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.

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Le récepteur A des peptides natriurétiques (NPRA) fait partie de la famille des guanylates cyclases membranaires. L’activation du NPRA par ses agonistes naturels, ANP et BNP, induit une production de GMPc qui est responsable de leur rôle dans l’homéostasie cardiovasculaire, l’inhibition de l’hypertrophie et de la fibrose cardiaques et la régulation de la lipolyse. Le NPRA est un homodimère non covalent composé d’un domaine extracellulaire de liaison du ligand (ECD), d’un unique domaine transmembranaire (TM), d’un domaine d’homologie aux kinases et d’un domaine guanylate cyclase. Bien que le NPRA ait un rôle physiologique important, les mécanismes moléculaires régissant son processus d’activation restent inconnus. Nous avons donc analysé les premières étapes du processus d’activation du NPRA. Nous avons d'abord étudié le rôle de la dimérisation des ECD dans l’activation du récepteur. Nous avons utilisé les techniques de liaison de radioligand, de FRET et de modélisation moléculaire, pour caractériser la liaison à l’ECD des agonistes naturels, d’un superagoniste et d’un antagoniste. L’ANP se lie à un dimère d’ECD préformé et la dimérisation spontanée est l’étape limitante du processus de liaison. De plus, comme le démontrent nos études de FRET, tous les peptides, incluant l’antagoniste, stabilisent le récepteur sous sa forme dimérique. Cependant, l’antagoniste A71915 stabilise le dimère d’ECD dans une conformation différente de celle induite par l’ANP. La dimérisation du NPRA semble donc nécessaire, mais non suffisante à l’activation du récepteur. L’état d’activation du NPRA dépend plutôt de l’orientation des sous unités dans le dimère. Nous avons ensuite étudié le mécanisme moléculaire de transduction du signal à travers la membrane. Plusieurs études ont suggéré que l’activation du NPRA implique un changement de conformation du domaine juxtamembranaire (JM). Cependant, les études de cristallographie de l’ECD soluble de NPRA n’ont pas permis de documenter la structure du JM et le changement de conformation impliqué dans la transduction du signal reste inconnu. Pour analyser ce changement de conformation, nous avons d’abord séquentiellement substitué les neuf acides aminés du JM par une cystéine. En étudiant la capacité des mutants à former des dimères covalents de façon constitutive ou induite par l’ANP, nous avons pu évaluer la proximité relative des résidus du JM, avant et après activation du NPRA. Ces résultats ont démontré la proximité élevée de certains résidus spécifiques et sont en contradiction avec les données cristallographiques. Nous avons également démontré que le domaine intracellulaire impose une contrainte conformationnelle au JM à l’état de base, qui est levée après liaison de l’ANP. En introduisant de 1 à 5 alanines dans l’hélice-α transmembranaire, nous avons montré qu’une rotation des TM de 40° induit une activation constitutive du NPRA. Le signal d’activation pourrait donc être transmis à travers la membrane par un mécanisme de rotation des TM. En utilisant nos données expérimentales, nous avons généré le premier modèle moléculaire illustrant la conformation active du NPRA, où les domaines JM et TM sont représentés. Dans son ensemble, cette étude apporte une meilleure compréhension des mécanismes moléculaires régissant les premières étapes du processus complexe d’activation du NPRA. / Natriuretic peptide receptor-A (NPRA) is a member of the particulate guanylate cyclase family. NPRA activation by natural agonists, ANP and BNP, leads to cGMP production, which is responsible for their role in cardiovascular homeostasis, cardiac hypertrophy and fibrosis inhibition and lipolysis regulation. NPRA is a non covalent dimer composed of an extracellular domain (ECD) with a ligand binding site, a single transmembrane region (TM), a kinase homology domain, and a guanylyl cyclase domain. Although NPRA plays an important physiologic role, molecular mecanisms driving its activation process are yet unknown. We thus analysed the first steps of NPRA’s activation process. First, we studied the role of ECD dimerization in receptor activation and determined the sequential steps of this dimerization process. We used radioligand binding, FRET and molecular modeling to characterize the interaction of ECD with natural agonists, a superagonist and an antagonist. ANP binds to preformed ECD dimers and spontaneous dimerization is the rate-limiting step of the ligand binding process. Furthermore, like demonstrated with fluorescence homoquenching, all the studied peptides, including A71915 antagonist, stabilize a dimeric form of the receptor. However, A71915 stabilizes the ECD dimer in a conformation distinct from those induced by ANP. Thus, ECD dimerization is necessary but not sufficient for NPRA activation. The activation state of NPRA seems to depend on the orientation of the receptor subunits within the dimer. Then, we tried to identify the molecular mechanism of signal transduction through the plasma membrane. Previous studies have shown that activation of NPRA involves a conformational change of the juxtamembrane domain (JM). However, crystallographic study of the soluble ECD of NPRA has failed to document JM structure, and the conformational change involved in transmembrane signal transduction is still unknown. To analyse this conformational change, we first sequentially substituted nine amino acids of JM by a cysteine residue. By studying the mutant’s capacity to form ANP-induced or constitutive covalent disulfide dimers, we evaluated the relative proximity of JM residues, before and after NPRA activation. These results demonstrate a high proximity of specific JM residues and are in disagreement with crystallography data. We also demonstrated that intracellular domain imposes a conformational constraint on JM at basal state, which becomes relaxed upon ANP binding. We finally confirmed, with a full-length receptor, that A71915 stabilizes NPRA in a dimeric form where JM are in a conformation distinct from the basal state. By introducing 1 to 5 alanine residues in the transmembrane α-helix, we showed that a TM rotation of 40° leads to constitutive NPRA activation. Activation signal could thus be transmitted through the membrane by a TM rotation mechanism. We finally studied the role of the TM in NPRA dimerization. By using the ToxR system, we demonstrated that the last JM residues are required to stabilize the TM dimer. Using these experimental data, we generated the first molecular model illustrating the active conformation of NPRA, where JM and TM are depicted. In summary, this study allows a better understanding of molecular mecanisms driving the first steps of NPRA’s complex activation process.

Ribosomal protein L27 is a component of the eubacterial large ribosomal subunit that has been shown to play a critical role in substrate stabilization during protein synthesis. This function is mediated by the L27 N-terminus, which protrudes into the peptidyl transferase center where it interacts with both A-site and P-site tRNAs as well as with 23S rRNA. We observed that L27 in S. aureus and other Firmicutes is encoded with a short N-terminal extension that is not present in most Gram-negative organisms, and is absent from mature ribosomes. The extension contains a conserved cleavage motif; nine N-terminal amino acids are post-translationally removed from L27 by a site-specific protease so that conserved residues important for tRNA stabilization at the peptidyl transferase center are exposed. We have identified a novel cysteine protease in S. aureus that performs this cleavage. This protease, which we have named Prp, is conserved in all bacteria containing the L27 N-terminal extension. L27 cleavage was shown to be essential in S. aureus; un-cleavable L27 did not complement an L27 deletion. Cleavage appears to play an essential regulatory role, as a variant of L27 lacking the cleavage motif could not complement. Ribosomal biology in eubacteria has largely been studied in E. coli; our findings indicate that there are aspects of the basic biology of the ribosome in S. aureus and other related bacteria that differ substantially from that of E. coli. This research lays the foundation for the development of new therapeutic approaches that target this novel, essential pathway.

A newly discovered cysteine protease, Prp, has been shown to perform an essential, site-specific cleavage of ribosomal protein L27 in Staphylococcus aureus. In Firmicutes and related bacteria, ribosomal protein L27 is encoded with a conserved N-terminal extension that must be removed to expose residues critical for ribosome function. Uncleavable and pre-cleaved variants were unable to complement an L27 deletion in S. aureus, indicating that this N-terminal processing event is essential and likely plays an important regulatory role. The gene encoding the responsible protease (prp) has been shown to be essential, and is found in all organisms encoding the N-terminal extension of L27. Cleavage of L27 by Prp represents a new target for potential antibiotic therapy. In order to characterize this protease, Prp has been overexpressed and purified. Using an assay we have developed, based on cleavage of a fluorogenic peptide derived from the conserved L27 cleavage sequence, we have undertaken an analysis of the enzyme kinetics and substrate specificity for Prp cleavage and tested predictions made based on a structural model using active-site mutants.

Colicin U is a protein produced by strains of bacterium Shigella boydii. It exhibits antibacterial activity against some bacterial strains Shigella and Escherichia. Based on sequence homology with colicins A, B and N, the colicin U is classified as a pore-forming colicin. Interaction of colicin U with attacked bacteria is ensured by three-step mechanism: 1) First colicin U interacts with surface receptors OmpA, OmpF and core of LPS. 2) Thereafter the colicin is translocated to periplasm through interaction with Tol proteins. 3) Finally colicin U interacts with the inner membrane of the attacked bacteria causing its depolarization. In this thesis I demonstrated pore-forming features of colicin U and further observed characteristics and properties of these pores. Using methods of measuring on black lipid membranes I determined a single channel conductance (19 pS), ion selectivity, the influence of various conditions on the behaviour of the pores. These findings, in many cases, correspond to the findings on other related colicins. Furthermore, I successfully determined the pore diameter of colicin U ( ≈ 0,8 nm). The next section of the thesis focuses on creation of single cysteine mutations of colicin U. Subsequently I produced five mutant variants of colicin U and verified their functionality so that...

Master of Science / Department of Grain Science and Industry / Sajid Alavi / Texturized vegetable protein (TVP) based foods offer several advantages compared to animal protein, including lower costs and improved health benefits. Wheat gluten is often processed using extrusion to produce TVP. Processing aids, such as reducing agents (example, cysteine and sodium metabisulfite) and pH modifiers (example, tetra potassium phosphate) aid in texturization. Reduction of sulfhydryl groups, cleavage of disulfide bonds, and reformation of bonds between elongated protein molecules results in protein aggregation and texturization. This study focused on development of a fundamental understanding of these mechanisms for texturization using analytical tools such as the phase transition analyzer (PTA), in combination with lab- and pilot-scale extrusion. The abovementioned three chemicals were added to four varieties of gluten. The control treatment had no additives. PTA was used to understand the operative flow properties of gluten in an environment similar to an extrusion system. Addition of sulfite (0.18%) and cysteine (0.18%) lowered the thermal softening (Ts:36.6-44.1 °C) and thermal flow (Tf:79.6-105.6 °C) temperatures of all varieties of gluten as compared to the controls (Ts:38.8-48.2 °C; Tf:91.7-112.2 °C). Phosphate (3%) did not have the same lowering effect on Ts (40.2-47.0 °C) and Tf (96.2-108.2 °C), indicating a different mechanism. Extrusion studies were conducted to gain an understanding of the reformation of disulfide bonds and texturization. Two of the varieties of gluten, a “superior” one that texturizes well and an “inferior” gluten requiring texturizing aids, were processed on a lab-scale extruder. Pilot scale extrusion was used to process the other two glutens (“superior” varieties) to obtain commercial quality products, which were evaluated for degree of texturization (hydration rate, absorption index and integrity). During lab-scale extrusion, texturization was observed only in the case of phosphate and corresponded with an increase in specific mechanical energy (SME) as compared to the control, indicating disulfide bond reformation. Phosphate also led to significantly (p<0.05) better texturization during pilot-scale extrusion, although SME trends were different due to higher in-barrel moisture and a more ideal extrusion system. Fourier Transform Infrared Spectroscopy was used to examine protein structural changes and indicated a loss of α-helix structure in TVP with an increase in β-sheet formation.

Nutrient availability regulates eukaryotic cell growth. This study focuses on two signaling pathways, involved in sensing amino acids and carbon sources, which allow cells to respond appropriately to their presence. The first part of this study shows that Ssy1, a plasma membrane localized sensor in the Ssy1-Ptr3-Ssy5 (SPS) amino acid sensing pathway, can detect 19 common L-amino acids with different potencies and affinities based on the physiochemical structure of amino acids. Substituents around alpha carbon are critical for amino acid sensing by Ssy1. Furthermore, a high concentration of cysteine is toxic to cells. Inactivation of SPS signaling confers resistance to cysteine. The second part focuses on the regulation of Hap4, the regulatory subunit of the Hap2/3/4/5 transcriptional factor complex. Many components of the 25-subunit Mediator complex negatively regulate HAP4 expression. Srb8 undergoes post-translational modification in response to changes of the carbon source. Gal11 and Med3 positively regulate HAP4 expression.

Os hidróxidos duplos lamelares (HDLs) compreendem uma extensa classe de materiais naturais e sintéticos, cujas estruturas e propriedades são frequentemente comparadas com as do mineral hidrotalcita. O estudo da intercalação de espécies de interesse farmacológico em HDLs tem ganhado a atenção da comunidade científica. O objetivo desta Dissertação foi o estudo da intercalação e liberação da espécie antioxidante N-acetil-L-cisteína (NAC) em HDLs de zinco-alumínio (Zn2Al-NAC) e magnésio-alumínio (Mg2Al-NAC). Espécies antioxidantes de modo geral apresentam características como baixa estabilidade química frente à luz e ao calor, sensibilidade ao valor do pH do meio e, algumas, baixa solubilidade. HDLs podem ser utilizados como carregadores de espécies antioxidantes para contornar as características indesejadas supracitadas. Os HDLs foram sintetizados através do método de coprecipitação, utilizando diferentes condições experimentais. Os materiais obtidos foram caracterizados por técnicas estruturais, espectroscópicas, térmicas, texturais e de análise química elementar. A liberação foi estudada através de experimentos in vitro de NAC intercalada ou imobilizada em HDL, empregando meio biológico simulado, nos métodos dinâmico e estático. Os difratrogramas de raios X das amostras de HDL de zinco mostram que a síntese realizada a 55&#176;C conduz à formação de material de alta cristalinidade e reflexão (003) igual a 16,3 &#197;. O material possui partículas planas e com baixo grau de agregação. Os resultados de espectroscopia vibracional e 13C-RMN confirmam a manutenção da integridade estrutural da NAC após intercalação e, ainda, sugerem que ocorreu a desprotonação dos grupos carboxílico e tiol. As lamelas possuem sítios distintos de alumínio hexacordenado, segundo o espectro de 27Al-RMN. O conjunto de técnicas de caracterização indicam a substituição de parte dos íons hidroxila das lamelas pelo oxigênio do grupo carboxilato da NAC. Os ensaios de liberação in vitro sugerem um processo modificado (prolongado) da NAC, visto que no método dinâmico foi liberado 35% dessa espécie em 96 horas, enquanto no método estático ocorreu a liberação de 20%. As análises estratigráficas após o ensaio comprovam que ocorreu a liberação apenas das regiões mais externas do comprimido. Os resultados das sínteses do HDL de magnésio não indicam a intercalação da NAC para essa matriz, mesmo empregando diferentes parâmetros experimentais. A espectroscopia Raman sugere que ocorreu a oxidação parcial dos ânions de NAC devido ao aparecimento da banda de estiramento &#957;S-S (508 cm-1). O espectro de 13C-RMN concorda com o resultado da espectroscopia Raman. Os dados de liberação in vitro corroboram a proposta de que a NAC está apenas imobilizada na superfície do HDL, visto que no método estático levou-se 12 horas para liberar 90% da NAC, sugerindo uma liberação rápida. As análises estratigráficas dos materiais após os testes de liberação dos dois métodos comprovam liberação total da NAC. / Layered double hydroxides (LDHs) comprise an extensive class of natural and synthetic materials, which structures and properties are often compared to those of hydrotalcite mineral. The study about intercalation of species of pharmacological interest into LDHs has gained the attention of the scientific community. The aim of this Dissertation was to investigate the intercalation and release of the antioxidant N-acetyl-L-cysteine (NAC) into LDHs of zinc-aluminum (Zn2Al-NAC) and magnesium-aluminum (Mg2Al-NAC) composition. Antioxidant species generally exhibit characteristics such as low chemical stability towards light and heat, sensitivity to the pH value of the medium and, some of them, low solubility. LDHs can be used as carriers of antioxidant species to circumvent the undesirable properties. LDHs were synthesized using the coprecipitation method and exploiting different experimental conditions. The obtained materials were characterized by structural, spectroscopic, thermal, textural and elemental chemical analysis techniques. The release of intercalated or immobilized NAC was studied by in vitro experiments in simulated biological medium, using the dynamic and static methods. The X-ray diffractograms of LDH samples of zinc show that the synthesis performed at 55&#176;C leads to a high crystalline material and the (003) reflection equal to 16.3 &#197;. The material has flat particles and a low degree of aggregation. The results of vibrational spectroscopy and 13C-NMR confirm the structural integrity of NAC after intercalation, and also suggest that the deprotonation of the carboxylic and thiol groups occurred. The LDH layer has distinct sites of hexacoordinate aluminum, according to the 27Al-NMR spectroscopy. The set of characterization techniques indicates the partial substitution of hydroxide ions in the layers by the oxygen of NAC carboxylate group. The in vitro assays of NAC release suggest a modified (prolonged) process, since 35% of this species was released in 96 h in the dynamic method while occurred 20% of release in the static method. Stratigraphic analyzes of the LDH-NAC tablet after the release test demonstrate that only the species of the outermost regions of the tablet were delivered. The results of magnesium-LDH syntheses do not indicate the intercalation of NAC into the matrix, even using different experimental parameters. Raman spectroscopy suggests that partial oxidation of NAC anions occurred due to the appearance of the band assigned to &#957;S-S (508 cm-1). The 13C-NMR spectrum of Mg2Al-NAC agrees with the result of Raman spectroscopy. In vitro release data corroborate the proposition that NAC is only immobilized on the LDH surface, since it took 12 h to release 90% of NAC in the static method, suggesting a rapid process. The stratigraphic analyzes of the material after the release tests by the two methods confirm the total release of NAC.

As cisteíno-proteases da família da papaína desempenham funções essenciais em processos biológicos, entre eles o desenvolvimento e crescimento do organismo, vias de sinalização celular e apoptose, invasão de parasitas em células hospedeiras. Assim, trata-se de uma classe de proteínas de grande interesse para as indústrias farmacêuticas, sendo utilizada como alvo para o tratamento de doenças como o câncer e metástases, osteoporose. Disfunções relacionadas ao sistema imune, doenças parasitárias como malária, leishmaniose, doença do sono e doença de Chagas. Esta última é uma enfermidade considerada negligenciada pelas grandes indústrias farmacêuticas, sem nenhum tratamento eficaz e seguro disponível, que gera um problema econômico de mais de sete bilhões de dólares anuais devido à perda de mão de obra e gastos com tratamento para amenizar os efeitos da doença. A cisteíno protease cruzaína de Trypanosoma cruzi, causador da Doença de Chagas, desponta como um alvo validado na busca de novos fármacos contra essa enfermidade. Essa enzima apresenta um par de aspartatos que interagem entre si, para os quais foi predito um pKa de 7, sendo possível a forma desprotonada desse par em condições biológicas. Neste caso, pode levar à exposição de uma nova cavidade por meio do movimento da alça entre os resíduos 57-62, segundo as simulações de dinâmica molecular desse trabalho, que se trata de uma possível candidata a ponto de seletividade de inibidores de cisteínoproteases de parasitos em relação às suas ortólogas em Homo sapiens que não possuem o par de aspartatos. Em pH ácido, foi mostrado por meio de análise de componentes principais de simulações de dinâmica molecular que as cisteíno protease apresentam uma restrição gradual na amostragem conformacional do sítio ativo quando complexadas com as formas não covalente e covalente de inibidores derivados de dipeptidil nitrilas. Isso sugere que esse sistema segue o modelo de seleção conformacional para flexibilidade de proteína. Notou-se também que o perfil de restrição de ligantes que inibem na faixa de nmol.L-1 difere daqueles a µmol.L-1 , o que possibilitou a construção de uma árvore de decisão para identificar os complexos que apresentam afinidade a nmol.L-1 . / The papain-like cysteine proteases are essentials for biological process, performing important roles on the parasite development, growth and also in the parasite invasion process on the host cell, in cellular signaling pathways and apoptosis, among others. Thus, the pharmaceutical industry widely uses this class of protein as target for the development of new drugs, against cancer and metastasis, osteoporosis and immune system disorders, resulting in many approved drugs. Additionally, these enzymes are validated target against parasitic diseases as leishmaniose, malaria and African and American trypanosomiasis. The last one, also known as Chagas\' disease, is neglected disease for which, further a century form this discovery, there is no effective and safe chemotherapy and is responsible for an economic loss of around seven billion dollars in the world per year due to the health care and lost productivity from infected people. Faced with this situation, the Cruzain, a cysteine protease from the Trypanosoma cruzi, the causative agent of Chagas\' disease, is emerging as interesting and validated target to the search for new drugs against this sickness. This enzyme has a pair of interactiong Asp for which was predicted a pKa of 7, by computational methods. By this way, this pair under neutral to alkaline pH adopts the deprotonated form, which exposed a new cavity through a movement of loop of residues 57-62, as we showed here by molecular dynamics simulations. This cavity emerges as a possible selectivity point of the cruzain inhibitors, once Homo sapiens enzynes does not present the aspartic acid - aspartate pair. In condition of acidic pH, principal component analysis of molecular dynamics simulations showed a gradual reduction of the conformational space covered by the active site of cruzain, cathepsin K and cathepsin L in it free form and complexed with dipeptidyl nitrilelike molecules in it noncovalent e covalent forms. This suggests these systems follows the conformational selection model of protein flexibility. Furthermore, we observed the ligands that inhibits the protein at nmol.L-1 induces the protein flexibility in a similar way, while the µmol.L-1 ones leads to another pattern. That made possible the construction of a decision tree which is able to identify nmol.L-1 from µmol.L-1 complexes.