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1
Schmid, Marco. "Conformational dynamics of G-quadruplex DNA probed by time-resolved circular dichroism." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLX107/document.
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Les quadruplexes de guanines (G4) sont des structures d’ADN non-canoniques qui résultent de l’empilement hydrophobe de tétrades de guanines, stabilisé par des cations métalliques (tels que Na+ et K+). Il existe aujourd’hui un nombre croissant de preuves expérimentales qui attestent de l’implication des G4 dans d’importantes fonctions cellulaires corrélées à leur mécanisme de repliement/dépliement. Toutefois, très peu d’études ont abordé les aspects dynamiques de leur formation. Aussi, nous avons entrepris l’étude de plusieurs G4 mono-moléculaires à l’aide d’une nouvelle extension d’expériences de saut de température, capable de mesurer la dynamique de dénaturation thermique et de renaturation consécutive de l’ADN, sur une fenêtre temporelle allant de quelques millisecondes aux secondes. Les changements conformationnels ont été sondés par dichroïsme circulaire (CD) résolu en temps, connu pour être très sensible à l’arrangement des guanines dans les G4. Au préalable des études résolues en temps, en collaboration avec DISCO/SOLEIL, nous avons mesuré les spectres CD statiques de différentes séquences G4 présentant des topologies distinctes, comme celles des télomères humains, de l’aptamère de la thrombine ou des promoteurs de c-MYC. Nous avons observé des cinétiques de dénaturation et renaturation biphasiques avec des constantes de temps de quelques centaines de millisecondes et quelques secondes. Ces cinétiques dépendent fortement de l’amplitude du saut de température et de la concentration de cations métalliques. L’ensemble de ces observations suggère l’existence de plusieurs voies de repliement/dépliement des G4 sur des surfaces de potentiel très rugueusesGuanine-quadruplexes (G4) are non-canonical DNA structures that result from the hydrophobic stacking of guanine quartets stabilized by metal cations (typically Na+ and K+). There is now an increasing body of experimental evidence of their occurrence in important cell functions correlated to their folding/unfolding mechanisms. However, only few studies have addressed the dynamical aspect of their formation. In this context, we have undertaken the study of several intramolecular G4 with a novel extension of temperature-jump experiments capable to measure the thermal denaturation and the consecutive renaturation of DNA over a time window spanning a few ten milliseconds to seconds. Conformational changes have been monitored by time-resolved circular dichroism (CD), which is known to be sensitive to the chiral arrangement of guanines in the G4 scaffolds.Prior to time-resolved measurements, within the frame of a collaboration with DISCO/SOLEIL, we have performed static synchrotron radiation CD measurements on several short G4-forming sequences, such as human telomere, thrombin-binding aptamer and c-MYC promoter sequences, displaying distinct topologies. Denaturation and renaturation kinetics are found to exhibit biphasic decays with time constants of a few hundred milliseconds and a few seconds, respectively. Those kinetics depend strongly on the amplitude of the temperature jump and the concentration of cations. Taken together these observations suggest the existence of multiple folding pathways on extremely rugged landscapes
2
Bulheller, Benjamin M. "Circular and linear dichroism spectroscopy of proteins." Thesis, University of Nottingham, 2009. http://eprints.nottingham.ac.uk/10866/.
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Circular dichroism (CD) is an important technique in the structural characterization of proteins, and especially for secondary structure determination. The CD of proteins can be calculated from first principles using the matrix method, with an accuracy that is almost quantitative for helical proteins. Thus, for proteins of unknown structure, CD calculations and experimental data can be used in conjunction to aid structure analysis. The vacuum-UV region (below 190 nm), where charge-transfer transitions have an influence on the CD spectra, can be accessed using synchrotron radiation circular dichroism (SRCD) spectroscopy. Calculations of the vacuum-UV CD spectra have been performed for 71 proteins, for which experimental SRCD spectra and X-ray crystal structures are available. The theoretical spectra are calculated considering charge-transfer and side chain transitions, which significantly improves the agreement with experiment, raising the Spearman correlation coefficient between the calculated and experimental intensity at 175 nm from 0.12 to 0.79. The influence of the different conformations used for the calculation of charge-transfer transitions is discussed in detail, focussing on the effect in the vacuum-UV. Linear dichroism (LD) provides information on the orientation of molecules but is more challenging to analyze than CD. To aid the interpretation of LD spectra, the calculation of protein LD using the matrix method is established and the results compared to experimental data. The orientations of five prototypical proteins are correctly reproduced by the calculations. Using a simplified approach, matrix method parameter sets for the nucleic bases and naphthalenediimide (NDI) have been created and are used to determine DNA/RNA conformations and to study NDI nanotubes. Finally, to make CD and LD calculations available for the scientific community in an easy-to-use fashion, the web interface DichroCalc is introduced.
3
Lees, Jonathan Gill. "Circular dichroism spectroscopy : informatics and new methodologies." Thesis, Birkbeck (University of London), 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.413799.
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Miles, Andrew John. "Synchrotron radiation circular dichroism : standardisation and new methods." Thesis, Birkbeck (University of London), 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.428084.
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George, S. J. "Magnetic circular dichroism studies of iron-sulphur proteins." Thesis, University of East Anglia, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.376059.
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Harding, Christopher John. "Photoelectron circular dichroism in gas phase chiral molecules." Thesis, University of Nottingham, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.430538.
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McCann, Jennifer L. "A vibrational circular dichroism study of optically active polymers." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp02/NQ34685.pdf.
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Orry, Andrew John Wooldridge. "Molecular modelling and circular dichroism studies of membrane proteins." Thesis, Birkbeck (University of London), 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.248128.
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On the basis of preliminary infonnation from genome projects it has been estimated that approximately 10000 different membrane proteins could exist in the human being. A membrane protein of some description is involved in nearly every biochemical pathway, therefore knowledge of their structure is essential for detennination of function and for rational drug design. Membrane proteins are extremely hard to crystallize due to their amphipathic nature and therefore we explore other structural detennination methods in order to gain infonnation about membrane proteins. These methods are, membrane protein sequence analysis, molecular modeling, conventional circular dichroism (CD) and synchrotron radiation circular dichroism spectroscopy (SRCD) which enable a detennination of structure, function and can be used as a basis for rational drug design. Sequence analysis studies were undertaken on the defective gene product of CLN2 which is involved in the neurodegenerative disease late infantile neuronal ceroid lipofuscinoses (LINCL). A one transmembrane helix structure is proposed for this membrane protein. A model is proposed for its structure in membranes, and how it may function as a proteinase to aid in the maturation of subunit c of the mitochondrial A TP complex. Its role is contrasted with that of the CLN3 protein, which is involved in the juvenile form of the disease. Molecular modeling studies were undertaken on the endothelin G-protein coupled receptor. The endothelins are important regulators of the vascular system and endothelin-l is the most potent vasoconstrictor yet characterized. Computational docking studies have been undertaken in order to detennine whether endothelins that have been isolated bind to the modeled receptor. The model of the receptor/ligand complexes produced forms a basis for rational drug design of agonists and antagonists for this G-protein coupled receptor. Conventional circular dichroism spectroscopy has been used to analyze the effects of organic solvents on the membrane protein bacteriorhodopsin. Circular dichroism analysis was also undertaken on membrane proteins whose crystal 2 structures have already been detennined. These studies involved using SRCD which enables low wavelength data to be obtained. Inclusion of data in this wavelength region in reference databases used for calculations of secondary structures could provide for much better accuracy in determination of the content of sheet, tum, polyproline II and aperiodic types of secondary structures.
9
Dang, Zhijing. "Theoretical studies of protein folding and circular dichroism spectroscopy." Thesis, University of Nottingham, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.406982.
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Saha, Supriya. "Circular dichroism and exotic pairing in heavy fermion superconductors." Thesis, University of Bristol, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.358031.
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Hewson, Daniel James. "Iridescence and circular dichroism in cellulose nanocrystal thin films." Thesis, University of Exeter, 2017. http://hdl.handle.net/10871/32480.
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Only in recent times has the true potential of cellulose as a high-end functional and sustainable material been realised. As the world’s most abundant resource cellulose has been utilised by man throughout history for timber, paper and yarns. It is found in every plant as a hierarchical material and can be extracted and converted into fibres which are of great use, especially in the form of nanofibrous materials. This thesis has focused on the utilisation and ability of cellulose nanocrystals (CNCs) to generate structural colour in fabricated thin films. This has been achieved in two ways: Firstly, the natural morphology of CNCs and their ability to form a suspension have been applied to a layer-by-layer (LbL) regime to produce tunable Bragg reflecting thin films. Secondly, a novel technique combining profilometry and spectroscopy has been developed to estimate the distribution of CNCs within EISA thin films and correlate this with the optical properties of the film. This thesis reports the successful fabrication of synthetic CNC LbL Bragg reflecting thin films. The film was compiled using an additive layer-by-layer technique which allowed the construction of a multi-layered thin film and control over individual layer thicknesses and refractive index. Also reported is the discovered reflection of both left and right handed circularly polarised light (CPL) from CNC EISA thin films. These reflections were found to correlate with CNC distribution within the thin films. The distribution of CNCs was estimated using a novel technique which combined spectroscopically measured film absorbance as a function of the volume of the film area under investigation. The specific volumes were calculated using profilometry measurements and the beam spot size used in the spectroscopy measurements.
12
Li, Zhuo. "Theoretical study of the circular dichroism spectroscopy of proteins." Thesis, University of Nottingham, 2018. http://eprints.nottingham.ac.uk/49128/.
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Circular dichroism (CD) spectroscopy is an important technique in studying protein structure, especially for protein secondary structures and conformational changes during biological processes. A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper interpretation and insight into biophysical and simulation studies of protein dynamics and folding. Vibrational structure in the electronic CD spectra of proteins is an important source of information on protein conformation and can be exploited to study structure and folding. We employ the state-averaged complete active space (CAS) method to calculate the ab initio electronic ground and excited states of N-methylacetamide (NMA), toluene, p-cresol and 3-methylindole (3-MI), which represent chromophores that are significant in the CD spectroscopy of proteins in the far- and near-ultraviolet (UV) regions. The results of these calculations are used to incorporate vibronic levels of the excited states into first principles calculations of CD using an exciton approach. The far-UV CD spectra of a set of 49 proteins, comprising a range of structural types, are calculated to assess the influence of the vibrational structure. The calculated spectra of -helical proteins are better resolved using the vibronic parameters and correlation between the experimental and the calculated intensity of less regular structure proteins improves over most wavelengths in the far-UV. No obvious improvement is observed in the calculated spectra of regular -sheet proteins. The near-UV CD spectra of 40 proteins are calculated with the new parameter set and the correlation between the computed and the experimental intensity from 270 to 290 nm is much improved. The contribution of individual chromophores to the CD spectra has been calculated for several mutants and in many cases helps rationalize changes in their experimental spectra. Considering conformational flexibility by using families of NMR structures leads to further improvements for some proteins and illustrates an informative level of sensitivity to side chain conformation. In several cases, the near-UV CD calculations can distinguish the native protein structure from a set of computer-generated misfolded decoy structures. CD spectra of proteins are better reproduced in both far- and near-UV by considering vibrational structures in electronic transitions of chromophores. This improvement can provide more details in connecting the spectroscopic data to the conformations of proteins and will encourage a broader use of CD in protein studies. Besides shedding light on the importance of vibronic transition, results in this thesis also show other aspects that may further improve CD calculations, such as developing parameters of disulfide bond, calculating CD using molecular dynamics (MD) trajectories and taking into account the influence of surroundings of chromophores.
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Bouldi, Nadejda. "Theory of X-ray circular dichroism and application to materials under pressure." Electronic Thesis or Diss., Paris 6, 2017. http://www.theses.fr/2017PA066491.
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Le but principal de cette thèse était de calculer les spectres de dichroïsme circulaire magnétique de rayons~X au seuil K afin de fournir un outil pour interpréter les spectres expérimentaux, jusqu'ici très déroutants. La détermination du dichroïsme circulaire nécessite le calcul précis des spectres d'absorption des rayons~X polarisés circulairement. Nous avons constaté que la théorie des perturbations semi-classique dépendante du temps, communément utilisée pour calculer les sections efficaces d'absorption et de diffusion, est incompatible à la fois, avec l'invariance de jauge et avec les descriptions semi-relativistes de la dynamique des électrons. Pour résoudre ces problèmes, on applique une transformation de Foldy-Wouthuysen aux sections efficaces relativistes données par l'électrodynamique quantique. Ainsi, un nouveau terme d'interaction lumière-matière émerge, que nous avons appelé "spin-position". Une approche performante a été développée pour calculer la section efficace d'absorption afin d'obtenir le dichroïsme circulaire magnétique de rayons~X (XMCD) et le dichroïsme circulaire naturel de rayons~X (XNCD). La méthode numérique repose sur la théorie de la fonctionnelle de la densité en ondes planes avec des pseudopotentiels. Nous constatons que le terme couplant l'opérateur dipolaire électrique avec l'opérateur spin-position contribue significativement au XMCD au seuil K du fer, du nickel et du cobalt ferromagnétiques et nous l'expliquons grâce aux règles de somme. Nous avons également appliqué la méthode aux calculs du XMCD dans FeH et CrO2. Dans les deux cas, la combinaison de l'expérience et de la théorie conduit à un enrichissement mutuelThe main purpose of this thesis was to compute X-ray magnetic circular dichroism spectra at the K-edge in order to provide a tool to interpret the, so far very puzzling, experimental spectra. Computation of circular dichroism requires precise calculations of X-ray absorption spectra (XAS) for circularly polarized light. We have found that there is an incompatibility of the semi-classical time-dependent perturbation theory commonly used to calculate light absorption and scattering cross-sections with both gauge invariance and semi-relativistic descriptions of the electron dynamics. The problems are solved by applying a Foldy-Wouthuysen transformation to the fully relativistic cross-sections given by quantum electrodynamics. In the process, a new light-matter interaction term emerges, that we named the "spin-position" interaction. An efficient first-principles approach was developed to compute the absorption cross-section in order to obtain X-ray magnetic circular dichroism (XMCD) and X-ray natural circular dichroism (XNCD). The numerical method relies on density-functional theory with plane waves and pseudopotentials. We find that the term coupling the electric dipole operator with the spin-position operator contributes significantly to the XMCD at the K-edge of ferromagnetic iron, cobalt, and nickel. We obtain a sum rule relating this term to the spin magnetic moment of the p states. We also applied the method to calculations of K-edge XMCD in FeH and CrO2. In both cases, the combination of experiment and theory leads to mutual enrichment
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Evans, Paul James. "Circular dichroism spectroscopy studies of the eye lens crystallin proteins." Thesis, Birkbeck (University of London), 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.437767.
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Circular dichroism spectroscopy is an established technique that is frequently used in the analysis of the confonnation of biological molecules. It has previously been reported that the deconvolution of circular dichroism spectra of vertebrate eye lens P'rcrystallin proteins gives exceptionally poor results, and that these spectra are heavily influenced by aromatic contributions in the far-ultraviolet. This thesis describes work undertaken to assess to what extent circular dichroism spectra of py-crystallins can be rationalised in tenus of secondary structure, and to determine if circular dichroism can be applied to investigations of the role of crystallin proteins in congenital and agerelated cataract. It Was found that in most py-crystallin spectra, aromatic interference is minor, and that the reported poor quality of py-crystallin deconvolution reflects inherent diffiCulties in deconvolution for most non-helical secondary structures. An instance of aromatic contributions to the far .. ultraviolet spectrum was identified, and investigated through mutagenesis. Synchrotron radiation circular dichroism was used in conjunction with other solution techniques to demonstrate that a loss in solubility of the folded P23T mutation of human yD .. crystallin is responsible for the congenital cataracts associated with this mutation. Finally, circular dichroism was used to investigate the stability and aggregation mechanisms of human fJB2-crystallin, and an assay method developed to show the interaction of fJB2-crystallin with the a.-crystallin molecular chaperone. Information from these experiments was used to describe the unfolding and subsequent aggregation and. chaperone-association of human PB2-crystallin.
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Bingham, Stephen John. "Magnetic circular dichroism and electron paramagnetic resonance of transition ions." Thesis, University of East Anglia, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.357179.
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Short, Geoffrey. "Study of magnetic anisotropy by Magnetic Circular X-ray Dichroism." Thesis, University of York, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.310961.
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Warner, Jeffrey A. (Jeffrey Andrew) Carleton University Dissertation Chemistry. "Detection of metalloporphyrins in crude petroleum using magnetic circular dichroism." Ottawa, 1992.
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Bouldi, Nadejda. "Theory of X-ray circular dichroism and application to materials under pressure." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066491/document.
Full textAbstract:
Le but principal de cette thèse était de calculer les spectres de dichroïsme circulaire magnétique de rayons~X au seuil K afin de fournir un outil pour interpréter les spectres expérimentaux, jusqu'ici très déroutants. La détermination du dichroïsme circulaire nécessite le calcul précis des spectres d'absorption des rayons~X polarisés circulairement. Nous avons constaté que la théorie des perturbations semi-classique dépendante du temps, communément utilisée pour calculer les sections efficaces d'absorption et de diffusion, est incompatible à la fois, avec l'invariance de jauge et avec les descriptions semi-relativistes de la dynamique des électrons. Pour résoudre ces problèmes, on applique une transformation de Foldy-Wouthuysen aux sections efficaces relativistes données par l'électrodynamique quantique. Ainsi, un nouveau terme d'interaction lumière-matière émerge, que nous avons appelé "spin-position". Une approche performante a été développée pour calculer la section efficace d'absorption afin d'obtenir le dichroïsme circulaire magnétique de rayons~X (XMCD) et le dichroïsme circulaire naturel de rayons~X (XNCD). La méthode numérique repose sur la théorie de la fonctionnelle de la densité en ondes planes avec des pseudopotentiels. Nous constatons que le terme couplant l'opérateur dipolaire électrique avec l'opérateur spin-position contribue significativement au XMCD au seuil K du fer, du nickel et du cobalt ferromagnétiques et nous l'expliquons grâce aux règles de somme. Nous avons également appliqué la méthode aux calculs du XMCD dans FeH et CrO2. Dans les deux cas, la combinaison de l'expérience et de la théorie conduit à un enrichissement mutuelThe main purpose of this thesis was to compute X-ray magnetic circular dichroism spectra at the K-edge in order to provide a tool to interpret the, so far very puzzling, experimental spectra. Computation of circular dichroism requires precise calculations of X-ray absorption spectra (XAS) for circularly polarized light. We have found that there is an incompatibility of the semi-classical time-dependent perturbation theory commonly used to calculate light absorption and scattering cross-sections with both gauge invariance and semi-relativistic descriptions of the electron dynamics. The problems are solved by applying a Foldy-Wouthuysen transformation to the fully relativistic cross-sections given by quantum electrodynamics. In the process, a new light-matter interaction term emerges, that we named the "spin-position" interaction. An efficient first-principles approach was developed to compute the absorption cross-section in order to obtain X-ray magnetic circular dichroism (XMCD) and X-ray natural circular dichroism (XNCD). The numerical method relies on density-functional theory with plane waves and pseudopotentials. We find that the term coupling the electric dipole operator with the spin-position operator contributes significantly to the XMCD at the K-edge of ferromagnetic iron, cobalt, and nickel. We obtain a sum rule relating this term to the spin magnetic moment of the p states. We also applied the method to calculations of K-edge XMCD in FeH and CrO2. In both cases, the combination of experiment and theory leads to mutual enrichment
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Vicente, Eduardo Festozo [UNESP]. "Uso de peptideos sintéticos no estudo da proteína diidrooratato desidrogenase humana (HsDHODH)." Universidade Estadual Paulista (UNESP), 2013. http://hdl.handle.net/11449/100730.
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000721605.pdf: 4723399 bytes, checksum: 29bea79ab4fbb0c39fdce178c6b55872 (MD5)A diidroorotato desidrogenase é uma enzima que apresenta um papel central na biossíntese de pirimidinas e catalisa a oxidação do diidroorotato a orotato. A enzima atua durante a via “de novo” de síntese de pirimidinas e está presente em quase todos os organismos vivos. A diidroorotato desidrogenase humana (HsDHODH) pode representar um importante alvo para o tratamento de doenças hiperproliferativas e inflamatórias, já que sua inibição bloqueia a síntese de ácidos nucléicos, impedindo a sua proliferação. Esta enzima tem uma estrutura monomérica e está associada com a membrana interna das mitocôndrias pela sua extensão N-terminal. Assim, entender em detalhes como esta enzima interage com a membrana poderia elucidar um alvo seletivo para drogas antiproliferativas, antiparasíticas e imunossupressivas. Esta região está também envolvida com a catálise central da enzima, sequestrando moléculas de ubiquinona presentes na membrana, fundamentais para as reações de oxirredução feitas pela enzima. Deste modo, para um melhor entendimento destes aspectos, neste trabalho foram sintetizados, por meio da Síntese de Peptídeos em Fase Sólida (SPFS) o peptídeo Ac-GDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLG-NH2, que corresponde ao microdomínio existente na porção N-terminal da HsDHODH, entre os resíduos 33 e 66. Três análogos marcados com o aminoácido paramagnético TOAC nas posições 0, 12 ou 20, além de dois análogos duplamente marcados também foram obtidos. Ambos os peptídeos com dupla marcação possuem uma cisteína ligada ao spin MTSSL na posição 35 (C-terminal) se diferenciando pela posição do segundo marcador: um contendo outra cisteína ligada ao MTSSL na posição 12 e o segundo possuindo o TOAC na posição 0 (ou N-terminal). Estes peptídeos foram estudados por técnicas...
The dihydroorotate dehydrogenase is an enzyme that has a central role on the pyrimidine biosynthesis and catalyses the oxidation of dihydrorotate to orotate. The enzyme acts on de novo pyrimidines nucleotides pathway and it is present in almost all the live organisms. The human dihydroorotate dehydrogenase (HsDHODH) can represent an important target for the treatment of hiperproliferative and inflammatory diseases, since its inhibition blocks the nucleic acid synthesis, which restrains the cell proliferation. This enzyme has a monomeric structure and it is associated into the inner mitochondrial membrane by the N-terminal extension. Thus, understanding in details how this enzyme interacts with the membrane could help to elucidate a selective target for antiproliferative, antineoplasic and immunosuppressive drugs. This region is also involved with the central enzyme catalysis, harboring quinones molecules that are in the membranes, which is essential for the oxidation-reduction reactions made by the HsDHODH. In this way, for a better evaluation of these aspects, in this work we synthesized through the Solid Phase Peptide Synthesis (SPPS) the peptide Ac-GDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLG-NH2, which corresponds to the HsDHODH N-terminal microdomain, between the residues 33 to 66. Three analogues labeled with the paramagnetic amino acid TOAC in the positions 0, 12 or 20 and two doubly labeled analogues were also synthesized. Both doubly labeled peptides contain a MTSSL-attached cysteine residue bounded to the position 35 (C-terminus), differing by the position of the second spin label: one possessing a cysteine with MTSSL at position 12 and the other contains TOAC at position 0 (N-terminus). These peptides were studied by spectroscopy techniques in order to obtain information about... (Complete abstract click electronic access below)
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Vicente, Eduardo Festozo. "Uso de peptideos sintéticos no estudo da proteína diidrooratato desidrogenase humana (HsDHODH) /." Araraquara, 2013. http://hdl.handle.net/11449/100730.
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Orientador: Eduardo Maffud CilliBanca: José Roberto Ernandes
Banca: Patricia Targon Campana
Banca: Antonio José da Costa Filho
Banca: Vani Xavier de Oliveira Junior
Resumo: A diidroorotato desidrogenase é uma enzima que apresenta um papel central na biossíntese de pirimidinas e catalisa a oxidação do diidroorotato a orotato. A enzima atua durante a via "de novo" de síntese de pirimidinas e está presente em quase todos os organismos vivos. A diidroorotato desidrogenase humana (HsDHODH) pode representar um importante alvo para o tratamento de doenças hiperproliferativas e inflamatórias, já que sua inibição bloqueia a síntese de ácidos nucléicos, impedindo a sua proliferação. Esta enzima tem uma estrutura monomérica e está associada com a membrana interna das mitocôndrias pela sua extensão N-terminal. Assim, entender em detalhes como esta enzima interage com a membrana poderia elucidar um alvo seletivo para drogas antiproliferativas, antiparasíticas e imunossupressivas. Esta região está também envolvida com a catálise central da enzima, sequestrando moléculas de ubiquinona presentes na membrana, fundamentais para as reações de oxirredução feitas pela enzima. Deste modo, para um melhor entendimento destes aspectos, neste trabalho foram sintetizados, por meio da Síntese de Peptídeos em Fase Sólida (SPFS) o peptídeo Ac-GDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLG-NH2, que corresponde ao microdomínio existente na porção N-terminal da HsDHODH, entre os resíduos 33 e 66. Três análogos marcados com o aminoácido paramagnético TOAC nas posições 0, 12 ou 20, além de dois análogos duplamente marcados também foram obtidos. Ambos os peptídeos com dupla marcação possuem uma cisteína ligada ao spin MTSSL na posição 35 (C-terminal) se diferenciando pela posição do segundo marcador: um contendo outra cisteína ligada ao MTSSL na posição 12 e o segundo possuindo o TOAC na posição 0 (ou N-terminal). Estes peptídeos foram estudados por técnicas... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: The dihydroorotate dehydrogenase is an enzyme that has a central role on the pyrimidine biosynthesis and catalyses the oxidation of dihydrorotate to orotate. The enzyme acts on "de novo" pyrimidines nucleotides pathway and it is present in almost all the live organisms. The human dihydroorotate dehydrogenase (HsDHODH) can represent an important target for the treatment of hiperproliferative and inflammatory diseases, since its inhibition blocks the nucleic acid synthesis, which restrains the cell proliferation. This enzyme has a monomeric structure and it is associated into the inner mitochondrial membrane by the N-terminal extension. Thus, understanding in details how this enzyme interacts with the membrane could help to elucidate a selective target for antiproliferative, antineoplasic and immunosuppressive drugs. This region is also involved with the central enzyme catalysis, harboring quinones molecules that are in the membranes, which is essential for the oxidation-reduction reactions made by the HsDHODH. In this way, for a better evaluation of these aspects, in this work we synthesized through the Solid Phase Peptide Synthesis (SPPS) the peptide Ac-GDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLG-NH2, which corresponds to the HsDHODH N-terminal microdomain, between the residues 33 to 66. Three analogues labeled with the paramagnetic amino acid TOAC in the positions 0, 12 or 20 and two doubly labeled analogues were also synthesized. Both doubly labeled peptides contain a MTSSL-attached cysteine residue bounded to the position 35 (C-terminus), differing by the position of the second spin label: one possessing a cysteine with MTSSL at position 12 and the other contains TOAC at position 0 (N-terminus). These peptides were studied by spectroscopy techniques in order to obtain information about... (Complete abstract click electronic access below)
Doutor
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Ellzy, Michael Wayne Kay Jack G. "Computational and experimental studies using absorption spectroscopy and vibrational circular dichroism /." Philadelphia, Pa. : Drexel University, 2006. http://hdl.handle.net/1860/1158.
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Zhao, Taiping Nafie Laurence A. Freedman Teresa B. "Near-infrared vibrational circular dichroism of polypeptides and small pharmaceutical molecules." Related electronic resource: Current Research at SU : database of SU dissertations, recent titles available full text, 2004. http://wwwlib.umi.com/cr/syr/main.
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Maharaj, Vanitha. "A vibrational circular dichroism study of deoxyoctanucleotides and their daunorubicin complexes." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp05/nq20751.pdf.
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Schneider, Claus M., Daniel E. Bürgler, Peter M. Oppeneer, Vancho Kocevski, Shigeo Arai, Roman Adam, Kazuyoshi Tatsumi, Ján Rusz, and Shunsuke Muto. "Quantitative characterization of nanoscale polycrystalline magnets with electron magnetic circular dichroism." nature publishing group, 2014. http://hdl.handle.net/2237/20835.
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Garcia-Macias, Gustavo Adolfo. "Molecular photoionisation using synchrotron radiation : photoelectron photoion coincidence and circular dichroism." Thesis, University of Nottingham, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.251988.
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Agrenius, Gustafsson Thomas. "A quantum chemical study of electronic circular dichroism in alanine oligopeptides." Thesis, KTH, Skolan för teknikvetenskap (SCI), 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-231763.
Full textAbstract:
Circular dichroism (CD) spectroscopy, exploiting the wavelength-dependentdifferential absorption of left- and right-handed circularly polarized light, isa popular method of protein characterization. Theoretically computed CDspectra from quantum mechanical computer models of peptides can widen theapplicability of the method. In this work, the usefulness of Time-DependentDensity Functional Theory (TD-DFT) with the CAM-B3LYP functional and6-31+G(d) basis set in obtaining CD spectra of model alanine α-helices 3to 15 residues long is investigated. It is found that including 10 excitedstates per residue in the TD-DFT calculation resolves the characteristic partof the spectra sufficiently. However, the results suffer from blueshift andimproper weakness of the 222 nm peak of the characteristic α-helix spectracorresponding to the n → π∗ transition, despite extension of the basis set to6-311++G(d,p) and use of the Polarizable Dielectric Continuum Model totreat solvent effects. In this case, these issues are limiting the usefulness ofTD-DFT for prediction of peptide CD spectra. More advanced methods totreat solvent interaction and benchmarking the performance of the functionalwith higher-level ab initio methods are suggestions for future studies. A introduction to electronic structure theory and the use of time-dependentperturbation theory to treat spectroscopy is also given in this work.Cirkulär dikroism (CD), den våglängdsberoende skillnaden i absorption avvänster- och högercirkulärpolariserat ljus, utnyttjas i populära spektroskopis-ka metoder för att karakterisera proteiner. Teoretiskt beräknade CD-spektraerhållna från kvantmekaniska datormodeller av peptider kan vidga metodensapplicerbarhet. I detta arbete undersöks användbarheten hos tidsberoendedensitetsfunktionalteori (TD-DFT) med funktionalen CAM-B3LYP och bas-mängden 6-31+G(d) för beräkning av CD-spektra för modeller av α-helixarav alanin, 3 till 15 aminosyror långa. Det visas att beräkningar som inkluderar 10 exciterade tillstånd per alanin är tillräckliga för att erhålla den karakteristiska delen av spektrat hos α-helixar. Resultaten lider dock av blåskiftoch felaktig svaghet hos toppen vid 222 nm i det karakteristiska α-helix-spektrat motsvarande övergången n → π∗, trots utvidgning av basmängdentill 6-311++G(d,p) och användning av metoden Polarizable Dielectric Continuum Model (PCM) för att behandla inverkan från lösningsmedel. Dessabrister begränsar i detta fall användbarheten av TD-DFT för bestämningav strukturbestämning från CD-spektran. Förslag för framtida studier är attbehandla interaktion från lösningsmedlet med mer avancerade metoder samtatt kontrollera prestandan hos funktionalen med ab initio-metoder av högrenivå. En introduktion till elektronstrukturteori och användningen av tidsberoendestörningsteori för att behandla spektroskopi ges även i detta verk.
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Yang, Lin. "Interaction of molecules and helical nanoparticles characterized by electronic circular dichroism." HKBU Institutional Repository, 2018. https://repository.hkbu.edu.hk/etd_oa/523.
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It is of fundamental significance to differentiate an enantiomer from its mirror image (i.e., enantiodifferentiation), through monitoring optical activity (OA) of enantiomers that is typically characterized by electronic circular dichroism (ECD or CD) in the UV-visible region. However, sub-wavelength molecular dimensions substantially prevent enantiomers from effectively perceiving the different circular polarization states, leading to low enantiomeric OA and weak enantiodifferentiation. Some approaches have been developed to amplify the enantiomeric OA; alternatively, on the basis of the emerging chiral metamaterials of metallic helical nanoparticles (HNPs) I devise two methods to enhance the enantiodifferentiation. First, I employ glancing angle deposition (GLAD) to deposit Ag HNPs with a helical pitch (P) larger than wire diameter (d) of the helical, i.e., Ag nanohelices (AgNHs). AgNHs exhibit strong plasmonic CD composed of a broadband longitudinal mode (i.e., L-mode) in the visible region, a transverse mode (i.e., T-mode) at a wavelength of ~370 nm, and a dielectric mode in the deep UV region (at a wavelength shorter than 320 nm). Adsorption of alkyl ligands on the AgNHs markedly weakens the two plasmonic CD modes, and the T-mode is weakened more seriously than the L-mode. The deterioration of the plasmonic CD is exacerbated with increasing the bonding energy of the Ag-alkyl ligand contacts, attributed to the increase of the dielectric constant of the medium of the AgNHs (εr) and the electron withdrawal from the AgNHs towards the alkyl ligands. Derived from the ligand-induced weakening of the plasmonic CD, enantiodifferentiation of L-Glutathione (L-GSH) from D-GSH is dramatically enhanced. The chiroptical weakening sensitively varies with the absolute configuration of GSH, resulting in an enantiodifferentiation anisotropic g factor of ~0.5 that is independent on the AgNH helicity. The AgNH-induced anisotropy g factor is superior to those obtained by other methods, by 2 - 4 orders of magnitude. It is the largest achieved up-to-date, as high as one-fourth of the theoretical maximum. Second, I operate GLAD with fast substrate rotation to reduce P less than d, to generate AgHNPs that exhibit negligible dielectric CD in the deep UV region, offering a helical substrate to directly amplify the OA of enantiomers grafted on the AgHNPs. The anchoring of enantiomers on AgHNPs with the sub-5 nm P leads to the enantioselective amplification of the enantiomeric OA in roughly ten folds; the LH- and RH-AgHNPs give rise to amplify the OA of (S)- and (R)-enantiomers, respectively. It is ascribed to the change of the dihedral angle of an enantiomer adsorbed on AgHNPs. Such the enantioselective amplification tends not to occur as long as P > 5 nm. Moreover, given the enantiodifferentiation of biomolecules that are typically dissolved in an aqueous solution, the effect of water on the plasmonic CD of AgHNPs is investigated and compared with that of AgNHs. Hydrophobic AgNHs with high structural porosity give rise to the irreversible water effect on the plasmonic CD; and hydrophilic AgHNPs with low structural porosity lead to the reversible water effect. At the end, I devise a new methodology to generate plasmonic CD through chirality transfer from chiral host to achiral guest, owing to the helicity duplication of the achiral guest from the chiral host. It leads to inducing chiroptical activity of the achiral guest made of some plasmonic materials that aren't facilely sculptured in the helical. The new methodology effectively broadens the range of materials made from the chiral nanostructures, which is on demand to develop diverse chirality-related bioapplications.
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Heavner, Sue Ellen. "Molecular modeling and experimental determination of the structure of C8-arylguanine modified oligonucleotides that preferentially adopt the Z-DNA conformation." Morgantown, W. Va. : [West Virginia University Libraries], 2004. https://etd.wvu.edu/etd/controller.jsp?moduleName=documentdata&jsp%5FetdId=3366.
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Thesis (Ph. D.)--West Virginia University, 2004.Title from document title page. Document formatted into pages; contains xv, 190 p. : ill. (some col.). Includes abstract. Includes bibliographical references (p. 153-180).
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Singer, R. "Matrix induced effects in the MCD spectra of isolated metal atoms." Thesis, University of East Anglia, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.374272.
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Deng, Junhong. "Numerical and analytical studies of ciricular dichroism of plasmonic nanospirals generated by glancing angle deposition /Deng Junhong." HKBU Institutional Repository, 2017. http://repository.hkbu.edu.hk/etd_oa/345.
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As emerging chiral metamaterials, plasmonic nanospirals (NSs) show strong optical activity that is expected to enhance the enantiodiscrimination of chiral molecules or help in the design of a new generation of integrated optical devices. The study of the optical activity of plasmonic NSs is still in its infancy, and no analytical model exists to describe their chiroptical mechanism. In this study, numerical and analytical simulations are devised to investigate the optical activity of plasmonic NSs that are generated by glancing-angle deposition. The findings will pave the way for the development of novel optical and optoelectronic devices with integrated functions. The CD spectrum of a closely packed random AgNS array has two CD peaks in the UV and visible regions with opposite signs. The pitch-normalized CD in the UV regime tends to be independent of the helical pitch, but that in the visible regime decreases in amplitude as helical pitch increases. The difference can be explained using an analytical LC circuit model and finite-element method simulation. The LC circuit model is used to quantitatively evaluate the chiroptical contribution. It is revealed that radiative loss makes an important chiroptical contribution to the two CD modes and that the visible CD mode receives a greater contribution from radiative loss than does the UV CD mode. Finally, the heterochiral biaxial AgNS arrays alter the sign of the visible CD by switching the incident direction, which shows that the arrays can function as circular polarizers in the visible regime. Furthermore, when AgNSs are deposited on a polymer substrate coated with indium tin oxide, the chiroptical flexible thin film has excellent chiroptical stability when exposed to forward mechanical bending, paving the way for the development of flexible or wearable chiroplasmonic devices.
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Gonçales, Garcia Luana [UNESP]. "Biologia estrutural: expressão e caracterização estrutural da proteína 25K do Cole latent virus." Universidade Estadual Paulista (UNESP), 2012. http://hdl.handle.net/11449/94849.
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goncalesgarcia_l_me_sjrp.pdf: 353281 bytes, checksum: 6786716aa7970dd6c603e25cad2d5709 (MD5)As atividades realizadas compreenderam a produção de cDNA utilizando primer anti-senso e RNA purificado, amplificação do gene codificador da proteína 25K do Cole latent virus (CoLV25K), purificação do fragmento amplificado, ligação em vetor de multiplicação pGEM-T, transformação em células competentes de Escherichia coli linhagem TOP 10, purificação do vetor, digestão enzimática com as enzimas Bam HI e Hind III, subclonagem no vetor de expressão pET28a, transformação em células competentes de E. coli linhagem BL21-RIL, sequenciamento do gene no vetor de expressão e expressão da proteína a 37 o C . Quando expressa a 37 ºC, a proteína, de 25 kDa, foi encontrada em sua totalidade nos corpos de inclusão. Dessa forma, a proteína foi purificada sob condição desnaturante (utilizando 8 M de uréia) e submetida à diálise para seu reenovelamento. Após o reenovelamento, a proteína foi concentrada para aproximadamente 3 mg/mL e foram realizadas medidas de dicroísmo circular, para verificar o seu conteúdo de estrutura secundária, e o espalhamento dinâmico de luz, para estimar a distribuição de tamanho das populações de partículas que estão presentes na solução. Os dados da deconvolução do experimento de dicroísmo circular indicam um percentual de 40-46% α-hélice, 12-14% folha-β, 15-22% voltas e 24-28% de outras estruturas, indicando que a proteína está estruturada; e os dados do espalhamento dinâmico de luz mostraram que a proteína encontra-se estável, monodispersa, mas apresenta um complexo de partículas que deve ser removido para que fique nas condições ideais de cristalização. Foram utilizadas também outras técnicas para tentar alcançar a solubilidade da proteína expressa: abaixando a temperatura...
The experiments performed were, the production of cDNA using anti-sense primers and purified RNA, amplification of the gene encoding the 25K protein of Cole latent virus (CoLV25K), purification of the amplified fragment, cloning in multiplication vector pGEM-T for cell transformation into competent Escherichia coli strain TOP 10, vector purification, enzymatic digestion using the enzymes Bam HI and Hind III, subcloning in expression vector pET28a, transformation into competent cells of E. coli strain BL21-RIL, sequencing of the gene cloned into the expression vector and protein expression at 37 o C. When expressed at 37 °C, the protein with a molecular mass of 25 kDa was detected in inclusion bodies. Thus, the protein was purified under denaturing conditions (using 8 M urea) and subjected to dialysis to stimulate refolding. After refolding, the protein was concentrated to approximately 3 mg / mL and the circular dichroism assay was performed to verify the content of secondary structure, and dynamic light scattering, to estimate the size distribution of particle populations which are present in solution. The data from the deconvolution of circular dichroism experiments indicate a percentage of 40-46% α-helix, 12-14% β-sheet, 15-22% turns and 24-28% of other structures, indicating a structured protein; and the data of the dynamic light scattering showed that the protein is stable, monodispersive, but forms a large complex of particles which must be separated to before crystallization experiments. Other techniques were used to solubilize the expressed protein: lowering the temperature of expression to 18 °C, using the method... (Complete abstract click electronic access below)
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Lim, Yee Chee. "Ultraviolet absorbance and circular dichroism analysis of DNA oligomers containing adenine tracts." Thesis, University of British Columbia, 2007. http://hdl.handle.net/2429/31762.
Full textAbstract:
"A-tract" is defined as phased runs of at least four consecutive adenines, i.e.
(dA)n-(dT)n , where n ≥ 4. The B*-form of DNA characteristic of A-tracts is distinct from
the canonical B-DNA, with high base propeller twist and a narrower minor groove. The
B*-form of DNA was examined using UV absorption and circular dichroism (CD)
spectroscopy in order to estimate the extent of B*-type conformation adopted by 12-mer
DNA oligomers containing different A-tract lengths. The systematic variation aims to
study how the propensity towards B*-DNA formation depends on different A-tract
lengths and different base compositions flanking the A-tract. CD and UV melting
experiments indicate that B*-form has distinctive spectral signatures. The structural
formation o f B*-DNA increases with A-tract length, but can be affected by the location
of the A-tract within the sequence as well as neighboring AA/TT, AT, and TA base pairs.
The spectroscopic results generally correlate well with differential scanning
calorimetry (DSC) data. The calorimetrically obtained results were compared with
thermodynamic parameters predicted by the Santa Lucia nearest-neighbor (NN) model.
Disagreements between experimental and predicted thermodynamic values exist
particularly for mixed AT sequences and those with the same number of NN parameters.
Such discrepancies may be caused by different stabilities resulting from various extent of
B*-type formation within a given DNA sequence. Since NN estimates of the melting
temperature do not adequately account for structural differences, the incorporation of
additional structural information may have a pronounced impact on thermodynamic
variables and will help to improve the NN model considerably. Consequently, this
allows for a more accurate prediction of the stability of short DNA sequences (< 25 base pairs), often used in molecular biology applications involving sequence dependent
hybridization reactions. In light of the increasing interest in the development of locked
nucleic acids (LNA) for probe and primer design and theurapeutic applications, the
thermodynamics and spectroscopic studies on the structural effects of the incorporation
of LNA nucleotides on the A-tract structure will also be presented.Science, Faculty of
Chemistry, Department of
Graduate
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Lambert, Karen A. "Solution studies of soybean protein isolate using circular dichroism and SDS-PAGE." Thesis, Georgia Institute of Technology, 1999. http://hdl.handle.net/1853/9495.
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Gonçales, Garcia Luana. "Biologia estrutural: expressão e caracterização estrutural da proteína 25K do Cole latent virus /." São José do Rio Preto : [s.n.], 2012. http://hdl.handle.net/11449/94849.
Full textAbstract:
Orientador: Raghuvir Krishnaswamy ArniCoorientador: José Osmar Gaspar
Banca: Marcelo Andrés Fossey
Banca: Priscila Belintani
Resumo: As atividades realizadas compreenderam a produção de cDNA utilizando primer anti-senso e RNA purificado, amplificação do gene codificador da proteína 25K do Cole latent virus (CoLV25K), purificação do fragmento amplificado, ligação em vetor de multiplicação pGEM-T, transformação em células competentes de Escherichia coli linhagem TOP 10, purificação do vetor, digestão enzimática com as enzimas Bam HI e Hind III, subclonagem no vetor de expressão pET28a, transformação em células competentes de E. coli linhagem BL21-RIL, sequenciamento do gene no vetor de expressão e expressão da proteína a 37 o C . Quando expressa a 37 ºC, a proteína, de 25 kDa, foi encontrada em sua totalidade nos corpos de inclusão. Dessa forma, a proteína foi purificada sob condição desnaturante (utilizando 8 M de uréia) e submetida à diálise para seu reenovelamento. Após o reenovelamento, a proteína foi concentrada para aproximadamente 3 mg/mL e foram realizadas medidas de dicroísmo circular, para verificar o seu conteúdo de estrutura secundária, e o espalhamento dinâmico de luz, para estimar a distribuição de tamanho das populações de partículas que estão presentes na solução. Os dados da deconvolução do experimento de dicroísmo circular indicam um percentual de 40-46% α-hélice, 12-14% folha-β, 15-22% voltas e 24-28% de outras estruturas, indicando que a proteína está estruturada; e os dados do espalhamento dinâmico de luz mostraram que a proteína encontra-se estável, monodispersa, mas apresenta um complexo de partículas que deve ser removido para que fique nas condições ideais de cristalização. Foram utilizadas também outras técnicas para tentar alcançar a solubilidade da proteína expressa: abaixando a temperatura... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: The experiments performed were, the production of cDNA using anti-sense primers and purified RNA, amplification of the gene encoding the 25K protein of Cole latent virus (CoLV25K), purification of the amplified fragment, cloning in multiplication vector pGEM-T for cell transformation into competent Escherichia coli strain TOP 10, vector purification, enzymatic digestion using the enzymes Bam HI and Hind III, subcloning in expression vector pET28a, transformation into competent cells of E. coli strain BL21-RIL, sequencing of the gene cloned into the expression vector and protein expression at 37 o C. When expressed at 37 °C, the protein with a molecular mass of 25 kDa was detected in inclusion bodies. Thus, the protein was purified under denaturing conditions (using 8 M urea) and subjected to dialysis to stimulate refolding. After refolding, the protein was concentrated to approximately 3 mg / mL and the circular dichroism assay was performed to verify the content of secondary structure, and dynamic light scattering, to estimate the size distribution of particle populations which are present in solution. The data from the deconvolution of circular dichroism experiments indicate a percentage of 40-46% α-helix, 12-14% β-sheet, 15-22% turns and 24-28% of other structures, indicating a structured protein; and the data of the dynamic light scattering showed that the protein is stable, monodispersive, but forms a large complex of particles which must be separated to before crystallization experiments. Other techniques were used to solubilize the expressed protein: lowering the temperature of expression to 18 °C, using the method... (Complete abstract click electronic access below)
Mestre
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Ernst, Margot Christiana. "Ab initio calculations on chiral cobalt (III) complexes." Diss., Georgia Institute of Technology, 1992. http://hdl.handle.net/1853/27429.
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Daly, Steven. "Study of the photoionization of chiral molecules using polarized VUV radiation." Thesis, University of Nottingham, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.594763.
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McHarg, Jane. "Investigations into the glycolytic enzyme phosphoglycerate kinase." Thesis, University of Exeter, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.390169.
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Miedzinska, K. M. E. (Katarzyna Malgorzata Ewa) Carleton University Dissertation Chemistry. "A dynamic ensemble model for intensity parameters in chiroelectronic spectroscopy." Ottawa, 1992.
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Deng, Yuanyuan, and 邓远源. "Magnetic circular dichroism and Hall measurement of cobalt-doped zinc oxide thin films." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B50434494.
Full textAbstract:
The observation of ferromagnetism of (Ga,Mn)As by Ohno in 1998 has inspired great interest in diluted magnetic semiconductors (DMS). DMS’s features combining ferromagnetism and semiconducting make them of great potential for conceptual spintronic devices, which is a promising field of research for the emerging electronics. The practical application of DMS requires a Curie temperature well above room temperature and an intrinsic ferromagnetism. There are several types of DMS materials. The typical ones are transition-metal (TM) doped GaAs, GaN and ZnO. The TM-doped ZnO has drawn particular attention due to the observation of room temperature ferromagnetism in this system including cobalt-doped ZnO.But the origin of ferromagnetic TM-doped ZnO is still unknown after a decade’s theoretical and experimental effort on this material.
In this thesis, we do the magnetic circular dichroism(MCD) and Hall measurement of high quality Cobalt-doped ZnO thin films grown by molecular beam epitaxy (MBE). Room temperature ferromagnetism is observed in these samples. Combining the data from MCD and Hall measurement, we attribute the room temperature ferromagnetism in this system to the impurity band of the doped Cobalt cations.published_or_final_version
Physics
Master
Master of Philosophy
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Jiemchooroj, Auayporn. "Long-range intermolecular dispersion forces and circular dichroism spectra from first-principles calculations." Doctoral thesis, Linköping : Department of Physics, Chemistry and Biology, Linköpings universitet, 2007. http://www.bibl.liu.se/liupubl/disp/disp2007/tek1118s.pdf.
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Wadley, Peter. "X-ray magnetic circular dichroism studies of III-Mn-V compounds and heterostructures." Thesis, University of Nottingham, 2012. http://eprints.nottingham.ac.uk/13451/.
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This thesis describes the characterisation of GaMnAs, related compounds and heterostructures. GaMnAs and other (III,Mn)V compounds have provided many interesting insights into fundamental physics, and are of considerable potential interest commercially in the field of spintronics. This study examines a set of samples grown by molecular beam epitaxy and characterised using several techniques: primarily this study makes use of the x-ray absorption techniques, x-ray magnetic circular dichroism(XMCD) and x-ray absorption spectroscopy (XAS). In addition, x-ray diffraction (XRD), transport measurements and super conducting quantum interference device (SQUID) magnetometry were used as complimentary techniques. GaMnAs layers with epitaxial Fe grown on top, are shown to have a sub-nanometre interfacial layer which remains polarised above room temperature. A detailed understanding of these systems is obtained by applying the element specific nature of XMCD in combination with two different probing depths to explore separately the nature of the coupling of the bulk and interfacial region. The coupling between the interfacial layer and the Fe is shown to be strongly antiferromagnetic (AF). A weaker coupling is also shown to exist between the Fe and the bulk of the \gamnas layer below the Curie temperature (Tc). This coupling is also AF at low fields, leading to an exchange bias for the entire layer. Doping of GaMnAs with P is shown to have several effects on the magnetic properties of the GaMnAs layer. Changes in the layer strain are observed using high resolution XRD. This strain also manifests itself in the Mn L_2,3 XMCD spectra and the relationship between the two is shown to be linear. A pronounced effect on the magnetic anisotropy is observed using SQUID measurements, with the easy axis switching from in-plane, in the compressively strained GaMnAs, to out-of-plane in the higher doped GaMnAsP layers. A decrease in total magnetic moment per Mn atom and Tc are observed with increased doping. This is inferred not to be due to a direct effect of the P on the local surrounding of the Mn ions, owing to the striking similarity of the XMCD spectra. This is instead attributed to reduced participation of Mn ions in the magnetic ordering. Finally, K edge XMCD is used to reveal the element specific nature of unoccupied states near the Fermi level in a set of GaMnAs and (In,Ga,Mn)As samples with differing Mn doping levels . The character of the holes in low-doped samples is shown to be markedly different than for those in the highly doped metallic samples. A transfer of orbital magnetic moment from the Mn to the As sites is observed on crossing the metal-insulator transition, with the large XMCD on Mn sites in low doped samples interpreted as a sign of hole localisation around the Mn ion.
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Ledger, G. "X-ray magnetic circular dichroism and scanning tunnelling microscopy applied to molecular spintronics." Thesis, University of Liverpool, 2017. http://livrepository.liverpool.ac.uk/3010415/.
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Tran, Duc-Thanh. "Novel aspects of topological insulators: Quasi-crystals, Floquet-engineered states and circular dichroism." Doctoral thesis, Universite Libre de Bruxelles, 2018. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/273410.
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Cette thèse traite d'aspects originaux ayant attrait au domaine des isolants topologiques et de leurs simulations par des systèmes d'atomes ultra-froids. Tout d'abord, ce travail aborde des concepts fondamentaux tels que la notion de géométrie et de topologie dans le contexte de la mécanique quantique ainsi que les techniques de simulations d'Hamiltonien avec les atomes ultra-froids. Ensuite on présentera trois travaux originaux liés aux isolants topologiques et leurs simulations.Doctorat en Sciences
info:eu-repo/semantics/nonPublished
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Castevens, Charles Montgomery IV. "Ligand Binding Energies And Magnetic Circular Dichroism of the Human Melatonin Receptor MT1." VCU Scholars Compass, 2003. http://scholarscompass.vcu.edu/etd_retro/134.
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The binding energies and Gibbs free energies ofbinding for melatonin and other indole-,naphthalene-, and benzene-moiety ligands totrans-membrane sections of the seven-helix humanmelatonin receptor MT1 have been calculated atthe ab initio and semi-empirical levels using GAMESS, and with molecular mechanics using Sybyl. A linear relationship was found between the Sybyl-calculated binding energies and theexperimentally-determined pKi values, and alinear fit of calculated HINT scores to theexperimentally-measured ΔG values givesdeltaG = -0.00263Hscore - 9.477, in kcal/mol. In addition, the interactions between individual residues in MT1 and various ligands were examined to determine why some ligands bind more strongly to MT1 than others. The magnetic circular dichroism spectra of melatonin bound tofragments of MT1 were also calculated, in theCNDO/S-D approximation.
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Fabini, Edoardo <1988>. "Characterization of Pharmaceutically Relevant Systems through Surface Plasmon Resonance and Circular Dichroism Spectroscopies." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2017. http://amsdottorato.unibo.it/7976/1/Fabini_Edoardo_Tesi.pdf.
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Studying biological interactions at a molecular level is crucial to rationally interpret pathophysiological conditions. Several analytical techniques have been engaged to elucidate different aspects of biological systems and, depending on the research question, medicinal chemists need to select the most tailored problem- solving approach. Among all possibilities, surface plasmon resonance (SPR) and circular dichroism (CD) spectroscopies offer intriguing potential. They can investigate both structural and functional aspects of biological targets and provide in return highly informative data output. In the present dissertation SPR and CD spectroscopies were employed to study different pharmaceutically relevant systems. The interaction between plant derivative Cucurbitacin, and serum albumins from different species (human and rat) was characterized with a combination of SPR direct binding assay and CD competition studies. Interestingly, two different binding profiles emerged. An extended SPR experimental set-up has been employed to investigate the interaction between the transcription factor from Helycobacter pylori NikR and the operator region of the urease promoter, revealing an isomerization of the protein–dsDNA complex occurring over time. SPR analysis was also employed to monitor the binding of Histone H4 residue to the methylation pocket of the epigenetic regulator SMYD3 in the presence of a selected small molecule (BCI-121). Results support in silico and in cellulo findings, confirming competition for the same binding site. CD detection was employed in combination with high performance liquid chromatography to achieve a full stereochemical characterization of Trans-3-(3,4- Dimethoxyphenyl)Glycidate enantiomers and to identify and quantify leva- and dexa-misole content in seized street cocaine samples. Studies reported in this dissertation highlighted how SPR and CD contribute to increase scientific knowledge on selected biological systems related to the field of life science. Moreover, assays developed here pose the basis for future inhibitors’ screening, which could eventually lead to the discovery of new chemical entities endowed with therapeutic properties.
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Rodger, Alison. "Molecular aspects of biomolecule structure and function." Thesis, The University of Sydney, 2002. http://hdl.handle.net/2123/516.
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All biological processes are fundamentally inter-molecular interactions. In order to understand, and hence control, biomolecular structure and function, methods are required that probe biological systems at the molecular level, ideally with those molecules being in their native environment. The research summarized herein has at its core the development and application of ultra violet (UV)-visible spectrophotometric techniquies for this prupose, in particular circular dichrosim (CD) and linear dichrosim (LD) but also absorbance, fluorescence and resonance light scattering. The spectroscopy is complemented by fundamental theoretical work on molecular structure and reactivity that forms the basis for designing molecules to bind to biomolecules for a particular structural or functional effect. A brief summary of the contributions of the listed publications to our understanding of 'Molecular aspects of biololecule structure and function' is given below under five headings: Circular dichroism theory Molecular geometry and reactivity Small molecule-macromolecule interactions: spectroscopic probes of inter-molecular geometries Molecular design for nucleic acid structure and control Spectroscopic probes of biomolecule structure: instrumentation and application In general terms these correspond to successive phases of the research programme, however, all areas have been present since the first publications in 1983 and can be traced weaving through all subsequent activity.
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Rodger, Alison. "Molecular aspects of biomolecule structure and function." University of Sydney. Chemistry, 2002. http://hdl.handle.net/2123/516.
Full textAbstract:
All biological processes are fundamentally inter-molecular interactions. In order to understand, and hence control, biomolecular structure and function, methods are required that probe biological systems at the molecular level, ideally with those molecules being in their native environment. The research summarized herein has at its core the development and application of ultra violet (UV)-visible spectrophotometric techniquies for this prupose, in particular circular dichrosim (CD) and linear dichrosim (LD) but also absorbance, fluorescence and resonance light scattering. The spectroscopy is complemented by fundamental theoretical work on molecular structure and reactivity that forms the basis for designing molecules to bind to biomolecules for a particular structural or functional effect. A brief summary of the contributions of the listed publications to our understanding of 'Molecular aspects of biololecule structure and function' is given below under five headings: Circular dichroism theory Molecular geometry and reactivity Small molecule-macromolecule interactions: spectroscopic probes of inter-molecular geometries Molecular design for nucleic acid structure and control Spectroscopic probes of biomolecule structure: instrumentation and application In general terms these correspond to successive phases of the research programme, however, all areas have been present since the first publications in 1983 and can be traced weaving through all subsequent activity.
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Capomaccio, Robin. "Interactions nanoparticules-protéines : caractérisation de la couronne protéique." Thesis, Lyon 1, 2015. http://www.theses.fr/2015LYO10323.
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De nos jours, les nanomatériaux sont utilisés dans de très nombreux domaines allant de l’agroalimentaire à la santé en passant par l’industrie automobile et le textile. Dans ce contexte, de nombreuses disciplines comme la métrologie et la nanotoxicologie se sont fortement développées. Dans les milieux biologiques, les protéines interagissent avec les nanoparticules pour former une couronne de protéines. Cette couronne de protéines joue un rôle important dans les interactions des nanoparticules avec leur environnement. Comprendre et caractériser les interactions des nanoparticules avec les protéines permettraient d’améliorer l’utilisation des nanoparticules dans différents domaines, notamment dans celui de la santé. Nous avons d’abord mis au point une méthode de purification des nanoparticules permettant de préserver la structure et la composition de la couronne protéique (Asymmetric flow field-flow fractionation, AF4). Nous avons ensuite caractérisé la couronne protéique associée à ces nanoparticules par plusieurs méthodes telles que la sédimentation centrifuge différentielle, la microscopie électronique, des méthodes basées sur la diffusion de la lumière (diffusion dynamique de la lumière (DLS) et la résonance plasmonique de surface localisée ou non), le dichroïsme circulaire classique et le Synchrotron Radiation Circular Dichroism (SRCD, Diamond, UK). Nous avons montré qu’une couronne d’albumine sérique humaine provoque une augmentation du diamètre hydrodynamique des nanoparticules d’or de 14 à 25,3 nm et une diminution de la densité d’un facteur 2. Ceci nous a permis de calculer que 19 molécules d’albumine en moyenne interagissent avec une nanoparticule. Les spectres de dichroïsme circulaire ont permis d’estimer que l’albumine conserve environ 70% de ses structures hélicoïdales lorsqu’elle est complexée avec les nanoparticules. Nous avons estimé l’affinité avec laquelle les nanoparticules d’or interagissent qui est d’environ 351 nM pour l’albumine et 513 nM pour la transthyrétine qui est riche en brins béta. Nous avons également optimisé une méthode de couplage de l’AF4 à un appareil de mesure de la diffusion dynamique de la lumière (DLS) pour améliorer la précision de la mesure du diamètre hydrodynamique des nanoparticules. Cette méthode précise et flexible permettra de caractériser de nombreuses modifications de surface des nanoparticules comme l’ajout de polyéthylène glycol, utilisées pour la conception de nano-médicamentsNowadays, nanomaterials are used in numerous areas ranging from food to health through cars and textile engineering. In this context, many disciplines such as metrology and nanotoxicology, have been developed. In biological fluids, proteins interact with nanoparticles to form the protein corona, which plays an important role in mediating the interactions of the nanoparticles with their environment. Understanding and characterizing the interactions of nanoparticles with proteins and the corona structure would improve their use in various fields and particularly in the health sector. We have first developed a method based on Asymmetric Flow Field Flow Fractionation (AF4) for purifying gold nanoparticles preserving the structure and composition of the protein corona. Then we have characterized the protein corona associated to these nanoparticles by differential centrifugal sedimentation, electron microscopy, light scattering (dynamic light scattering, DLS), surface plasmon resonance (SPR) and localized SPR and by circular dichroism (classical CD and Synchrotron Radiation Circular Dichroism, SRCD, Diamond, UK). We have shown that human serum albumin corona increased the hydrodynamic diameter of the gold nanoparticles from 14 to 25.3 nm and decreases their density by a factor of 2. This enabled us to calculate that 19 albumin molecules on average interact with a nanoparticle. We have estimated by circular dichroism that albumin maintains about 70% of its helical structures when complexed with nanoparticles. The affinity between gold nanoparticles and proteins, is about 351 nM for albumin and 513 nM for transthyretin, which are enriched in helices and beta strands respectively. We have also optimized a coupling method between the AF4 system and the dynamic light scattering apparatus to improve the measurement accuracy of the hydrodynamic diameter of the nanoparticles. This accurate and flexible method will be helpful to characterize many surface modifications of the nanoparticles such as the addition of polyethylene glycol used for the design of nanodrugs
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Li, Tian-Yi, You-Xuan Zheng, and Yong-Hui Zhou. "Iridium(III) phosphorescent complexes with dual stereogenic centers: single crystal, electronic circular dichroism evidence and circularly polarized luminescence properties." Royal Society of Chemistry, 2016. https://tud.qucosa.de/id/qucosa%3A36123.
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Iridium complexes with a chiral metal center and chiral carbons, Λ/Δ-(dfppy)₂Ir(chty-R) and Λ/Δ-(dfppy)2Ir(chty-S), were synthesized and characterized. These isomers have the same steadystate photophysical properties, and obvious offsets in ECD spectra highlight both the chiral sources. Each enantiomeric couple shows mirror-image CPL bands with a dissymmetry factor in the order of 10ˉ³.
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Tran, Viet-Dung. "Modélisation du dichroïsme circulaire des protéines : modèle simple et applications." Thesis, Orléans, 2015. http://www.theses.fr/2015ORLE2076.
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La spectroscopie de dichroïsme circulaire (CD) est une des techniques fondamentales en biologie structurale qui permet la détermination du contenu en structures secondaires d'une protéine. Le rayonnement synchrotron a considérablement augmenté l’utilité de la méthode, car il permet de travailler avec une gamme spectrale étendue et à meilleure intensité. Le développement de modèles permettant d’établir une relation entre la structure d’une protéine et son spectre CD d’une manière efficace n’a pourtant pas suivi l’évolution technique et l’analyse de spectres CD de protéines entières reste un défi sur le plan théorique. Dans ce contexte, nous avons développé un modèle "minimaliste" pour la spectroscopie CD des protéines, où chaque atome C-alpha de la chaîne principale porte un oscillateur de Lorentz classique, i.e. une charge mobile qui est tenue par un potentiel quadratique. Les oscillateurs sont couplés par un potentiel coulombien et leurs déplacements suivent les tangentes locales respectives de la courbe spatiale décrite par les atomes C-alpha. Le système d'oscillateurs est couplé à une onde électromagnétique plane décrivant la source de lumière et le phénomène d'absorption est modélisé par des forces de friction. Nous montrons que le modèle reproduit correctement le phénomène CD d'une chaîne polypeptidique hélicoïdale et en particulier son signe en fonction de l'orientation de la chaîne. Comme première application, nous présentons l'ajustement du modèle au spectre CD d'un polypeptide composé de 15 résidus qui se plie sous forme d'une hélice alpha. La transférabilité de ces paramètres est ensuite évaluée pour la myoglobine, une protéine de 153 résidus contenant 8 hélices alphaCircular dichroism (CD) spectroscopy is one of the fundamental techniques in structural biology that allows us to investigate the secondary structure of proteins. Synchrotron radiation has considerably increased the usefulness of the method because it allows to work with a wider range of spectrum and much greater signal-to-noise ratios. The development of a theoretical model to establish a relationship between the structure of a protein and its CD spectra in an efficient manner proved to be a complex task. The calculation of the CD spectra of large molecules, such as protein, remains a challenge, due to the size and flexibility of the molecules. In this context, we have developed a “minimal” model to explain the CD spectroscopy of proteins, which associates each C-alpha position on the protein backbone with a classical Lorentz oscillator i.e. a mobile charge attaches to a corresponding atom by a quadratic potential. The coupling between charges is through the Coulomb potential and their displacements follow the direction of the respective local tangents to the Calpha space curve. This system is coupled to a planar electromagnetic wave describing the light source and the absorption phenomenon is modeled by frictional forces. We show that the model correctly reproduces the CD phenomenon of a helical polypeptide chain and in particular its sign depending on the orientation of the chain. At first, we have fitted a model to CD spectra of a polypeptide chain of 15 residues folded into alpha helix. The transferability of these parameters is then evaluated with myoglobin, a protein of 153 residues containing eight alpha helices