Dissertations / Theses on the topic 'Sulfur Peptide'

Adsorption is a versatile purification technique to selectively separate different peptide fractions from a mixture using mild operation conditions. Porous carbons are ideally suited to separate ACE-inhibiting dipeptides by combining tailored size exclusion and polarity selectivity. The desired peptide fraction is mostly hydrophobic and very small and should adsorb inside hydrophobic micropores. The second topic of this thesis is linked to energy storage. The lithium-sulfur battery is a promising alternative to common lithium-ion batteries with theoretical capacities of up to 1672 mAh g−1 sulfur. The second aim of this thesis is to conduct an in-depth investigation of polysulfides interacting with selected carbon materials in a simplified battery electrolyte environment. The focus of this study is laid on the impact of surface polarity and pore size distribution of the carbon to develop a quantitative correlation between polysulfide retention and porosity metrics. Both, the enrichment of ACE-inhibitors and the retention of polysulfides rely on liquid phase adsorption in porous materials, linking the above mentioned topics. This thesis not only aims to develop an enrichment process or to find a superior battery cathode but also strives to explore structure-property relationships that are universally valid. Understanding the complex interplay of pore size and polarity leading to selective interactions between pore wall and the adsorbed species is given a high priority.

T cell activation is critical for the initiation of the adaptive immune response against both pathogens and malignant cells. This process depends on a complex set of finely tuned interactions, not only between the T cell receptor (TCR) and peptide-MHC complexes, but also between numerous accessory molecules. Chapter 2 of this thesis examines CD6, a transmembrane glycoprotein predominantly found on the surface of T cells, and its interaction with CD166, another transmembrane glycoprotein found on the surface of antigen presenting cells (APCs), amongst others. This interaction is required for optimal T cell activation. I have solved the X-ray crystal structures of the three extracellular SRCR domains of CD6 and the two membrane distal IgSF domains of CD166. In collaboration with colleagues, the ligand binding sites on both CD6 and CD166 have been further defined. We have also shown that a single nucleotide polymorphism (SNP) in CD6 caused glycosylation, hindering the CD6/CD166 interaction. Finally, native mass spectrometry revealed competition between the heterophilic CD6/CD166 interaction and the homophilic CD166 interaction.

Iron-sulfur clusters play a fundamental role in biology and are believed to be ancient cofactors that could have played a role in early protometabolic systems. Thus far, redox active, prebiotically plausible iron-sulfur clusters have always been obtained through cysteine coordination to the iron ions. However, extant iron-sulfur proteins can be found to exploit other modes of binding, including ligation by histidine residues, as seen with [2Fe-2S] Rieske and MitoNEET proteins. In this thesis, we investigated the ability of cysteine- and histidine-containing proteins and peptides to coordinate mononuclear [1Fe-0S] centers and a [2Fe-2S] clusters. The iron-sulfur peptides were characterized by UV-vis, circular dichroism, and paramagnetic NMR spectroscopies and cyclic voltammetry. Small (≤ 6 amino acids) peptides can coordinate [2Fe-2S] clusters through a combination of cysteine and histidine residues with similar reduction potentials as their corresponding proteins. Such complexes may have been important for early cell-like systems.

La catalyse permet de réaliser des transformations efficaces à un coût énergétique plus faible qu'avec des réactions non catalysées. Le développement d’un catalyseur peut souvent être inspiré par la Nature qui parvient à réaliser des transformations chimiques difficiles avec de hauts rendements et une grande sélectivité et ce en milieu aqueux dans des conditions douces. Par exemple, les protéines dépendantes du cuivre peuvent oxyder une large gamme de substrats. Inspirés par les systèmes biologiques, les metallopeptides ont récemment émergés en tant que plate-forme fiable pour développer de nouveaux catalyseurs grâce à leur facilité d’accès, de maniement et d’affinage de leurs propriétés. Dans cette thèse, nous décrivons la synthèse d’une famille de décapeptides bio-inspirés, qui contiennent des résidus His et Asp permettant de coordiner des ions métalliques. Les données indiquent que tous les peptides se lient au cuivre et qu’ils forment, à un pH proche de la neutralité, une espèce cuivre (II) majoritaire, similaire entre tous les peptides. Dans ces complexes, les peptides lient le cuivre (II) par les chaines latérales des résidus His et Asp. Pour finir, la capacité de ces systèmes ainsi que des complexes cuivre (II)-amyloid-β à catalyser des transformations oxydantes en solution aqueuse en utilisant H2O2 comme oxydants a été évaluée. Cette étude révèle que i) la structure des peptides à un impact sur les rendements catalytiques et sur l’obtention d’excès énantiomérique, et que ii) les complexes cuivre (II)-amyloid-β sont moins performants que nos systèmes cuivre (II)-peptide
Catalysis gives access to efficient transformations at a lower cost in energy and generally offers possibilities to reduce or eliminate the need for and the generation of hazardous compounds . The development of a catalyst is often inspired by Nature that performs challenging chemical transformations with high rates and high selectivity under mild conditions and aqueous media. For example, copper dependent proteins can react to oxidize a broad range of substrates. Inspired by biological systems, metallopeptides have recently emerged as reliable platforms to evolve new catalysts because they are chemically accessible, easy to handle and fine-tune.In this work we synthetized a family of bioinspired decapeptides containing His and Asp residues as metal ion coordinating amino acids. Their copper coordination properties were studied using pH potentiometry, and different spectroscopic techniques (UV-Vis, CD, EPR, NMR). The data indicates that all the peptides bind copper and form similar major copper(II) species at a pH close to neutrality where copper (II) is coordinated by the side-chains of His and Asp residues. Finally, the capabilities of these metallopeptides to perform a variety of oxidative transformations in aqueous solution at room temperature, using H2O2 as the oxidant were evaluated in parallel with that of amyloid-β peptides copper (II) complexes. This study revealed that i) the scaffold of the designed peptides had an impact on the catalytic efficiencies and enantiomeric excess and ii) the amyloid-β peptides copper (II) complexes are less active than our designed copper(II) peptide systems

L'étude des membranes biologiques nécessite l'examen des différentes propriétés de ses composantes principales: les lipides et les protéines. Dans ce manuscrit, l'interaction lipide- lipide et lipide-protéine ont été suivies par spectroscopie vibrationnelle (Raman, Infrarouge). Nous sommes intéressés en premier lieu à l'étude de la structure et l'organisation des phospholipides dans leur phase gel et leur phase cristalline liquide en utilisant la spectroscopie moyen infrarouge. En outre, l'effet de la composition du groupement hydrophiles des lipides sur le comportement de la liaison hydrogène des mélanges lipidiques a été sondé en utilisant la spectroscopie lointain infrarouge. Dans la seconde partie, l'interaction de la protéine NADH ubiquinone oxydoréductase et du mutant NuoL (D563N) avec le zinc ont été étudiés par spectroscopie différentielle et les changements conformationnels induits par la liaison du zinc avec les protéines ont été examinés. Enfin, les vibrations métal-ligand des groupements fer-soufre dans le mutant de NuoB (C64A G100C) à différents pH ont été analysées par spectroscopie Raman
The study of biological membranes involves the examination of the different properties of its main components: as lipids and proteins. In this manuscript, the lipid-lipid interaction and the lipid-protein interaction were monitored by vibrational spectroscopy (Raman and Infrared). We have been interested in the first part in studying the structure and organization of phospholipids in the gel phase and the liquid crystalline phase using mid infrared spectroscopy. In addition, the effect of the head group composition on the hydrogen bonding behaviour of lipid mixtures was probed using far infrared spectroscopy. In the second part, the interaction of the NADH ubiquinone oxidoreductase protein and NuoL mutant (D563N) with zinc was investigated through FTIR difference spectroscopy where the conformational changes upon zinc binding were monitored. Finally, the metal-ligand vibrations of the iron- sulfur clusters in NuoB mutants (C64A G100C) at different pH were analysed using Raman spectroscopy

Metabolism is a subset of chemistry that allows cells to defy thermodynamic equilibrium, a fundamental process that must have been in place from the very beginning of biology. Before evolution produced efficient catalysts in the form of complex protein machinery, short metal binding peptides might have preceded modern metalloproteins. Such prebiotic, metal-binding motifs have been hypothesized to have existed through analyses of extant protein sequences. However, it is unclear how metal-binding motifs might have evolved in the harsh prebiotic environment. Here, we show how certain environments, in particular seawater-like environments rich in divalent cations and especially Mg2+, support the survival of short peptides upon extreme temperatures as high as 150 °C. Moreover, while Mg2+ does not offer the same protection from UV light, peptides are protected from both heat and irradiation when bound to a metal ion. The results suggest that specific environments rich in metal ions may be better suited for the emergence of complex systems in the path toward life. Additionally, the conditional degradation of peptides depending on their ability of binding metals might have enabled a selection mechanism that would favor the survival of metal-binding motifs which resemble the motifs found in modern proteins. These short sequences could have acted as early, simple catalysts able to facilitate a restricted set of chemical reactions, which would shape the emergence and biology of the Last Universal Common Ancestor.

Les interactions non covalentes jouent un rôle clé dans des phénomènes de la biologie chimique tel que la stabilisation de la structure tertiaire et quaternaire des protéines ou la reconnaissance entre des biomolécules tel que protéine-protéine et protéine-ligand. Parmi ces interactions, la liaison hydrogène classique de type amide NH···O=C a fait l’objet de nombreuses études approfondies. En revanche, l’étude d’autres types de liaisons hydrogène impliquant le NH de la fonction amide est plus rare. Nos travaux ont été focalisés sur l’impact d’une liaison NH···S sur les préférences conformationnelles d’amino acides soufrés et de leurs oligomères courts. Nous avons préparé un panel de dérivés protégés des amino acides soufrés non-canoniques suivants : Cys(Me) (acyclique), Attc (thiétane), Atlc (thiolane), Atc (thiane). Ces dérivés ont été caractérisés par des calculs théoriques, par spectroscopie double résonance IR/UV en phase gazeuse, par spectroscopie IR et RMN en solution, et à l’état solide. Nous avons mis en évidence pour ces quatre composés l’existence concomitante d’une liaison hydrogène NH···S inter-résidus formant une structure C6ˠ et d’une interaction NH···O=C formant une structure C5. Une succession de ces motifs combinés C5-C6ˠ stabilisants a été retrouvée dans les oligomères d’Attc. Un autre type de liaison hydrogène NH···S, cette fois-ci intra-résidu et formant une structure C5ˠ, a été caractérisé dans des dimères d’Atlc et d’Atc, associée parfois à une interaction NH···O=C formant un coude ˠ. La force de l’interaction NH···X dans le motif structural combiné C5-C6ˠ a été évaluée par comparaison avec des dérivés protégés amino acides cycliques à 4 chaînons : Attc (X = soufre), (Aatc(Me) (X = azoté), Aotc (X = oxygéné). Le motif C5-C6ˠ était présent dans les trois cas et la comparaison des spectres IR en phase gazeuse et en solution, aidée par des calculs théoriques, nous a permis de déduire une force croissante de la liaison hydrogène NH···X en allant de X=O vers X=S puis X=N
Non-covalent interactions play a key role in chemical biology phenomena such as the stabilization of protein tertiary and quaternary structure or protein-protein and protein-substrate recognition. Among these interactions, the classical amide-type NH···O=C hydrogen bond has been thoroughly studied. The study of other types of non-covalent interactions implicating peptide backbone NH groups is much rarer. This work focused on the impact of NH···S hydrogen bonding on the conformational preferences of thioether amino acid residues and their short oligomers. A panel of capped derivatives of the following non-canonical sulfur-containing amino acids was prepared: Cys(Me) (acyclic), Attc (thietane), Atlc (thiolane), Atc (thiane). These derivatives were characterized computationally, by IR/UV double resonance laser spectroscopy in the gas phase, by IR and NMR spectroscopy in solution, and in the solid state. We demonstrated the concomitant existence of inter-residue C6ˠ NH···S hydrogen bonds and C5 NH···O=C interactions in each of these four compounds. This combined stabilizing feature was also prevalent in Attc oligomers. A different intra-residue C5ˠ NH···S hydrogen bond was characterized in short oligomers of Atlc and Atc, in some cases associated with a ˠ-turn NH···O=C interaction. The significance of NH···S bonding in the combined C5-C6ˠ structural feature of Attc was evaluated by comparison with capped derivatives of other four-membered ring amino acids: Ac4c (cyclobutane), Aatc(Me) (azetidine), Aotc (oxetane). The C5–C6ˠ feature was present in the three heterocyclic residues: comparison of their IR spectra in gas phase and in solution, aided by theoretical calculations, allowed us to identify an increasing strength of NH···X hydrogen bonding from X=O to X=S to X=N

Muitas espécies de pimentas vermelhas do gênero Capsicum são utilizadas em práticas medicinais tradicionais. Essas plantas são empregadas em algumas preparações para tratar uma variedade de doenças, incluindo infecções. Algumas bactérias produzem biofilme como um importante fator de virulência, pois a estrutura do biofilme intermedia a adesão bacteriana a superfícies, como em dispositivos implantados, sondas e cateteres além de promover proteção física contra os antibióticos ou as respostas do sistema imunológico. Dessa maneira, este estudo investigou a capacidade do extrato e de produtos isolados das sementes de Capsicum baccatum como agentes antibiofilme. Este estudo demonstra, pela primeira vez, que um extrato de C. baccatum apresentou importante atividade antibiofilme contra Staphylococcus epidermidis e Pseudomonas aeruginosa. A fração ativa foi obtida através de ensaios bioguiados e analisada por HPLC-DAD-MS, MALDI-TOF MS e MALDI-MS/MS, identificando-a como peptídeos da proteína 2S sulfur-rich seed storage protein 2-like. Estes peptídeos (2mg/ml) foram potentes no controle da formação de biofilme de S. epidermidis (>96%) em solução e adsorvidos em lâminas de Permanox® recobertas. De modo interessante, não inibiram o crescimento bacteriano, indicando que a inibição do biofilme é independente da morte celular bacteriana. Ainda, esses peptídeos foram capazes de preservar eritrócitos, bem como a integridade de linfócitos humanos após 24 e 48 horas de exposição, demonstrando que o fracionamento do extrato de C. baccatum potencializou a sua atividade antibiofilme e reduziu significativamente a sua citotoxicidade. Nossos resultados corroboram com a pesquisa de novas estratégias não antibióticas para combater microrganismos com reduzida possibilidade para o desenvolvimento de resistência.
Many species of Capsicum red peppers are used in traditional medicinal practices. These plants are utilized in a number of preparations to treat a variety of illnesses including infections. Some bacteria produce biofilm as an important virulence factor, due to this its structure mediates the adhesion to surfaces as implanted devices, probes, catheters and also promotes physical protection against the antibiotics or the immune system response. Accordingly, this study investigated the ability of the extract and isolated products from seeds of Capsicum baccatum as anti-biofilm agent. This study demonstrates by the first time that an extract from C. baccatum presented relevant anti-biofilm activity against Staphylococcus epidermidis and Pseudomonas aeruginosa. The active fraction was obtained by bio-guided assays and analyzed by HPLC-DAD-MS, MALDI-TOF MS and MALDI-MS/MS, identifying it as peptides from 2S sulfur-rich seed storage protein 2-like. It strongly controlled (2mg/ml) the S. epidermidis biofilm formation (>96%) when the compound was in solution and adsorbed on Permanox™ slides. Interestingly, it did not inhibit the growth of this bacterium, indicating the inhibition of biofilm is independent of bacterial cell death. Moreover, this peptides preserved human erythrocytes and lymphocytes integrity after 24-48 h of exposure, suggesting the fractionation potentiated the anti-biofilm activity of the C. baccatum crude extract while absolutely reduced its cytotoxicity. Our results corroborate to the search of new non-antibiotic strategies to combat microorganisms with a reduced pressure for resistance development.

L’ubiquinone, ou coenzyme Q (CoQ ou UQ), est un lipide polyprénylé qui joue un rôle important dans le transport des électrons dans les chaînes respiratoires chez E. coli. La biosynthèse de l'UQ en aérobie chez E. coli nécessite huit réactions et implique au moins douze protéines (UbiA-UbiK et UbiX). Dans ce travail, nous démontrons que les protéines Ubi forment le complexe Ubi, un métabolon stable qui catalyse les six dernières réactions de la voie de biosynthèse. La structure tridimensionnelle du domaine SCP2 d’UbiJ forme une cavité hydrophobe étendue qui lie les intermédiaires de l’UQ à l'intérieur du complexe d’1-MDa. Le complexe Ubi est purifié à partir des extraits cytoplasmiques et la biosynthèse de l'UQ a lieu dans cette fraction, remettant en question l’hypothèse actuelle d'un processus de biosynthèse associé à la membrane. L’UQ est connue pour être synthétisée en aérobie et anaérobie. Nous caractérisons une nouvelle voie de biosynthèse de l’UQ indépendante de l'O2. Cette voie repose sur trois protéines, UbiT, UbiU et UbiV. UbiT possède un domaine de liaison aux lipides SCP2 et est probablement un facteur accessoire de la voie de biosynthèse, tandis qu’UbiU et UbiV (UbiU-UbiV) sont impliqués dans les réactions d'hydroxylation et représentent une nouvelle classe d'hydroxylases indépendantes de l’O2. Nous démontrons qu’UbiU-UbiV d’E.coli forme un hétérodimère, chaque protéine se lie à un centre [4Fe-4S] via des cystéines conservées essentielles à l'activité. De plus, nous montrons qu’UbiU purifié de P. aeruginosa est capable de lier de l’UQ, suggérant un rôle différent d’UbiU et d’UbiV. UbiU et UbiV appartiennent à la famille des peptidases U32, dont la fonction reste discutable. Nous démontrons, par des analyses bioinformatiques, que les protéines U32 sont caractérisées par quatre cystéines conservées très importantes pour leurs activités enzymatiques et par des outils biochimiques, nous confirmons que RlhA et TrhP, deux autres protéines de la famille U32, comme UbiU et UbiV, sont des protéines Fe-S
Ubiquinone (UQ) is a polyprenylated lipid that plays an important role in electron transport in the respiratory chains of E. coli. The aerobic biosynthesis of UQ in E. coli requires eight reactions and involves at least twelve proteins (UbiA-UbiK and UbiX). In this work, we demonstrate that seven Ubi proteins form the Ubi complex, a stable metabolon that catalyzes the last six reactions of the UQ biosynthetic pathway. The X-Ray structure of the SCP2 domain of UbiJ forms an extended hydrophobic cavity that could bind UQ intermediates inside the 1-MDa Ubi complex. The Ubi complex is purified from cytoplasmic extracts and UQ biosynthesis occurs in this fraction, challenging the current thinking of a membrane-associated biosynthetic process. UQ is reported to be biosynthesized under both anerobic and anaerobic conditions. We characterize a novel, O2-independent pathway for the biosynthesis of UQ. This pathway relies on three proteins, UbiT, UbiU, and UbiV. UbiT contains an SCP2 lipid-binding domain and is likely an accessory factor of the biosynthetic pathway, while UbiU and UbiV (UbiU-UbiV) are involved in hydroxylation reactions and represent a novel class of O2-independent hydroxylases. We demonstrate that UbiU-UbiV from E.coli form a heterodimer, wherein each protein binds a [4Fe-4S] cluster via conserved cysteines that are essential for activity. Moreover, we show that purified UbiU from P. aeruginosa is able to bind UQ, suggesting a different role of UbiU and UbiV. UbiU and UbiV belong to peptidase U32 family whose function remains questionable. By bioinformatic analyses, we demonstrated that U32 proteins were characterized by four conserved cysteines important for their enzymatic activities and by biochemical tools, we confirmed that RlhA and TrhP, two others U32 subfamilies, like UbiU and UbiV, are all Fe-S proteins

Foi estudada a fração não-protéica de sementes de feijão (Phaseolus vulgaris L. ), tendo por objetivo identificar a presença e conhecer o teor de (γ-glutamil peptídeos sulfurados. Estes peptídeos (γ-glutamil-S-metilcisteína e (γ-glutamil metionina) podem interferir com o doseamento da metionina pelo método da clivagem com brometo de cianogênio e análise do metiltiocianato por cromatografia em fase gasosa. O extrato etanólico contém 21 % do nitrogênio total do feijão. A lavagem do extrato com clorofórmio reduziu o teor de nitrogênio para 5,5%, pela remoção de proteínas co-extraídas. O extrato não-proteico assim obtido foi purificado sucessivamente por resinas de troca catiônica e aniônica, ocorrendo a separação dos constituintes pelos seus valores de pK. A purificação foi acompanhada por testes químicos, cromatografia em camada delgada e análise de aminoácidos. Foi identificada com base nas suas características químicas, a presença de S-metilcisteína, principalmente na forma de dipeptídeo com ácido glutâmico. A quantificação do peptídeo após hidrólise ácida (3h / 110° C), resultou num teor de S-metilcisteína total de 0,67g /100g proteína, que corresponde a aproximadamente 50% do teor de metionina no feijão, determinado por cromatografia de troca iônica. Estes resultados podem indicar que o teor de metiltiocianato total, liberado pela metionina e pela S-metilcisteína do feijão (1 ,6%) (determinado em trabalho anterior), descontado do teor de S-metilcisteína (0 ,7%), equivale à metionina quimicamente disponível, correspondendo a aproximadamente 64% da metionina total presente no feijão. No ensaio de germinação das sementes do feijão foi observado um decréscimo da (γ-glutamil-Smetilcisteína, indicando uma mobilização dos aminoácidos constitutintes.
The non-protein fraction of Phaseolus vulgrias L. seeds has been analysed to obtain information on the identity and level of (γ-glutamyl peptides containing a sulfur amino acid. These peptides (γ-glutamyl-S-methylcysteine and (γ-glutamyl methionine) could interfere with the determination of methionine measured by cleavage with cyanogen bromide and subsequent gas-chromatographic identification of methylthiocyanate. The ethanolic extract of (γ-glutamyl peptides contains 21% of the total seed nitrogen, which decrease to 5,5%, by removing the coextracted bean proteins with chloroform. This non-protein extract was then purified by ion-exchange chromatography on basic and acid resins, taking advantage of the different pK values of the amino acids. The isolation procedure was followed up by chemical analysis, thin layer chromatography and amino acid analysis. Based on their chemical properties we were able to identify the presence of S-methylcysteine, mainly in the form of a dipeptide with glutamic acid. Quantitative analysis of the peptide after acid hydrolysis (3h /110° C) showed a level of 0,67g /total S-methylcysteine /100gbean protein. This content accounted for approximately 50% of the bean methionine content, determined by ion-exchange chromatography. These results might indicate that total methylthiocyanate released from both, methionine and S-methylcysteine of beans, (1,6%) (from a previous paper) subtracted from S-methylcysteine (0,7%) could be recognized as chemically available methionine, corresponding to approximately 64% of total methionine. During seed germination the (γ-glutamyl-S-methylcysteine undergo a degradative process resulting in loss of the dipeptide.

Adsorption is a versatile purification technique to selectively separate different peptide fractions from a mixture using mild operation conditions. Porous carbons are ideally suited to separate ACE-inhibiting dipeptides by combining tailored size exclusion and polarity selectivity. The desired peptide fraction is mostly hydrophobic and very small and should adsorb inside hydrophobic micropores. The second topic of this thesis is linked to energy storage. The lithium-sulfur battery is a promising alternative to common lithium-ion batteries with theoretical capacities of up to 1672 mAh g−1 sulfur. The second aim of this thesis is to conduct an in-depth investigation of polysulfides interacting with selected carbon materials in a simplified battery electrolyte environment. The focus of this study is laid on the impact of surface polarity and pore size distribution of the carbon to develop a quantitative correlation between polysulfide retention and porosity metrics. Both, the enrichment of ACE-inhibitors and the retention of polysulfides rely on liquid phase adsorption in porous materials, linking the above mentioned topics. This thesis not only aims to develop an enrichment process or to find a superior battery cathode but also strives to explore structure-property relationships that are universally valid. Understanding the complex interplay of pore size and polarity leading to selective interactions between pore wall and the adsorbed species is given a high priority.