The gas-phase hydrogen/deuterium (H/D) exchange of protonated di- and tripeptides containing a basic amino acid residue has been studied with a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Bimolecular reactions are monitored as a function of time providing exchange efficiencies and temporal distributions for the peptide ions. Results from these experiments indicated that position of the basic residue within the peptide (i.e. N-terminal, internal, or C-terminal) influences gas-phase H/D exchange, suggesting unique peptide ion conformations. The FT-ICR mass spectrometer employed for these gas-phase H/D exchange studies was modified from its original design. Instrument modifications include development of an internal matrix assisted laser desorption ionization (MALDI) source for peptide protonation. In addition, a two-section cell was utilized, allowing control of ion motion and factors affecting gas-phase ion molecule reactions. Systems investigated in these gas-phase H/D exchange studies are peptides containing the same amino acid residues but different sequences. These sequence isomers display dissimilar reaction efficiencies and temporal distributions for deuterium incorporation depending on the primary structure of the peptide ion. Specifically, [M+H]+ peptide ions containing a N-terminal basic residue demonstrate unique H/D exchange behavior when compared to their internal and C-terminal counterparts. These differences are attributed to dissimilar intramolecular bridging interactions involved with inductive stabilization of the charge site. Gas-phase H/D exchange of peptide sequence isomers was also probed with various deuterium reagents. Findings suggest that different reagents also influence H/D exchange reaction rate efficiencies and temporal distributions. These dissimilarities are ascribed to relative gas-phase basicity and proposed mechanistic exchange differences for the deuterium reagents.

Resumo: Neste trabalho estudou-se a estrutura, função e mecanismo de ação do peptídeo antibacteriano Protonectarina-MP (isolado de veneno da vespa social Protonectarina sylveirae) tendo seu resíduo C-terminal nas formas ácida (-OH) e amidada (-NH2). Os peptídeos foram sintetizados, utilizando-se a estratégia Fmoc, purificados por cromatografia líquida de alta performance. O monitoramento do material sintético foi feito por espectrometria de massas ESI-MS e por seqüenciamento através de Química Degradativa de Edman. A estrutura secundária foi investigada pelo uso de espectroscopia de dicroísmo circular e modelagem molecular. Atividade lítica (extravasamento) e interação do resíduo de triptofano em vesículas foram investigadas pelo uso de espectrômetro de fluorescência. Foram realizados ensaios sobre as interações desses peptídeos em meio de vesículas zwitteriônicas e aniônica, formando complexos proteolipossomos que foram submetidos à troca isotópica H/D monitorada por espectrometria de massas ESI-MS e MS/MS. Além disso, foram realizados ensaios biológicos de atividade hemolítica, de desgranulação de mastócito, de liberação da enzima citoplasmática Lactato Desidrogenase e de atividade antimicrobianas. Os dados de CD revelam uma tendência dos peptídeos se estruturarem em hélice-α em ambiente hidrofóbico e em ambiente de membranas. Porém, o mesmo não pode ser observado em meio aquoso. Os modelos obtidos para ambos os peptídeos por modelagem molecular mostram uma estruturação em hélice-α anfipática. Nos ensaios de atividade lítica em vesículas, os peptídeos apresentaram um processo com cooperatividade positiva, com curvas de dose-resposta que mostram uma dependência sigmoidal com a concentração do peptídeo. Os resultados da fluorescência do triptofanos mostram um deslocamento da emissão para a região de onda do azul para o peptídeo... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: In the present work was studied the structure, function and mechanism of action of the antibacterial peptide Protonectarina-MP (isolated from venom of social wasp Protonectarina sylveirae) with its carboxyamidation (-NH2) and carboxyl-free (-OH) Cterminal forms. The peptides were manually synthesized on-solid phase by using Fmoc strategy and purified under HPLC. The homogeneity of the synthetic material was analyzed by ESI mass spectrometry and Edman Degradation Chemistry. The secondary structure was investigated through circular dichroism (CD) spectroscopy and molecular modeling. Lytic activity and peptides interaction with the membranes was also investigated through tryptophan emission, by fluorescence spectrometry. The interaction of peptides with zwitterionic and anionic vesicles was investigated through the combination of H/D exchange and ESI-mass spectrometry. Some biological activities, like: mast cell degranulation, release of cytoplasmic enzyme lactate dehydrogenase, hemolysis and antibiosis were investigated for both peptides. The CD spectra revealed that the peptides in hydrophobic environments or in presence of biological membranes have the tendency to form helix conformations; however, organized structures were not observed in aqueous or buffer solutions. The models obtained by molecular modeling show that both peptides form an amphipathic α-helix. The peptides presented a positive cooperative process in the lytic activity of vesicles, with dose-response curves presenting a sigmoidal dependence with the peptide concentration. The results of the fluorescence of tryptophans showed a shift of the emission wavelength to the blue region of the peptide Protonectarina-MP (-NH2), which was not observed for its analogue presenting the C-terminal residue in free acid form. This is indicating a greater interaction of the amidated peptide in membranes, when compared to the peptide... (Complete abstract click electronic access below) / Orientador: Mario Sergio Palma / Coorientador: João Ruggiero Neto / Banca: Ivo Lebrun / Banca: Pietro Ciancaglini / Mestre

Depuis les années 2000, le domaine de l’organocatalyse est en plein essor. Une vue d’ensemble des différents modes d’activation organocatalytique fera l’objet du premier chapitre. Malgré les avancées considérables faites dans l’activation par liaison covalente, particulièrement dans l’aminocatalyse par activation iminium, des progrès sont encore possibles au niveau de l’activité catalytique des organocatalyseurs. Une large partie du travail détaillé dans le deuxième chapitre concerne le design puis le développement de deux voies de synthèse permettant de préparer une nouvelle classe d’organocatalyseurs pour l’activation iminium ainsi que leurs tests d’activité catalytique. Enfin, le troisième chapitre est consacré à l’étude de réactions d’échange H/D organocatalysées par les carbènes N-hétérocycliques. / Since the begining of 2000, the field of organocatalysis has performed a lot of improvements. An overview of the different modes of activation of this field will constitute the first chapter. Despite the improvements in the domain of activation by covalent bond, specially for the iminium activation, some enhancements of the catalytic activity of organocatalysts are still possible. A major part of the work developped in the second chapter will be focused on the design then the synthesis of a new class of organocatalysts for iminium activation and their catalytic activity tests. Then the third chapter will be dedicated to the H/D exchange reactions organocatalyzed by N-heterocyclic carbenes.

<p>Many of the biological roles of proteins are modulated through protein-ligand interactions, making proteins important targets for drug therapies and diagnostic imaging probes. The discovery of novel ligands for a protein of interest often relies on the use of high throughput screening (HTS) technologies designed to detect protein-ligand binding. The basis of one such technology is a recently reported mass spectrometry-based assay termed SUPREX (stability of unpurified proteins from rates of H/D exchange). SUPREX is a technique that uses H/D exchange and MALDI-mass spectrometry for the measurement of protein stabilities and protein-ligand binding affinities. The single-point SUPREX assay is an abbreviated form of SUPREX that is capable of detecting protein-ligand interactions in a high throughput manner by exploiting the change in protein stability that occurs upon ligand binding.</p><p>This work is focused on the development and application of high throughput SUPREX protocols for the detection of protein-ligand binding. The first step in this process was to explore the scope of SUPREX for the analysis of non-two-state proteins to determine whether this large subset of proteins would be amenable to SUPREX analyses. Studies conducted on two model proteins, Bcl-xL and alanine:glyoxylate aminotransferase, indicate that SUPREX can be used to detect and quantify the strength of protein-ligand binding interactions in non-two-state proteins.</p><p>The throughput and efficiency of a high throughput SUPREX protocol (i.e., single-point SUPREX) was also evaluated in this work. As part of this evaluation, cyclophilin A, a protein target of diagnostic and therapeutic significance, was screened against the 880-member Prestwick Chemical Library to identify novel ligands that might be useful as therapeutics or imaging agents for lung cancer. This screening not only established the analytical parameters of the assay, but it revealed a limitation of the technique: the efficiency of the assay is highly dependent on the precision of each mass measurement, which generally decreases as protein size increases. </p><p>To overcome this limitation and improve the efficiency and generality of the assay, a new SUPREX protocol was developed that incorporated a protease digestion step into the single-point SUPREX protocol. This new protocol was tested on two model proteins, cyclophilin A and alanine:glyoxylate aminotransferase, and was found to result in a significant improvement in the efficiency of the SUPREX assay in HTS applications. This body of work resulted in advancements in the use of SUPREX for high throughput applications and laid the groundwork for future HTS campaigns on target proteins of medical significance.</p> / Dissertation

Some proteins require presence of their specific ligand, cofactor or prosthetic group for their activity. Binding of this specific molecule can cause conformational changes which permit to perform their function. In some occasions the identification of conformational changes could be really challenging task. In this thesis we describe the novel approach for monitoring structural changes in proteins using chemical cross-linking and high resolution mass spectrometry and its application on model calmodulin system. It is demonstrated that analysis using isotope-labelled cross-linking agents enabled us to get insight into the structural rearrangement caused by presence or absence of the protein ligand. However, it is shown that the method has potential drawback due to limited enzymatic proteolysis. The novel approach that also makes it possible to quantify the changes in protein structure was used together with other methods for characterization of the neutral trehalase Nth1 in complex with Bmh1 protein (yeast isoform of protein 14-3-3). The results revealed that Bmh1 induce structural rearrangement of Nth1 molecule with changes within the EF- hand like motif which is essential for the activation process.

To investigate how protein folding is affected by sequence connectivity five topological variants of the ribosomal protein S6 were constructed through circular permutation.  In these constructs, the chain connectivity (i.e. the order of secondary-structure elements) is changed without changing the native-state topology.  The effects of the permutations on the folding process were then characterised by φ-value analysis, which estimates the extent of contact formations in the transition-state ensemble.  The results show that the folding nuclei of the wild-type and permutant proteins comprises a common motif of one α-helix docking against two β-sheets, i.e. the minimal structure for folding.  However, this motif is recruited in different parts of the S6 structure depending on the permutation, either in the α1 or α2 half of the protein.  This minimal structure is not unique for S6 but can also be seen in other proteins.  As an effect of the dual nucleation possibilities, the transition-state changes describe a competition between two parallel pathways, which both include the central β-stand 1.  This strand constitutes thus a structural overlap between the two competing nuclei.  As similar overlap between competing nuclei is also seen in other proteins, I hypothesise that the coupling of several small nuclei into extended ‘super nuclei’ represents a general principle for propagating folding cooperativity across large structural distances.  Moreover, I demonstrate by NMR analysis that the existence of multiple folding nuclei renders the H/D-exchange kinetics independent of the folding pathway. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper IV: Manuscript

Made available in DSpace on 2014-06-11T19:22:59Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-06-08Bitstream added on 2014-06-13T20:29:34Z : No. of bitstreams: 1 silva_avr_me_rcla.pdf: 1706887 bytes, checksum: eda68ea29b93397b581e427121535611 (MD5) / Neste trabalho estudou-se a estrutura, função e mecanismo de ação do peptídeo antibacteriano Protonectarina-MP (isolado de veneno da vespa social Protonectarina sylveirae) tendo seu resíduo C-terminal nas formas ácida (-OH) e amidada (-NH2). Os peptídeos foram sintetizados, utilizando-se a estratégia Fmoc, purificados por cromatografia líquida de alta performance. O monitoramento do material sintético foi feito por espectrometria de massas ESI-MS e por seqüenciamento através de Química Degradativa de Edman. A estrutura secundária foi investigada pelo uso de espectroscopia de dicroísmo circular e modelagem molecular. Atividade lítica (extravasamento) e interação do resíduo de triptofano em vesículas foram investigadas pelo uso de espectrômetro de fluorescência. Foram realizados ensaios sobre as interações desses peptídeos em meio de vesículas zwitteriônicas e aniônica, formando complexos proteolipossomos que foram submetidos à troca isotópica H/D monitorada por espectrometria de massas ESI-MS e MS/MS. Além disso, foram realizados ensaios biológicos de atividade hemolítica, de desgranulação de mastócito, de liberação da enzima citoplasmática Lactato Desidrogenase e de atividade antimicrobianas. Os dados de CD revelam uma tendência dos peptídeos se estruturarem em hélice-α em ambiente hidrofóbico e em ambiente de membranas. Porém, o mesmo não pode ser observado em meio aquoso. Os modelos obtidos para ambos os peptídeos por modelagem molecular mostram uma estruturação em hélice-α anfipática. Nos ensaios de atividade lítica em vesículas, os peptídeos apresentaram um processo com cooperatividade positiva, com curvas de dose-resposta que mostram uma dependência sigmoidal com a concentração do peptídeo. Os resultados da fluorescência do triptofanos mostram um deslocamento da emissão para a região de onda do azul para o peptídeo... / In the present work was studied the structure, function and mechanism of action of the antibacterial peptide Protonectarina-MP (isolated from venom of social wasp Protonectarina sylveirae) with its carboxyamidation (-NH2) and carboxyl-free (-OH) Cterminal forms. The peptides were manually synthesized on-solid phase by using Fmoc strategy and purified under HPLC. The homogeneity of the synthetic material was analyzed by ESI mass spectrometry and Edman Degradation Chemistry. The secondary structure was investigated through circular dichroism (CD) spectroscopy and molecular modeling. Lytic activity and peptides interaction with the membranes was also investigated through tryptophan emission, by fluorescence spectrometry. The interaction of peptides with zwitterionic and anionic vesicles was investigated through the combination of H/D exchange and ESI-mass spectrometry. Some biological activities, like: mast cell degranulation, release of cytoplasmic enzyme lactate dehydrogenase, hemolysis and antibiosis were investigated for both peptides. The CD spectra revealed that the peptides in hydrophobic environments or in presence of biological membranes have the tendency to form helix conformations; however, organized structures were not observed in aqueous or buffer solutions. The models obtained by molecular modeling show that both peptides form an amphipathic α-helix. The peptides presented a positive cooperative process in the lytic activity of vesicles, with dose-response curves presenting a sigmoidal dependence with the peptide concentration. The results of the fluorescence of tryptophans showed a shift of the emission wavelength to the blue region of the peptide Protonectarina-MP (-NH2), which was not observed for its analogue presenting the C-terminal residue in free acid form. This is indicating a greater interaction of the amidated peptide in membranes, when compared to the peptide... (Complete abstract click electronic access below)

<p>Dimerization and oligomerization reactions of alkenes are promising catalytic strategies to convert light alkenes, which can be derived from light alkane hydrocarbons (ethane, propane, butane) abundant in shale gas resources, into heavier hydrocarbons used as chemical intermediates and transportation fuels. Nickel cations supported on aluminosilicate zeotypes (zeolites and molecular sieves) selectivity catalyze ethene dimerization over oligomerization given their mechanistic preference for chain termination over chain propagation, relative to other transition metals commonly used for alkene oligomerization and polymerization reactions. Ni-derived sites initiate dimerization catalytic cycles in the absence of external activators or co-catalysts, which are required for most homogeneous Ni complexes and Ni²⁺ cations on metal organic frameworks (MOFs) that operate according to the coordination-insertion mechanism, but are not required for homogeneous Ni complexes that operate according to the metallacycle mechanism. Efforts to probe the mechanistic details of ethene dimerization on Ni-containing zeotypes are further complicated by the presence of residual H⁺ sites that form a mixture of 1-butene and 2-butene isomers in parallel acid-catalyzed pathways, as expected for the coordination-insertion mechanism but not for the metallacycle mechanism. As a result, the mechanistic origins of alkene dimerization on Ni cations have been ascribed to both the coordination-insertion and metallacycle-based cycles. Further, different Ni site structures such as exchanged Ni²⁺, grafted Ni²⁺ and NiOH⁺ cations are proposed as precursors to the dimerization active sites, based on analysis of kinetic data measured in different kinetic regimes and corrupted by site deactivation, leading to unclear and contradictory proposals of the effect of Ni precursor site structures on dimerization catalysis.</p> <p> Dimerization of ethene (453 K) was studied on Ni cations exchanged within Beta zeotypes in the absence of externally supplied activators, by suppressing the catalytic contributions of residual H⁺ sites via selective pre-poisoning with Li⁺ cations and using a zincosilicate support that contains H⁺ sites of weaker acid strength than those on aluminosilicate supports. Isolated Ni²⁺ sites were predominantly present, consistent with a 1:2 Ni²⁺:Li⁺ ion-exchange stoichiometry, CO infrared spectroscopy, diffuse reflectance UV-Visible spectroscopy and <i>ex-situ</i> X-ray absorption spectroscopy. Isobutene serves a kinetic marker for alkene isomerization reactions at H⁺ sites, which allows distinguishing regimes in which 2-butene isomers formed at Ni sites alone, or from Ni sites and H⁺ sites in parallel. 1-butene and 2-butenes formed at Ni sites were not equilibrated and their distribution was invariant with ethene site-time, revealing the primary nature of butene double-bond isomerization at Ni sites as expected from the coordination-insertion mechanism. <i>In-situ</i> X-ray absorption spectroscopy showed that the Ni oxidation state was 2+ during dimerization, also consistent with the coordination-insertion mechanism. Moreover, butene site-time yields measured at dilute ethene pressures (<0.4 kPa) increased with time-on-stream (activation transient) during initial reaction times, and this activation transient was eliminated at higher ethene pressures (≥ 0.4 kPa) and while co-feeding H₂. These observations are consistent with the <i>in-situ</i> formation of [Ni(II)-H]⁺ intermediates involved in the coordination-insertion mechanism, as verified by H/D isotopic scrambling and H₂-D₂ exchange experiments that quantified the number of [Ni(II)-H]⁺ intermediates formed.</p> <p> The prevalence of the coordination-insertion cycles at Ni²⁺ cations provides a framework to interpret the kinetic consequences of the structure of Ni²⁺ sites that are precursors to the dimerization active sites. Beta zeotypes predominantly containing either exchanged Ni²⁺ cations or grafted Ni²⁺ cations show noteworthy differences for ethene dimerization catalysis. The deactivation transients for butene site-time yields on exchanged Ni²⁺ cations indicate two sites are involved in each deactivation event, while those for grafted Ni²⁺ cations indicate involvement of a single site. The site-time yields of butenes extrapolated to initial time, and then further extrapolated to zero ethene site-time, rigorously determined initial ethene dimerization rates (453 K, per Ni) that showed a first-order dependence in ethene pressure (0.05-1 kPa). This kinetic dependence implies the β-agostic [Ni(II)-ethyl]⁺complex to be the most abundant reactive intermediate for the Beta zeolites containing exchanged and grafted Ni²⁺ cations. Further, the apparent first-order dimerization rate constant was two orders of magnitude higher for exchanged Ni²⁺ cations than for grafted Ni²⁺ cations, reflecting differences in ethene adsorption or dimerization transition state free energies at these two types of Ni sites. </p> <p> The presence of residual H⁺ sites on aluminosilicate zeotypes, in addition to the Ni²⁺ sites, causes formation of saturated hydrocarbons and oligomers that are heavier than butenes and those containing odd numbers of carbon atoms. The reaction pathways on Ni²⁺ and H⁺ sites are systematically probed on a model Ni-exchanged Beta catalyst that forms a 1:1 composition of these sites <i>in-situ</i>. The quantitative determination of apparent deactivation orders for the decay of product space-time yields provides insights into the site origins of the products formed. Further, Delplot analysis systematically identifies the primary and secondary products in the reaction network. This strategy shows linear butene isomers to be primary products formed at Ni²⁺-derived sites, while isobutene is formed as a secondary product by skeletal isomerization at H⁺ sites. In addition, propene is formed as a secondary product, purportedly by cross-metathesis between linear butene isomers and the reactant ethene at Ni²⁺-derived sites. Also, ethane is a secondary product that forms by hydrogenation of ethene at H⁺ sites, with the requisite H₂ generated <i>in-situ</i> likely by dehydrogenation and aromatization of ethene at H⁺ sites.</p> <a>The predominance of the coordination-insertion mechanism at Ni²⁺-derived sites implies kinetic factors influence isomer distributions within the dimer products, providing an opportunity to influence the selectivity toward linear and terminal alkene products of dimerization. In the case of bifunctional materials, reaction pathways on the Ni²⁺ and H⁺sites dictate the interplay between kinetically-controlled product selectivity at Ni sites and thermodynamic preference of product isomers formed at the H⁺ sites. </a>In summary, through synthesis of control catalytic materials and rigorous treatment of transient kinetic data, this work presents a detailed mechanistic understanding of the reaction pathways at the Ni²⁺ and H⁺ sites, stipulating design parameters that have predictable consequences on the product composition of alkene dimerization and oligomerization.

Les composés deutérés sont d’un intérêt grandissant dans des domaines variés. Par exemple, en pharmacologie, l'échange H/D peut améliorer les propriétés pharmacocinétiques de certains médicaments ou réduire leur toxicité. Les composés deuterés peuvent également être utilisés comme étalons internes en spectroscopie de masse. Il est donc important de trouver un moyen simple et sélectif d'échanger l'hydrogène avec le deutérium sur des molécules d’intérêt biologique. Les nanoparticules, de ruthénium en particulier, se sont révélées être des systèmes efficaces pour catalyser cet échange. Cependant, étant très actives, elles conduisent souvent à la réduction de substrats aromatiques. L'objectif principal du doctorat est l’élaboration de nouvelles nanoparticules permettant de contrôler la réactivité en échange isotopique H/D. Nous avons d’abord synthétisé des alliages Ru-Pt afin d’introduire du platine, moins actif en échange H/D, et donc empoisonner la surface du Ru. Nous avons montré qu’en changeant le précurseur de platine, on pouvait changer la distribution atomique de surface, et ainsi moduler la réactivité des nanoparticules. Nous avons finalement synthétisé des nanoparticules de nickel et d'iridium. Ces nanoparticules se sont avérées être des catalyseurs efficaces pour l'échange H/D, sans réduction de fonctions aromatiques. De plus, des sélectivités différentes ont été obtenues en fonction du métal utilisé. / Deuterated compounds are molecules of great interest in various fields. In pharmacology, the H/D exchange can improve the pharmacokinetic properties of some drugs or reduce their toxicity. In addition, deuterium-labelled compounds can be used as internal standards for mass spectroscopy, or as tracers for the understanding of different reaction mechanisms. Therefore, it is important to find a way to exchange hydrogen with deuterium in a simple, selective and efficient way. The main goal of the PhD project is the synthesis of novel nanoparticles for isotopic exchange (H/D). Metal nanoparticles and more particularly ruthenium nanoparticles, has shown their efficiency to catalyze this exchange. However, ruthenium nanoparticles are very active in arene hydrogenation, and often lead to the reduction of aromatic substrates. In a second part of the work, we synthesized Ru-Pt alloys in an attempt to passivate the Ru surface with platinum, which is less-active in H/D exchange. We have shown that by changing the platinum precursor, we can change the atomic distribution of the surface, and thus we were able to modulate the reactivity of nanoparticles. We finally synthesized Ni and Ir nanoparticles. These nanoparticles have proven to be efficient catalysts for H/D exchange, without reducing aromatic functions. In addition, different selectivity was obtained depending on the metal used.

The field of molecular bioenergetics deals with the energy transduction in biological cells. In this project, respiration and more specifically proton and sodium pumping enzymes and their coupling to electron transfer have been in focus. First we have been interested in the Na+-pumping NADH:quinone reductase from Vibrio cholerae which is the entry site of electrons in the respiratory chain of several pathogens. The role of specific flavin cofactors and amino acids involved in Na+ transfer has been shown in a combined IR spectroscopic and electrochemical approach. The interaction between proteins, namely the cytochrome c552 and the CuA fragment from the terminal ba3 oxidase from the organism Thermus thermophilus was then investigated. Structural reorganization during electron transfer was revealed by IR spectroscopy. Finally, in the third part of the project the interaction within the bc1-aa3 supercomplex from the respiratory chain from Corynebacterium glutamicum was analyzed.