSIAN 03. Por meio deles, determinaram-se as energias e geometrias dos confôrmeros mais estáveis na fase isolada e em solução aquosa. Para alguns compostos, a análise dos efeitos hiperconjugativos por meio dos cálculos de NBO também indicou que algumas interações de orbitais presentes estabilizam o sistema. Para a dopamina protonada, através da RMN de 1H, não foi possível relacionar o efeito do solvente nem da temperatura com possíveis mudanças nas populações dos confôrmeros. No caso das duas formas da L-dopa, o comportamento dos acoplamentos 3JHH em diferentes solventes e diferentes temperaturas não pôde nos dizer que houve variação de população com a mudança de polaridade do meio. Entretanto, seus valores permitiram afirmar que em solução a forma predominante no equilíbrio é a trans, corroborando com os dados teóricos obtidos. Com espectros no Infravermelho na região do fundamental do estiramento da carbonila, para a L-dopa, novamente não pudemos verificar a variação de população no equilíbrio, mas a significativa assimetria e largura destas bandas permitiu verificar que o equilíbrio está composto por vários confôrmeros, como é o caso. Finalmente, fez-se o uso de mapas de potencial eletrostático para demonstrar nos confôrmeros mais estáveis quais as regiões de maior e menor densidade eletrônica.

ATP-dependent chromatin remodelers have been proposed to act sequentially, and to a certain extent non-redundantly, in the priming stages of the DNA Damage Response pathways by establishing chromatin in lesion sites ready to act as a scaffold for repair factors or to be displaced in order to allow DNA repair. Among remodeling factors proposed to play a role in DNA repair is SMARCAD1, a poorly characterized, non-canonical member of the SWR1-like family of SNF2/SWI2 superfamily of ATPases, which has recently been identified as a potential target for ATM/ATR phosphorylation at canonical and non-canonical sites upon DNA damage. The actual mechanism for SMARCAD1 recruitment and involvement in DNA remodeling is still unknown, and unlike most other chromatin remodelers, SMARCAD1 does not contain DNA- or histone-binding domains frequently accompanying such proteins. Instead, in addition to the core ATPase domain, only two CUE domains (a type of helical ubiquitin-binding domain) have been identified. This thesis presents the findings of an investigation intended to structurally characterize SMARCAD1 by dissecting and identifying its domain architecture, and examining the activity and ligand selectivity of its binding domains in the functional context of DNA damage repair. The solution NMR structure of the CUE1 domain is presented, describing a triple helix bundle consistent with other members of the family. Furthermore, a novel SUMO interacting motif was identified and through a combination of NMR titrations and phospho-proteomics analysis, shown to be constitutively phosphorylated which excludes the possibility of DNA damage dependent ATM targeting as the recruitment mechanism for DNA repair. Additionally, it is demonstrated that both CUE domains are poor binders of mono-ubiquitin, however CUE1 specifically mediates the high affinity binary interaction with the transcriptionally repressive master regulator KAP1. This interaction was shown to be independent of post-translational ubiquitylation but rather sustained through direct interaction with the dimeric RBCC domain of KAP1. Finally, mass spectrometry profiling of domain-dependent interactions (based on differential abundance relative to changes due to chemically induced DNA damage) suggests SMARCAD1 may be involved in p53 transcriptional regulation through interactions maintained with CUE1 prior to DNA damage, whereas the SIM domain selectively targets protein interactions upon DNA damage that simultaneously activate p53 transcriptional control and recruit SMARCAD1 to DNA damage repair pathways.

Avec l'âge, les propriétés mécaniques des os se détériorent, conduisant à un risque accru de fracture. Bien que les mesures de densité minérale osseuse permettent de prédire, dans une certaine mesure, ces risques, elles restent insuffisantes dans un grand nombre de cas. Une compréhension plus complète des différents facteurs permettant de définir la « qualité » d'un os est donc souhaitable. Il est connu que la résistance à la fracture de tissus osseux est affectée non seulement par la glycosylation non-enzymatique du collagène, mais aussi par des protéines non collagéneuses comme l'ostéocalcine (OC) et l'ostéopontine (OPN). Cependant, le rôle structural de ces deux protéines dans l'os est mal connu, de même que la façon dont elles contribuent aux propriétés mécaniques globales. L'objectif de cette thèse est donc de répondre à ces deux points. Un modèle synthétique a ainsi été développé pour élucider quelles sont les interactions-clés gouvernant l'interaction de l'OC et l'OPN avec la phase minérale osseuse. Par ailleurs, en utilisant des os de souris génétiquement modifiées (déficientes en OC et/ou OPN), des études RMN solide ont été menées, pour élucider le rôle de l'OC et l'OPN à l'interface organique-inorganique. Leur lien avec les propriétés mécaniques a aussi été étudié en détail, via des tests de rupture, de fatigue et de fluage. Les résultats obtenus montrent que l'OC et l'OPN ont un rôle structural important dans les tissus osseux, et qu'elles contribuent aux propriétés mécaniques par le biais de leurs interactions ioniques, au niveau des interfaces entre les fibrilles de collagène minéralisés. / The decrease in bone mechanical properties occurs with age. The associated fragility fractures present a global public health concern. The use of bone mineral density as a predictor of risk of fracture is, however, limited. A more comprehensive understanding of bone quality and its link to bone fragility is thus desirable. Besides the brittleness caused by nonenzymatic glycation of collagen, bone fracture resistance is also influenced by noncollagenous components such as osteocalcin (OC) and osteopontin (OPN). The structural role of OC and OPN in bone and how they contribute to mechanical properties is however unclear. The objective of this thesis is to elucidate these two aspects. Key interactions associated with the binding of OC and OPN to bone mineral were studied in a synthetic model. Using genetically modified animal model lacking OC and/or OPN, the role of OC and OPN in organic-inorganic interface was examined by solid state NMR, and their link to mechanical properties was studied via a series of tissue level mechanical tests, measuring fracture toughness, creep, or fatigue. Based on the results obtained, it is concluded that OC and OPN are present as structural elements in bone and contribute to tissue mechanical properties via ionic interactions at the interfaces between mineralized fibrils.

Spectrally sparse signals arise in many applications of signal processing. A spectrally sparse signal is a mixture of a few undamped or damped complex sinusoids. An important problem from practice is to reconstruct such a signal from partial time domain samples. Previous convex methods have the drawback that the computation and storage costs do not scale well with respect to the signal length. This common drawback restricts their applicabilities to large and high-dimensional signals. The reconstruction of a spectrally sparse signal from partial samples can be formulated as a low-rank Hankel matrix completion problem. We develop two fast and provable non-convex solvers, FIHT and PGD. FIHT is based on Riemannian optimization while PGD is based on Burer-Monteiro factorization with projected gradient descent. Suppose the underlying spectrally sparse signal is of model order r and length n. We prove that O(r^2log^2(n)) and O(r^2log(n)) random samples are sufficient for FIHT and PGD respectively to achieve exact recovery with overwhelming probability. Every iteration, the computation and storage costs of both methods are linear with respect to signal length n. Therefore they are suitable for handling spectrally sparse signals of large size, which may be prohibited for previous convex methods. Extensive numerical experiments verify their recovery abilities as well as computation efficiency, and also show that the algorithms are robust to noise and mis-specification of the model order. Comparing the two solvers, FIHT is faster for easier problems while PGD has a better recovery ability.

Perfluoroalkyl substances (PFASs) are contaminants of emerging concern, and have been detected in drinking water, wildlife, humans, and the environment. Cyclodextrins (CDs), cyclic sugars composed of glucose monomers, are proposed as a potential remediation strategy. CDs can form host-guest complexes with hydrophobic molecules; this complexation could be capitalized on for PFAS removal and sequestration. These dissertation projects aim to study the fundamental host-guest interactions between a variety of PFASs and CDs for eventual applications in environmental and biological remediation. 1D and 2D Nuclear magnetic resonance (NMR) spectroscopic methods were employed to determine the strength, dynamics, and structure of the CD:PFAS host-guest complexes. Legacy and emerging PFASs were studied with the three native CDs (α-, β-, and γ-CDs) as well as β-CD derivatives. β-CD and its derivatives exhibit the strongest complexation with all studied PFASs, with association constants of 102-105 M-1, depending on PFAS chain length, functional groups, and branching. The host-guest complex was not significantly disturbed under different environmental conditions, such as changing pH, ionic strength, and in the presence of humic acid. A competition study between perfluorooctanoic acid (PFOA), β-CD, and human serum albumin (HSA), the most abundant protein in blood serum, was then conducted using NMR, circular dichroism, and fluorescence spectroscopies. Excess β-CD was able to totally reverse all PFOA binding to HSA. Finally, the host-guest complex was studied within a biological organism to test its viability as a remediation strategy. The attenuation of the toxicity of PFOA in zebrafish embryos, a model organism for toxicology studies, was tested with β-CD. Excess β-CD increased the LC50 (lethal concentration for 50 % of the population) of PFOA compared to PFOA in the absence of β-CD (p < 0.0001). These dissertation projects suggest that the encapsulation of PFASs by CDs has potential in PFAS remediation strategies.