Thesis (Ph. D.)--West Virginia University, 1999. / Title from document title page. Document formatted into pages; contains xii, 96 p. : ill. Includes abstract. Includes bibliographical references.

Thesis--Uppsala. / In Periodical Room.

Submitted by KELLY TASSO DE PAULA null (kelly_tasso@hotmail.com) on 2016-02-02T18:47:39Z No. of bitstreams: 1 Dissertação Kelly 2015 v6 .pdf: 6882664 bytes, checksum: 58b55229d09b2ae6003279a8396261d6 (MD5) / Approved for entry into archive by Juliano Benedito Ferreira (julianoferreira@reitoria.unesp.br) on 2016-02-02T19:47:27Z (GMT) No. of bitstreams: 1 paula_kt_me_rcla.pdf: 6882664 bytes, checksum: 58b55229d09b2ae6003279a8396261d6 (MD5) / Made available in DSpace on 2016-02-02T19:47:27Z (GMT). No. of bitstreams: 1 paula_kt_me_rcla.pdf: 6882664 bytes, checksum: 58b55229d09b2ae6003279a8396261d6 (MD5) Previous issue date: 2016-01-28 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / A isomerização fotoinduzida transcis reversível de azocompostos tem sido extensivamente estudada nas últimas décadas. A fotoisomerização transcis das moléculas azoaromáticas ocorre quando estas moléculas fotocromáticas são expostas à irradiação de luz com comprimento de onda apropriado. A incorporação desses azocompostos em matrizes poliméricas tem originado materiais com potenciais aplicações em diversos campos como óptica não linear e sistemas de armazenamento óptico. Esse trabalho é dedicado à preparação e caracterização óptica de filmes de ORMOSIL (silicatos organicamente modificados) dopados com os azocorantes Methyl Red (MR) e Methyl Orange (MO). Estes materiais híbridos combinam as vantagens do processo sol-gel, com características específicas de polímeros orgânicos, permitindo o processamento de filmes finos, sem fraturas e fissuras. As amostras foram preparadas via processo sol-gel, a partir do alcóxido 3-glicidoxipropiltrimetoxissilano (GPTMS) dopado com MR e MO. A matriz foi depositada em forma de filmes finos sobre lâminas de vidro pela técnica de revestimento por imersão (dip coating). Para as caracterizações ópticas dos filmes foram realizadas medidas de espectroscopia de absorção UV/Vis, que permitiu a identificação das bandas de absorção e sua variação quando expostas a um feixe de luz. Os filmes mostraram mudanças reversíveis no seu espectro de UV/Vis de absorção relacionada com a fotoisomerização de trans-cis induzida pela luz quando expostos a um LED branco de alta intensidade. O efeito fotocrômico apresentado pelas amostras foi analisado em diferentes irradiâncias do feixe de excitação, onde foi possível a determinação das constantes de tempo para cada irradiância. Também foi analisado o fotocromismo na presença de bombeio óptico em diferentes temperaturas, o que permitiu a determinação da energia de ativação do processo de fotoisomerização cis-trans(em ausência de luz) (91,4 kJ/mol para a amostra dopada com MR e 82,6 kJ/mol para a amostra dopada com MO). / The reversible photoinduced trans  cis isomerization of azo dye-doped compounds has been extensively studied in the last decades. The trans  cis photoisomerization of azodye molecules occurs when these photochromic molecules are photo-selected by linearly polarized light of appropriate wavelength. The incorporation of these azo compounds in polymeric matrices has given rise to materials with potential applications in various fields as nonlinear optics and optical storage systems. This work is dedicated to the preparation and optical characterization of ORMOSIL (Organic Modified Silicates) films doped with Methyl Red (MR) and Methyl Orange (MO) azo dyes. These hybrids materials combine the advantages of sol-gel process with specifics characteristics of organic polymers, allowing the preparation of thin films without fractures or cracks. ORMOSIL samples were prepared by sol-gel process derived from 3-Glycidoxypropyltrimethoxysilane (GPTS) alkoxide doped with MR and MO. MR and MO-doped GPTS-derived thin films were deposited onto glass slides by dip-coating technique. In order to characterize optically, UV/Vis absorption spectroscopy measurements were performed, which allowed the identification of the absorption bands, and its variation when exposed to a light beam. Films samples showed reversible changes in its UV-Vis absorption spectrum related to the trans-cis photoisomerization induced by light when exposed to a cold white LED. The photochromic effect of the samples was analyzed at different light intensities of the excitation beam, where it was possible to determine the time constants for each irradiance. It was also analyzed in the presence of optical pumping at different temperatures, allowing the determination of the activation energy of the cis-trans photoisomerization process (in the dark) (91.4 kJ/mol for the MR-doped and 82.6 kJ/mol for the MO-doped GPTMS-derived thin films).

NMR spectroscopy with in situ laser irradiation has been used to investigate the photo- and thermal isomerisation of eight azobenzene derivatives; diphenyldiazene (azobenzene), p-phenylazoaniline (p-aminoazobenzene), 4-(dimethylamino)azobenzene (Methyl Yellow), 4-dimethylamino-2-methylazobenzene (o-Methyl-Methyl Yellow), p-nitroazobenzene, 4-nitro-4’-dimethylaminoazobeneze (Dimethyl-nitroazobenzene), 4-(4-nitrophenylazo)aniline (Disperse Orange 3) and N-ethyl-N-(2-hydroxyethyl)-4-(4-nitrophenylazo) (Disperse Red 1). The rate constants and activation parameters of the thermal cis-to-trans isomerisation have been measured experimentally and correlated to the mechanism of isomerisation in two solvents. The experimental data show that the values of the activation energy (related to the enthalpy of activation) and the entropy of activation (related to the Arrhenius pre-exponential factor) vary significantly from molecule to molecule and thus both of these parameters influence the inter-molecule variation of the rate constant. Similarly, both of these parameters influence the solvent-dependence of the rate constant. Complementary computational studies have been carried out in the gas phase and in solution using density functional theory (DFT) to predict the structures of the cis and trans isomers and the transition state, and to explore the reaction coordinate. The theoretically predicted activation parameters are compared with those determined experimentally, and the utility of DFT calculations in predicting the effects of molecular structure and solvation on the kinetics of cis-to-trans isomerisation assessed. The DFT-predicted values of the activation energy and Gibbs free energy of activation in DMSO are in good agreement with the experimental values, while the values in benzene tend to be in less good agreement. The DFT calculations are unsuccessful at predicting the entropy of activation, where in all cases there is a large discrepancy between the theoretical and experimental values. The DFT- calculated energy differences between the activation energies of the two inversion pathways for the asymmetric azobenzenes suggests the favourable phenyl ring for inversion. The formation of a linear transition state from a dihedral rotation potential energy curve is explained in terms of the lower activation barrier of the more favourable inversion route (α-inversion) than that of the dihedral rotation pathway, and suggests the inversion through the α-phenyl ring to be the favoured pathway for substituted azobenzene. DFT calculations are able to obtain a transition state corresponding to pure rotation pathway for two azobenzene derivatives. The higher activation barrier for the formation of the transition state corresponding to this pathway compared to that of the formation of the α-transition state confirmed the previous conclusion. DFT predictions of the effect of protonation on the thermal rates of isomerisation of azobenzenes substituted with electron-donating group were in good agreement with the experimental results; both conclude faster isomerisation and lower activation barriers on protonation. However, DFT calculations could not confirm the postulation of rotational transition state for the isomerisation of the protonated molecule, as a result of weakening of the N=N bond by protonation.

The amino acid (2S, 4R)-4-hydroxyproline (Hyp) plays a critical role in animal kingdom as structural protein collagen. It is ubiquitous in plant cell walls performing various functions such as structural assembly, plant hormones, plant growth, defense against pathogens, etc. Glycosylation of Hyp is often seen in plant cell walls with L-Arabinofuranose and D-Galactopyranose and not in animal kingdom. Glycosylation is a post-translational modification, which affects characteristics of proteins and peptides. The main objective of this thesis is to synthesize various L-arabinofuranosylated hydroxyproline model amides and investigate their thermodynamic and kinetic properties of cis/trans amide isomerization. These results are compared with the previous research of D-galactopyranosylated hydroxyproline model amides, which may provide an insight to structural implications for their stability and conformations of peptides and specificity in plants. Both - and -L-arabinosylation of Hyp resulted in the stabilization of trans rotameric state at room temperature while the α-anomer leads to cis rotamer stabilization at higher temperature. Similarly, both unnatural 4S-hydroxyproline (hyp) building blocks resulted in stabilization of trans rotamer but α-anomer shows exo configuration instead of endo. This result shows a reverse trend when compared to galactosylated hydroxyproline building blocks as previous research results in our group. Our results may provide further insight to the role of glycosylation on protein structure and stability in plants.

Zugl.: Göttingen, Univ., Diss., 2009

Pin1 is an enzyme central to cell signaling pathways because it catalyzes the cis–trans isomerization of the peptide ω-bond in phosphorylated serine/threonine-proline motifs in many proteins. This regulatory function makes Pin1 a drug target in the treatment of various diseases. The effects of phosphorylation on Pin1 substrates and the basis for Pin1 recognition are not well understood. The conformational consequences of phosphorylation on Pin1 substrate analogues and the mechanism of recognition by the catalytic domain of Pin1 were determined using molecular dynamics simulations. Phosphorylation perturbs the backbone conformational space of Pin1 substrate analogues. It is also shown that Pin1 recognizes specific conformations of its substrate by conformational selection. Dynamical correlated motions in the free Pin1 enzyme are present in the enzyme of the enzyme–substrate complex when the substrate is in the transition state configuration. This suggests that these motions play a significant role during catalysis. These results provide a detailed mechanistic understanding of Pin1 substrate recognition that can be exploited for drug design purposes and further our understanding of the subtleties of post-translational phosphorylation and cis–trans isomerization. Results from accelerated molecular dynamics simulations indicate that catalysis occurs along a restricted path of the backbone configuration of the substrate, selecting specific subpopulations of the conformational space of the substrate in the active site of Pin1. The simulations show that the enzyme–substrate interactions are coupled to the state of the prolyl peptide bond during catalysis. The transition-state configuration of the substrate binds better than the cis and trans states to the catalytic domain of Pin1. This suggests that Pin1 catalyzes its substrate by noncovalently stabilizing the transition state. These results suggest an atomistic detail understanding of the catalytic mechanism of Pin1 that is necessary for the design of novel inhibitors and the treatment of several diseases. Additionally, a set of constant force biased molecular dynamics simulations are presented to explore the kinetic properties of a Pin1 substrate and its unphosphorylated analogue. The simulations indicate that the phosphorylated Pin1 substrate isomerizes slower than the unphosphorylated analogue. This is due to the lower diffusion constant for the phosphorylated Pin1 substrate.

Among the peptidyl prolyl isomerases, the Cyclophilin family of proteins has been linked to various cellular activities such as regulation of homeostasis, mitochondrial permeability, and cell death. Their functionality spans throughout the cell and throughout all cell types as different isoforms. Previous studies done on Cyclophilin A revealed an interesting contact ensemble when bound to a substrate. Because of the similarity of CypA to its homologues, it is believed that they too will exhibit the same contact dynamics. We have defined the dynamics of cyclophilin isoforms through Molecular Dynamics simulations and determined their contact dynamics, characterizing their contact ensembles, and their relative dynamical conservation to each other.

Les switches multimodulables sont des systèmes qui, sous l'action d'un ou de plusieurs stimuli extérieurs, donnent naissance à un ensemble d'états aux propriétés physico-chimiques différentes. Au cours de cette thèse, plusieurs voies de synthèse permettant l'obtention d'une nouvelle famille de biphotochromes organiques constitués d'un dithiényléthène relié à une indolino[2,1-b]oxazolidine ont été mises au point. Les dithiényléthènes préparés présentent d'excellentes performances photochromiques et s'interconvertissent de façon réversible entre deux états stables thermiquement. Les 10-styryl-indolino[2,1-b]oxazolidines sont des molécules acidochromiques et doublement photochromiques par ouverture du cycle oxazolidine ou isomérisation de la double liaison. Ce système moléculaire compte jusqu'à huit états multicolores aux propriétés physico-chimiques différentes, accessibles par irradiations lumineuses et variation de l'acidité. Les propriétés ont été étudiées en solution et en matrice polymère, tous les états des biphotochromes étant caractérisés par spectroscopie d'absorption électronique et RMN. Cette thèse a été l'occasion de développer le premier système multimodulable incorporant huit états différents au sein d'une même molécule. / Multi-addressable switches are systems that give rise to a set of states with different physical-chemical properties upon the effect at least one external stimulus. During this thesis, several synthetic routes to a new family of organic biphotochromes composed of a dithienylethene linked to an indolino[2,1-b]oxazolidine have been developed. Synthesized dithienylethenes exhibit excellent photochromic properties and can be reversibly photoswitched between two thermally stable states. 10-styryl-indolino[2,1-b]oxazolidines are acidochromic molecules and photochromic by opening of the oxazolidine ring or cis/trans isomerization of the double bond. This molecular system exhibits up to eight multicoloured states with different physical-chemical properties, interchangeable by different sequences of light irradiation and pH variation steps. Properties were studied in solution and in a polymer matrix and all biphotochromes states have been characterised by electronic absorption spectroscopy and NMR. Additionally, the first multi-addressable system incorporating eight different states within the same molecule is described.

Cyclophilins are ubiquitous enzymes that are involved in protein folding, signal transduction, viral proliferation, oncogenesis, and regulation of the immune system. Cyclophilin A is the prototype of the cyclophilin family. We use molecular dynamics to describe the catalytic mechanism of cyclophilin A in full atomistic detail by sampling critical points along the reaction coordinate, and use accelerated molecular dynamics to sample cis-trans interconversions. At these critical points, we analyze the conformational space sampled by the active site, flexibility of the enzyme backbone, and modulation of binding interactions.We use Kramer’s rate theory to determine how diffusion and free energy contribute to lowering the activation energy of prolyl isomerization. We also find preferential binding modes of several cyclophiln A inhibitors, and compare the conformational space sampled by inhibited cyclophilin A to the conformational space sampled during wild-type interactions. We also analyze the mechanism of the next family member cyclophilin B in order to probe differences in enzyme dynamics and intermolecular interactions that could possibly be exploited in isoform-specific drug design. Our results indicate that cyclophilin proceeds by a conformational selection binding mechanism that manipulates substrate sterics, electrostatic interactions, and multiple reaction timescales in order to speed up reaction rate. Conformational space sampled by cyclophilin when inhibited and when undergoing wild-type interactions share significant similarity. Cyclophilins A and B do have notable differences in enzyme dynamics, due to variation in intramolecular interactions that arise from variation in primary structures. This work demonstrates how computational methods can be used to clarify catalytic mechanisms.