Dissertations / Theses on the topic 'Proteins thiol'

Bioconjugation chemistry generally refers to the covalent derivatisation of biomolecules. Derivatisation of cysteine’s thiol of peptides and proteins is a common method in bioconjugation chemistry as the thiolate is an excellent nucleophile in aqueous conditions. The propensity for thiols to oxidise in an aqueous environment necessitates the need for a disulfide reduction step prior to the addition of ligands derivatised with thiol alkylating linkers. Disulfide reducing agents such as tris(2-carboxyethyl)phosphine (TCEP) and tris(3-hydroxypropyl)phosphine (THPP) are disulfide reducing agents that are often marketed as being non-reactive with thiol alkylating reagents. The reaction of TCEP and THPP with thiol alkylation linkers was therefore investigated. Characterisation of reaction products and mechanistic studies revealed that TCEP and THPP both react with thiol alkylation reagents. A novel protocol was, therefore, developed utilising the Staudinger reaction to oxidise excess TCEP and THPP prior to the addition of thiol alkylating reagents. The protocol offers a simple “one-pot” method for effecting conjugate production via thiol alkylation, without the need for an intermediate purification step for the removal of excess disulfide reducing agents. 4-Vinyl pyridine (4-VP) derivatives were developed and explored as an alternative Michael acceptor class for thiol alkylation of peptides and proteins. The 4-VP derivatives exhibited high reactivity and specificity for thiol alkylation between pH = 7 and pH = 8. A selection of 4-VP linkers were subsequently functionalised with either carbohydrates or polyethylene glycol (PEG) and successfully utilised to produce peptide or protein conjugates via thiol alkylation reactions.

The terms "aging" and "neurodegeneration" are often used in a broad and generalized manner. Actually, they are particularly complex and multifaceted processes, involving different biochemical systems. Increasing evidence supports the notion that reduction of cellular expression and activity of antioxidant proteins and the resulting increase of oxidative stress are fundamental causes in the aging processes and neurodegenerative diseases. Within the frame of free radical hypothesis of aging, several lines of evidence suggest that accumulation of oxidative molecular damage is a causal factor in senescence. It is also increasingly evident that the mitochondrial genome may play a key role in aging and neurodegenerative diseases. Mitochondrial dysfunction is characteristic of several neurodegenerative disorders, and evidence for mitochondria being a site of damage in neurodegenerative disorders is partially based on decreases in respiratory chain complex activities in Parkinson s disease (PD), Alzheimer s disease (AD), and Huntington s disease (HD). Such defects in respiratory complex activities, possibly associated with oxidant/antioxidant balance perturbation, are thought to underlie defects in energy metabolism and induce cellular degeneration. Efficient functioning of mantainance and repair process seems to be crucial for both survival and physical quality of life. This is accomplished by a complex network of the so-called "longevity assurance processes", which are composed of several genes, termed vitagenes. Among these, heat shock proteins, also known as stress proteins and molecular chaperones, are highly conserved proteins for the preservation and repair of the correct conformation of cellular macromolecules, such as proteins, RNAs and DNA. Chaperone-buffered silent mutations may be activated during the aging process and lead to the phenotypic exposure of previously hidden features and contribute to the onset of multigenic diseases, such as age-related disorders, atherosclerosis and cancer. Recent studies have shown that the heat-shock response contributes to establishing a cytoprotective state in a wide variety of human diseases, including ischemia and reperfusion damage, inflammation, metabolic disorders, cancer, infection, trauma, and aging. The major neurodegenerative diseases, Alzheimer s disease (AD), Parkinson s disease (PD), amyotrophic lateral sclerosis (ALS), Huntington s disease (HD), and Friedreich s ataxia (FA), are all associated with the presence of abnormal. Given the broad cytoprotective properties of the heat-shock response, there is now strong interest in discovering and developing pharmacological agents capable of inducing the heat-shock response. These findings have opened up new perspectives in medicine and pharmacology, as molecules inducing this defense mechanism appear to be possible candidates for novel cytoprotective strategies. Particularly, modulation of endogenous cellular defense mechanisms such as the heat-shock response, and the proteasomal system, through nutritional antioxidants or pharmacological compounds may represent an innovative approach to therapeutic intervention in diseases causing tissue damage, such as neurodegeneration. Moreover, by maintaining or recovering the activity of vitagenes, it would be possible to delay the aging process and decrease the occurrence of age-related diseases with resulting prolongation of a healthy life span.

In higher plants oxygenic photosynthesis primarily takes place in the chloroplasts of leaves. Within the chloroplasts is an intricate membrane system, the thylakoid membrane, which is the site of light harvesting and photosynthetic electron transport. Enclosed by this membrane is the lumen space, which initially was believed to only contain a few proteins, but now is known to house a distinct set of >50 proteins, many for which there is still no proposed function. The work presented in this thesis is focused on understanding the functions of the proteins in the lumen space. Using proteomic methods, we investigated first the regulation of lumenal proteins by light and secondly by dithiol-disulphide exchange, mediated by the disulphide reductase protein thioredoxin. We furthermore performed structural and functional studies of the lumenal pentapeptide repeat proteins and of the PsbP-domain protein PPD6. When studying the diurnal expression pattern of the lumen proteins, using difference gel electrophoresis, we observed an increased abundance of fifteen lumen protein in light-adapted Arabidopsis thaliana plants. Among these proteins were subunits of the oxygen evolving complex, plastocyanin and proteins of unknown function. In our analysis of putative lumenal targets of thioredoxin, we identified nineteen proteins, constituting more than 40 % of the lumen proteins observable by our methods. A subset of these putative target proteins were selected for further studies, including structure determination by x-ray crystallography. The crystal structure of the pentapeptide repeat protein TL15 was solved to 1.3 Å resolution and further biochemical characterization suggested that it may function as a novel type of redox regulated molecular chaperone in the lumen. PPD6, a member of the PsbP-family of proteins, which is unique in that it possesses a conserved disulphide bond not found in any other PsbP-family protein, was also expressed, purified and crystallized. A preliminary x-ray analysis suggests that PPD6 exists as a dimer in the crystalline state and binds zinc ions. The high representation of targets of thioredoxin among the lumen proteins, along with the characterization of the pentapeptide repeat protein family, implies that dithiol-disulphide exchange reactions play an important role in the thylakoid lumen of higher plants, regulating processes such as photoprotection, protein turnover and protein folding.

There is increasing evidence that hydrogen peroxide (H2O2) can act as a signalling molecule capable of modulating a variety of biochemical and genetic systems. Using Jurkat T-lymphocytes, this study initially investigated the involvement of H2O2 in the activation of a specific signalling protein extracellular signal-regulated protein kinase (ERK). It was found that as a result of H2O2 treatment, mitochondrial complex activities decreased which led to subsequent increase of mitochondrial reactive oxygen species (ROS) production. The increase of ROS resulted in higher cellular H2O2 as well as increased ERK activation. This study demonstrated that in an oxidative stress setting, H2O2 production from the mitochondria was an essential component in maintaining the activation of a signalling protein. One way in which H2O2 could influence protein function is by the oxidation of susceptible thiol groups of cysteine residues. To further understand the variety of signalling pathways that H2O2 may be involved in, an improved proteomics technique was developed to globally identify proteins with susceptible thiol groups. The

Aqueous Phase Partitioning has a long history of applications to the analytical characterisation of biomolecules. However process applications have attracted the most interest in biotechnology where it has become widely recognized as a cost-effective technique. The main aim of this work was to explore the proposition that partition in Aqueous Two Phase Systems (ATPS) can be used as an analytical tool to detect protein isoforms and to assess the applicability of the method in clinical assays and for quality control in bioprocessing through examination of several analytical problems. The work also examined the development of automated methods of system preparation and sampling techniques to determine the partition coefficient in ATPS. The study demonstrated that the geometrical form of the phase diagram co-existence curve was of crucial importance since this directly affected the accuracy with which systems of defined Tie Line Length and Mass Ratio could be constructed. The TLL %Bias (accuracy) of a theoretical system range in the PEG1000-(NH4)2SO4 system at shorter TLL (12.2) was in the range +80.6% to -100% while at a longer TLL (53.1) the %Bias (accuracy) was reduced to +0.1% to -1.9%. At the same time the MR %Bias (accuracy) at shorter TLL (12.2) was in the range +59.5% to -21.3% while at the longer TLL (53.1) this was reduced to +2.7% to -2.6%. By contrast in the PEG8000-Dextran500 system the TLL %Bias (accuracy) at shorter TLL (13.1) was in the range +3.7% to -4.12%, while at a longer TLL (31.1) the range was +0.74% to -0.67%. The MR %Bias (accuracy) at the shorter TLL (13.1) was in the range +3.6% to -3% while at the longer TLL (31.1) the range was +1.1% to -1.4%. This illustrated that it is more difficult to work with a high degree of accuracy (e.g. %Bias <5%) close to the critical point in PEG-salt systems than in PEG-dextran systems. Two different approaches were taken to examine analytical phase partitioning. In the first approach the structure of the isoforms of a model protein (ovalbumin) were altered enzymatically. Analytical methods involving Strong Anion-Exchange chromatography were developed and applied to the separation of the ovalbumin isoforms. Removal of the phosphorylated groups (dephosphorylation of ovalbumin) was undertaken using alkaline phosphatase and de-glycosylation was attempted using neuraminidase and Endo-glycosidase F. However, both enzymatic approaches to deglycosylation were unsuccessful. Dephosphorylated isoforms were successfully produced and characterised. After partitioning in ATPS a clear difference was demonstrated between the behaviour of the native and dephosphorylated forms of ovalbumin. The mean % recovery in a PEG-salt ATPS was 99.8% (± 3.59) for the naive protein and 75.6% (± 4.03) for the dephosphorylated form. On the other hand, in a PEG3350-Dextran500 system, where solubility was maintained, a significant difference in the partition coefficient (K) of native and dephosphorylated ovalbumin was found. K for native ovalbumin was 0.85 while the partition coefficient of the dephosphorylated ovalbumin was 0.61. Analysis of covariance (ANCOVA) indicated that the regression coefficients of the respective partition isotherms were significantly different (p value < 0.05). In a second approach to examine analytical phase partitioning, chemical modification of a specific target surface amino acid of another model protein (serum albumin) was used to determine the degree of conjugation of the protein and also to determine its oxidative state. The method examined the reactivity of a free surface thiol to a wide range of labels ( (a) 2-methylsulfonyl-5-phenyl -1,3,4 oxidiazole reagent, (b) N-Ethylmaleimide (NEM) reagent, (c) 5, 5’-dithiobis (2-nitrobenzoate)(DTNB) (Ellman’s reagent), (d) N-pyrenylmaleimide (NPM) reagent, (e) Fluorescein-5-maleimide (F-5-M) Reagent). Only DTNB was found to modify the surface free thiol of serum albumin in a highly specific and quantitative manner. In the course of the development of a partitioning assay for surface free thiols of serum albumin significant oxidative properties were found to be associated with poly(ethylene glycol) PEG solutions and several attempts were made to find an oxidatively safe partitioning system by including antioxidants and by removal of contaminants by freeze drying. PEG3350-Dextran500 was found to provide an oxidatively safe environment for the development of a partitioning assay for the determination of albumin free thiols. A phase partitioning assay system capable of quantitatively resolving protein associated free thiols and low molecular weight thiols from a mixture of the two was developed. Correlation coefficients (R2) for the regression of experimentally determined protein free thiols in the presence of different levels of added LMW free thiol on the known addition of protein ranged from 0.77 to 0.83. The results demonstrated that the assay could quantify and distinguish both types of thiol in a simple two-step procedure.

Protein adsorption on solid surfaces is a common yet complicated phenomenon that is not fully understood. Self-assembled monolayers have been utilized in many studies, as well-defined model systems for studying protein-surface interactions in the atomic level. Various strategies, including the use of single component SAMs[1, 2], combinations of long and short alkanethiolates with methyl- and hydroxyl- terminal groups[3, 4], and using mixtures of alkanethiolates with similar chain length and varying terminal functional group [5] have been used to effectively control the surface wettability and determine the effect of surface composition and wettability on protein adsorption. In this dissertation we report key new findings on the effect of surface density of functional groups on protein adsorption phenomenon. In The first phase of this research, we developed a novel approach for preparation of low-density self-assembled monolayers(LD-SAMs) on gold surfaces, based on radical-initiated thiol-yne click chemistry. This approach provides exceptional adsorbate stability and conformational freedom of interfacial functional groups, and is readily adapted for low-density monolayers of varied functionality. The resulting monolayers have two distinct phases: a highly crystalline head phase adjacent to the gold substrate, and a reduced density tail phase, which is in contact with the environment. First, we investigated the feasibility of the proposed chemistry in solution-phase. In this approach, we synthesized “Y” shaped carboxylate-terminated thiol adsorbates via radical-initiated thiol-yne reaction. The LD-SAMs were then prepared through immersion of gold substrates into the solution of synthesized adsorbate molecules in hexane. The chemical structuring and electrochemical properties of resultant LD-SAMs were analyzed and compared with those of analogous traditional well-packed monolayers, using techniques such as Fourier transform infrared spectroscopy, ellipsometry, electrochemical impedance spectroscopy, reductive desorption, and contact angle goniometry. Characterization results indicated that resulting LD-SAMs have a lower average crystallinity, and higher electrochemical stability compared to well-packed monolayers. In addition, using a three-electrode system, we were able to show a reversible change in LD-SAM surface wettability, in response to an applied voltage. This remodeling capacity confirms the low density of the surface region of LD-SAM coatings. The second area of work was focused on using the developed chemistry in solid-phase. The solid-phase approach minimized the required synthesis steps in solution-phase method, and used the photo-initiated thiol-yne click-reaction for grafting of acid-terminated alkynes to thiol-terminated monolayers on a gold substrate to create similar LD-SAMs as what were prepared through solution-phase process. We characterized the resulting monolayers and compared them to analogous well-packed SAMs and the also low-density monolayers prepared through the solution phase approach. The results confirmed the proposed two-phase structure, with a well-packed phase head phase and a loosely-packed tail phase. In addition, the electrochemical studies, indicated that the resultant monolayers were less stable than the monolayers prepared via solution-phase, but they are yet significantly more stable than typical well-packed monolayers. The less stability of these monolayers were attributed to the partial desorption of adsorbates from the gold substrate due to UV irradiation during the grafting process. Building on the established chemistry, we studied the effect of lateral packing density of functional groups in a monolayer on the adsorption of Bovine serum albumin protein. we used surface plasmon resonance spectroscopy (SPR) and spectroscopic ellipsometry, to evaluate BSA adsorption on carboxylate‑, hydroxyl-, or alkyl- terminated LD-SAMs. It was found that for the LD-SAMs, the magnitude of protein adsorption is consistently higher than that of a pure component, well-packed SAM for all functionalities studied. In addition, it was seen that the magnitude of BSA adsorption the LD-SAMs, was consistently higher than that of a pure component, well-packed SAM for all functionalities studied. The difference of protein adsorption on LD-SAMs and SAMs can not be associated to difference in lateral packing density, unless we eliminate the impact of other contributing factors in protein adsorption such as surface energy. In order to better understand the impact of packing density on protein-surface interactions, we prepared the mixed SAMs of (carboxylate/alkyl) and (hydroxyl/alkyl) with matching surface energy as the carboxylate and hydroxyl terminated LD-SAMs. It was found that the energy-matched mixed SAMs of carboxylate and hydroxyl functionality adsorbed more protein than the LD-SAMs. However, an opposite trend was seen for the alkyl surfaces, where surface energies are comparable for LD-SAMs and pure component SAMs, indicating that BSA proteins have higher affinity for methyl- terminated LD-SAMs than well-packed SAMs.

The present study sought to compare the in vitro antioxidant potentials of a newly synthesized organodiselenide, dicholesteroyl diselenide (DCDS) and diphenyl diselenide (DPDS) and their possible interactions with some thiol containing enzymes in different tissues from mammalian system. In addition, the potency of DPDS as antioxidant and antihyperglycaemic agents, and its interaction with thiol containing proteins in various mammalian tissues and organs (hepatic, renal and spleenic and more importantly cerebral tissues) were evaluated in animal models of streptozotocin induced diabetic rats. The in vitro results show that DPDS exhibited a higher glutathione-peroxidase mimetic activity as well as increased ability to oxidize both mono- and di- thiols than DCDS. In addition, while DPDS inhibited thiobarbituric acid reactive substances (TBARS) and protein carbonyls formations in both cerebral and hepatic tissues, induced by either iron (II) or SNP, DCDS exhibited a prooxidant effect in both cerebral and hepatic tissues when iron (II) serves as the prooxidant, However, when TBARS was induced by SNP, DCDS slightly modify TBARS formation in both hepatic and cerebral tissues. Also the activities of cerebral and hepatic delata aminolevulinic acid dehydratase (ð-ALA-D), cerebral Na+/K+- ATPase were significantly inhibited by DPDS and only weakly inhibited by the DCDS. Further studies reveal that the inhibition caused by organodiselenides (in this case, DPDS) on Na+/K+-ATPase activity likely involves the modification of the thiol groups at the ATP binding site of the enzyme. Similarly, different isoforms of lactate dehydrogenase (LDH) were significantly inhibited by both DPDS and DCDS in vitro. Likewise, we observed that the in vitro inhibition of different isoforms of lactate dehydrogenase by DCDS and DPDS likely involves the modification of the -SH groups at the NAD+ binding site of the enzyme. Oral administration of DPDS dissolved in soya bean oil administered to streptozotocin induced diabetes in male albino rats shows that there was significant reduction in blood glucose levels accompanied by a marked reduction of glycated proteins in streptozotocin induced diabetic rats treated with DPDS in relation to untreated streptozotocin induced diabetic. In addition, DPDS was able to significantly ameliorate the levels of Vitamin C and GSH (liver, kidney and spleen), which were decreased in streptozotocin treated rats. Similarly, treatment with DPDS was able to markedly abolish the increase levels of TBARS that were observed in STZ diabetes group. Finally, the inhibition of both ð-ALA-D and some isoforms of LDH caused by hyperglycaemia were prevented by DPDS. We also observed that although streptozotocin evoke a significant diminution on brain s antioxidant status and activity of Na+/K+-ATPase, but the activity of acetylcholineesterase and glutamate uptake and release were not altered. However, DPDS was able to markedly restore the observed imbalance in antioxidant status and sodium pump. Finally, we conclude that organodiselenides are promising antioxidant remedy in the management of diseases caused by oxidative stress. However, their toxicity involves an interaction with thiols on proteins and this study has further demonstrated that the sulphydryl groups in question are critical to the normal function of the protein or enzymes. Most likely, these -SH are associated with thiols at the substrate binding (active site) sites of the enzymes. Interestingly, pharmacological doses of organodiselenides 3mg/kg bw for the study on diabetes do not present any observed toxicity.
O presente estudo quis comparar os potenciais antioxidants in vitro de organoselênios novamente sintetizados, diseleneto dicolesterol e diseleneto de difenila e suas possíveis interações com algumas enzimas contendo tióis em diferentes tecidos de mamíferos. Além disso, o potencial de DPDS como agente antioxidante e antihiperglicêmico, e sua interação com proteínas contendo tióis em vários tecidos e órgãos de mamíferos (hepático, renal, esplênico e, mais importante, tecido cerebral) foram avaliados em modelos animais de streptozotocina induzindo diabetes em ratos. Os resultados in vitro mostram que DPDS exibiu uma maior atividade mimética da glutationa peroxidase bem como aumentada habilidade para oxidar mono e di-tióis que DPDS. Além disso, enquanto o DPDS inibiu substâncias reativas ao ácido tiobarbitpúrico (TBARS) e formação de proteínas carboniladas em tecidos cerebral e hepático, induzidas por ferro(II) ou SNP, DCDS exibiu um efeito pró-oxidante em cérebro e tecido hepático quando ferro(II) serviu como próoxidante, porém, quando TBARS foi induzido por SNP, DCDS modificou a formação de TBARS tanto em tecido cerebral como hepático. Também, as atividades da deltaaminolevulinato desidratase (ð-ALA-D) cerebral e hepática e Na+/K+-ATPase cerebral foram significativamente inibidas por DPDS e somente fracamente inibida por DCDS. Mas estudos revelam que a inibição causada por organodiselenetos (neste caso, DPDS) na atividade da Na+/K+-ATPase envolve a modificação de grupos tiólicos ligados ao sítio ATP da enzima. Similarmente, diferentes isoformas da lactato desidrogenase (LDH) foram significativamente inibidas por DPDS e DCDS in vitro. nós observamos que a inibição in vitro de diferentes isoformas da LDH por DCDS e DPDS envolve a modificação de grupos SH no sítio ligante NAD+ da enzima. a administração oral de DPDS dissolvido em óleo soya administrado a ratos albino machos com diabetes induzida por streptozotocina mostrou que houve uma redução significante nos níveis de glicose sanguínea acompanhada por uma marcada redução nas proteínas glicadas em ratos diabéticos induzidos com streptozitocina tratados com DPDS em relação aos não diabéticos. Além disso, DPDS melhorou significativamente os níveis de vitamina C e GSH (fígado, rim e baço), que foram diminuídos em ratos tratados com streptozotocina. Similarmente, tratamento com DPDS marcadamente aboliu os níveis elevados de TBARS que foram observados no grupo diabético. Finalmente, a inibição da ð-ALA-D e algumas isoformas da LDH causada pela hiperglicemia foram prevenidas por DPDS. Nós também observamos que STZ provocou uma significante diminuição no status antioxidante do cérebro e atividade da Na+/K+- ATPase, mas a atividade da acetilcolinesterase e captação e liberação de glutamato não foram alteradas. Porém, DPDS marcadamente restaurou o desequilíbrio observado no status antioxidante e bomba de sódio. Finalmente, nós concluímos que organoselenetos são remédios antioxidantes promissores no manejo de doenças causadas por estresse oxidativo. Porém, sua toxicidade envolve uma interação com tióis em proteínas e este estudo demonstrou que os grupos sulfidril em questão são críticos para a função normal de enzimas e proteínas. Estes SH são associados com tióis dos sítios de ligação do substrato (sítio ativo) de enzimas. interessantemente, doses farmacológicas de organodiselenetos (3mg/kg para o estudo de diabetes) não apresentou nenhuma toxicidade observada.

A Esclerose Lateral Amiotrófica (ELA) é uma doença progressiva e fatal causada pela degeneração seletiva dos neurônios motores do cérebro e medula. Dos casos familiares de ELA (fELA), 20% são causados por mutações pontuais no gene da sod1. O ácido docosahexaenoico (C22:6, n-3, DHA) é um ácido graxo altamente insaturado, sendo um dos principais ácidos graxos da massa cinzenta do cérebro. Estudos têm correlacionado mutações de SOD1 com a formação de agregados que poderiam ser induzidos por ácidos graxos insaturados. O objetivo deste estudo foi avaliar os efeitos e mecanismos do DHA e de seus hidroperóxidos (DHAOOH) na agregação de SOD1 in vitro. As análises de dicroísmo circular (CD) mostraram mudanças na estrutura secundária de ambas as proteínas apo-SOD1WT e G93A promovidas pelo DHA, resultando em aumento de superfície hidrofóbica e formação de estruturas do tipo beta-amilóide, como mostrado pelos ensaios do bis- ANS e Tioflavina, respectivamente. Estas mudanças resultam na formação de agregados amorfos como observado por microscopia eletrônica de varredura (MEV). Espécies de alto peso molecular foram observadas nas incubações do DHA com as formas apo da SOD1 por SDS-PAGE sob condições não redutoras e também por cromatografia de exclusão por tamanho. A formação dos agregados mostrou-se dependente de resíduos de Cys na sua forma desprotonada, visto que agregados não foram observados na presença de beta-mercaptoetanol e sua formação foi inibida na presença de bloqueador de tióis e em pH ácido. Além disso, análises por cromatografia de exclusão mostraram que a agregação é dependente da insaturação e conformação cis dos ácidos graxos. Comparativamente ao DHA, os hidroperóxidos do DHA tiveram um efeito menor na agregação de SOD1, porém revelaram a propriedade de induzir a dimerização covalente de SOD1. No geral, os dados mostram que o DHA induz a agregação de SOD1, através de um processo envolvendo a exposição de superfícies hidrofóbicas, formação de pontes dissulfeto e também de possíveis cross-links envolvendo reações do tipo \"ene-tiol\".
ALS is a progressive and fatal disease caused by selective degeneration of motor neurons in the brain and spinal cord. Twenty percent of familial ALS (fALS) cases are caused mainly by point mutations in the sod1 gene. Docosahexaenoic acid (C22:6, n-3, DHA) is a highly unsaturated fatty acid, wich is one of the main fatty acids in the cerebral gray matter. Studies have linked SOD1 mutations to the formation of aggregates that could be induced by unsaturated fatty acids. The aim of this study was to evaluate the effect of DHA on aggregation of SOD1 fALS mutants in vitro and its mechanisms. CD analysis shows changes in the secondary structure of both apo-SOD1WT and G93A promoted by DHA resulting in an increase in the surface hydrophobicity and formation of structures such as beta amyloid, which was also confirmed by bis-ANS assay and Thioflavin, respectively. These changes enhance the interaction of SOD1 and DHA, leading to amorphous aggregates as revealed by FESEM. Incubation of DHA with apo-SOD1 forms results in high-molecular weight species as detected by SDS-PAGE analyses under non-reducing conditions and also by size exclusion chromatography. This appears to require Cys residues in their thiolate forms because high aggregates are not observed under reducing conditions and also by size exclusion chromatography or at acidic pH. Also, size-exclusion chromatography indicates that the mutant apo-SOD1 aggregation is dependent on the unsaturation and cis-conformation of fatty acids. Compared to the DHA, DHAOOH had a minor effect on SOD1 aggregation, however revealed the ability to induce covalent dimerization of SOD1. Overall, the data suggest a mechanism of DHA aggregation, by a process involving exposure to hydrophobic surfaces, formation of disulfide bonds and also for possible cross-links involving reactions such \"thiol-ene\".

CKD is diagnosed when there’s a decreased kidney function shown by a GFR less than 60 ml / min (established for a reference man with 1.73 m² body surface area), or markers of kidney damage, or both, of at least 3 months duration. The severity of complications increases in parallel with the GFR decline. We focused on three comorbidities extremely common in CKD patients: oxidative stress and inflammation; anemia and dysbiosis. We investigated these CKD comorbidities both with in vitro and in vivo approaches. More in detail, regarding in vivo studies, we measured oxidative stress biomarkers in a population of ESRD patients before and after the hemodialysis treatment, comparing the results with a population of healthy subjects; we evaluated oxidative stress biomarkers in the plasma of HD patients before, during and after two type of iron treatments (intravenous and sucrosomial iron). Regarding in vitro experiments, we focused on two uremic toxins, urea and indoxyl sulphate, and we evaluated their effects on a human endothelial cell line (Human Microvascular Endothelial Cells 1, HMEC-1).

The focus of this thesis is to investigate the interactions of mitochondrial protein thiols with ROS and examine the oxidation of these thiols in response to oxidative stress. Among these protein thiol modifications, an area of great interest is the interactions of mitochondrial protein thiols with glutathione, therefore possible connections between the modifications and cell death were investigated. I explored the possibility that staurosporine (STS) induces apoptosis via the mitochondrial pathway, causing early changes in the mitochondrial membrane potential (Δψ), by changing the thiol redox status of the cell. The hypothesis tested was that there may be a common link between oxidative stress and thiol changes of mitochondrial proteins and oxidation of the cellular glutathione pool which then initiates the critical mitochondrial events that lead to apoptosis. STS caused apoptosis after 2-4 hours of treatment and caused a decrease in total glutathione measured in cells, with the depletion of cellular glutathione occurring after the induction of apoptosis. There were no changes in glutathione (GSH)/glutathione disulphide (GSSG) redox state up to one hour of STS treatment, and thus no association of cellular GSH oxidation with the early mitochondrial Δψ changes observed. However, the GSH pool was significantly oxidised after 2 hours. Even so, no significant changes in protein glutathionylation by STS were observed at 2 hours. I next explored the possibility that protein thiol modifications might respond to oxidative stress for the purpose of redox signalling, whereby redox-sensitive modifications might contribute to biological regulation. Therefore, I went on to quantify total and exposed protein thiols in subcellular fractions including mitochondria. This analysis showed that 74% of total liver cell lysate protein thiols are exposed compared to 57% of mitochondrial proteins, 67% of cytosolic proteins and 62% of soluble proteins. The amount of exposed thiols as a percentage of total thiols in each of the four fractions did not differ when comparing rat liver and rat heart tissue. I then further characterised the distribution of protein thiols in the mitochondria and found that approximately two-thirds of protein thiols present in the mitochondrial membrane fraction were exposed compared to 78% in the mitochondrial matrix fraction. In addition, by using two membrane-impermeant thiol-alkylating agents, I was able to show that approximately a third of all the exposed protein thiols in the mitochondrial membrane fraction were either on the outer membrane, facing outward into the cytosol or facing inward into the intermembrane space, within the intermembrane space itself or on the outer leaflet of the inner membrane. The possibility that protein thiols might have a protective role acting as a redox buffer was also explored, and loss of exposed protein thiols during oxidative stress was investigated.

O hidroperóxido de urato (HOOU) é o produto da oxidação do ácido úrico por peroxidases. Sua produção é favorecida durante a inflamação e hiperuricemia, uma vez que há grande quantidade de ácido úrico, peroxidases inflamatórias e superóxido. Neste sentido, o objetivo deste estudo foi avaliar o efeito do hidroperóxido de urato sobre proteínas sensíveis à modulação redox em um ambiente inflamatório asséptico e outro que imita infecção. Assim, nesta tese comparou-se a estrutura química do HOOU obtido fotoquimicamente daquele obtido através da catálise enzimática pela mieloperoxidase. A obtenção do HOOU por foto-oxidação permitiu o melhor isolamento do composto. Este oxidante foi capaz de reagir especificamente com os aminoácidos contendo enxofre (metionina e cisteína). Neste sentido, foi investigada sua reatividade com tiol-peroxidases detoxificadoras de peróxido, a peroxiredoxina 1 e 2 (Prx1 e Prx2). O HOOU apresentou cinética rápida de reação com a Prx1, k = 4,9 × 105 M-1s-1 e Prx2, k = 2,3 × 106 M-1s-1, o que as torna um provável alvo celular, além disso, foi capaz de oxidar a Prx2 de eritrócitos humanos, mostrando ser capaz de atravessar a membrana plasmática. Além das Prxs, a albumina do soro também desempenha papel importante na homeostase redox. O HOOU foi capaz de oxidar a albumina com constante de velocidade de 0,2 × 102 M-1s- 1. Outra tiol-proteína com importante função na homeostase e sinalização redox é a tioredoxina (Trx). A Trx foi oxidada pelo HOOU com constante de reação de 2,8 × 102 M-1s-1 e foi liberada juntamente com a Prx1 e Prx2 das células de macrófagos humanos (linhagem THP-1) quando estas células foram incubadas com HOOU. A liberação dessas proteínas é reconhecidamente um sinal de estresse celular. Assim o HOOU pode estar envolvido na exacerbação do estresse oxidativo em ambiente inflamatório. Quando neutrófilos (linhagem HL- 60) e macrófagos humanos (linhagem THP-1) foram incubados na presença de ácido úrico e Pseudomonas aeruginosa houve uma diminuição na produção de ácido hipocloroso (HOCl). Isto se deveu à competição entre ácido úrico e cloreto pela mieloperoxidase e resultou em menor atividade microbicida pelas células, demonstrando que a formação do HOOU não contribui e, ao contrário, prejudica a atividade microbicida das células inflamatórias. Dessa forma, a oxidação do ácido úrico e formação do hidroperóxido de urato tanto altera a atividade microbicida das células inflamtárias, quanto leva à oxidação de tiósproteínas importantes para manutenção da homeostase redox. Assim, o HOOU pode ser o responsável pelos efeitos pró-oxidantes e pró-inflamatórios do ácido úrico solúvel, e isso indica que o papel antioxidante do ácido úrico deve ser revisto em situações de inflamação.
Urate hydroperoxide (HOOU) is the product of the oxidation of uric acid by peroxidases. The formation of HOOU is favored during inflammation and in hyperuricemia, where there is plenty amount of uric acid, inflammatory peroxidases and superoxide. Therefore, the aim of the present study was to evaluate the effect of urate hydroperoxide on redox sensitive proteins in an inflammatory environment and another that mimics infection. In this thesis the chemical structure of the HOOU produced by photo-oxidation was compared to that obtained by myeloperoxidase catalysis. The chemical production of HOOU allowed a better purification of the compound. This oxidant was able to specifically react with sulfur containing amino acids (methionine and cysteine). In this sense, its reactivity with peroxiredoxins (Prx1 and Prx2) was investigated. HOOU reacted fast with Prx1 k = 4.9 × 105 M-1s-1 and Prx2 k = 2.3 × 106 M-1s-1. In addition, HOOU was able to oxidize Prx2 from intact erythrocytes at the same extend as does hydrogen peroxide. Albumin is an important thiol-containing protein to redox homeostasis in plasma. HOOU was able to oxidize albumin with a rate constant of 0.2 × 102 M-1s-1. Another protein with important function in redox homeostasis is thioredoxin (Trx). Trx was oxidized by HOOU with a rate constant of 2.8 × 102 M-1s-1 and was released together with Prx1 and Prx2 from human macrophages cells (THP-1 cell line) that were incubated with HOOU. The release of these proteins is a signal of cellular stress. Thus, HOOU may be involved in the exacerbation of oxidative stress in inflammatory environments. When neutrophil (HL-60 cell line) and macrophages (THP-1 cell line) were incubated with uric acid and Pseudomonas aeruginosa there was a decrease in hypochlorous acid (HOCl) production because of the competition between chloride and uric acid by myeloperoxidase. It decreased HOCl and impaired the microbicidal activity of the cells, showing that HOOU does not contribute in bacteria clearance. Therefore, the oxidation of uric acid to urate hydroperoxide impairs microbicidal activity and oxidizes thiol-proteins in inflammatory cells contributing to a pro-oxidant status. In this context, the antioxidant role of uric acid in inflammatory response should be reviwed.

Most pharmaceutically relevant proteins and many extracellular proteins contain disulfide bonds. Formation of the correct disulfide bonds is essential for stability in almost all cases. Disulfide containing proteins can be rapidly and inexpensively overexpressed in bacteria. However, the overexpressed proteins usually form aggregates inside the bacteria, called inclusion bodies, which contains inactive and non-native protein. To obtain native protein, inclusion bodies need to be isolated and resolubilized, and then the resulting protein refolded in vitro. In vitro protein folding is aided by the addition of a redox buffer, which is composed of a small molecule disulfide and/or a small molecule thiol. The most commonly used redox buffer contains reduced and oxidized glutathione. Recently, aliphatic dithiols and aromatic monothiols have been employed as redox buffers. Aliphatic dithiols improved the yield of native protein as compared to the aliphatic thiol, glutathione. Dithiols mimic the in vivo protein folding catalyst, protein disulfide isomerase, which has two thiols per active site. Furthermore, aromatic monothiols increased the folding rate and yield of lysozyme and RNase A relative to glutathione. By combining the beneficial properties of aliphatic dithiols and aromatic monothiols, aromatic dithiols were designed and were expected to increase in vitro protein folding rates and yields. Aromatic monothiols (1-4) and their corresponding disulfides (5-8), two series of ortho- and para-substituted ethylene glycol dithiols (9-15), and a series of aromatic quaternary ammonium salt dithiols (16-17) were synthesized on a multigram scale. Monothiols and disulfides (1-8) were utilized to fold lysozyme and bovine pancreatic trypsin inhibitor. Dithiols (11-17) were tested for their ability to fold lysozyme. At pH 7.0 and pH 8.0, and high protein concentration (1 mg/mL), aromatic dithiols (16, 17) and a monothiol (3) significantly enhanced the in vitro folding rate and yield of lysozyme relative to the aliphatic thiol, glutathione. Additionally, aromatic dithiols (16, 17) significantly enhance the folding yield as compared to the corresponding aromatic monothiol (3). Thus, the folding rate and yield enhancements achieved in in vitro protein folding at high protein concentration will decrease the volume of renaturation solution required for large scale processes and consequently reduce processing time and cost.

京都大学
0048
新制・課程博士
博士(農学)
甲第20008号
農博第2192号
新制||農||1045(附属図書館)
学位論文||H28||N5017(農学部図書室)
33104
京都大学大学院農学研究科農学専攻
(主査)教授 裏出 令子, 教授 松村 康生, 教授 三上 文三
学位規則第4条第1項該当
Doctor of Agricultural Science
Kyoto University
DFAM

Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第20008号
農博第2192号
新制||農||1045(附属図書館)
学位論文||H28||N5017(農学部図書室)
33104
京都大学大学院農学研究科農学専攻
(主査)教授 裏出 令子, 教授 松村 康生, 教授 三上 文三
学位規則第4条第1項該当

Thrombospondin 1 (TSP1) is a 450 kDa homotrimeric multidomain glycoprotein with fundamental roles in many cell-cell and cell-matrix interactions. These varied, and sometimes conflicting, functions are mediated by specific domains in TSP1. One region with diverse biological roles is the Ca2+ binding loops (or type 3 repeats). The biological activity of this region is determined through a complex assembly of disulfide bonds linking structure and function. Disulfide interchange in a protein is usually very specific and quite slow, unless catalysed. I have found that protein disulfide isomerase (PDI) is expressed on the surface of platelets and endothelial cells in a reduced active conformation. The presence of enzymatically active PDI on the surface of TSP1-secreting cells suggests PDI is well positioned to catalyse disulfide interchange in, and regulate the structure/function relationships of, TSP1. PDI was observed to form disulfide-linked complexes with TSP1. Moreover, incubation of platelet or fibroblast TSP1 with PDI enhanced binding of an isomer-specific anti-TSP1 antibody whose epitope is in the Ca2+ binding loops. These findings suggest that PDI may mediate disulfide bond rearrangement in both the soluble and extracellular matrix-bound forms of TSP1. TSP1 is a tight-binding competitive inhibitor of neutrophil cathepsin G; however, incubation with PDI increased the Ki for the interaction ???10-14-fold. TSP1 bound platelet-derived growth factor (PDGF) tightly in the region of the Ca2+ binding loops and supported binding of PDGF to its receptor. PDI-mediated disulfide interchange in TSP1 ablated PDGF binding, indicating that PDI-catalysed disulfide interchange in TSP1 may modulate PDGF-TSP1 complex formation and the biological activity of PDGF. Finally, PDI-catalysed isomerization of TSP1 potently affected its cell adhesive properties. Treatment of TSP1 with PDI enhanced adhesion and spreading of endothelial cells through the ??v??3 integrin receptor to TSP1, by exposure of a cryptic RGD sequence. Thus, endothelial cell surface PDI may be a physiological regulator of RGD-dependent binding to TSP1. These data suggest that cell-surface PDI may regulate the disulfide-bonded structure and certain biological functions of TSP1. In conclusion, I propose a novel mechanism for the post-translational regulation of TSP1 structure/function, which in turn may regulate certain aspects of TSP1 in vascular biology.

Thesis (Ph. D.)--Ohio State University, 2003.
Title from first page of PDF file. Document formatted into pages; contains xxiii, 325 p.; also contains graphics (some col.). Includes abstract and vita. Advisor: Gary E. Means, Dept. of Biochemistry. Includes bibliographical references (p. 206-225).

Thesis (Ph. D.)--University of Oregon, 2005.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 75-82). Also available for download via the World Wide Web; free to University of Oregon users.

This work investigates the reactions of proteins with ROS when mitochondria are exposed to H₂O₂ or when they generate ROS endogenously. Using isolated mitochondria, those proteins that are particularly sensitive to low concentrations of H₂O₂ and to ROS generated by the mitochondrial electron transport chain were first identified using a method called Redox-Difference Gel Electrophoresis (Redox-DIGE). Most redox sensitive thiol proteins identified by Redox-DIGE were involved either in fatty acid oxidation or in the regulation of the pyruvate dehydrogenase complex. Next the mechanisms by which ROS selectively oxidise mitochondrial thiol proteins were investigated; it was determined that H₂O₂ generated by the electron transport chain may either oxidise mitochondrial thiol proteins directly or indirectly, through oxidation of the peroxiredoxin and thioredoxin redox couples. To determine if ROS generated by mitochondria might act as a redox signal by altering the functions of mitochondrial proteins, the effect of protein thiol oxidation was tested on the activity of two proteins: pyruvate dehydrogenase kinase and propionyl-CoA carboxylase. Loss of pyruvate dehydrogenase kinase and propionyl-CoA carboxylase activity correlated with protein thiol oxidation and was very sensitive to ROS, suggesting a plausible mechanism of redox regulation of these proteins in vivo. Lastly, glutathionylation of complex I was investigated in intact mitochondria exposed to a glutathione oxidant; two cysteine residues on the 75 kDa subunit of complex I were shown to become glutathionylated. The functional effect of glutathionylation of these two cysteine residues on complex I activity is currently under investigation.

2-Cys Prx compõem um grupo de enzimas antioxidantes homodiméricas que atuam na decomposição de hidroperóxidos utilizando uma cisteína reativa (cisteína peroxidásica - CysP). A alta reatividade da CysP é alcançada com o envolvimento de dois aminoácidos vicinais à CysP: uma treonina e uma arginina, que constituem a tríade catalítica. Após a decomposição do hidroperóxido, a CysP forma um dissulfeto intermolecular com um segundo resíduo de cisteína (cisteína de resolução - CysR), o qual é reduzido pela tiorredoxina (Trx). Durante o ciclo redox, estas enzimas sofrem alterações estruturais, mas os mecanismos envolvidos neste processo eram pouco compreendidos. Neste trabalho foi obtida a estrutura cristalográfica de Tsa1 de Saccharomyces cerevisiae, uma 2-Cys Prx. Através de abordagens envolvendo bioquímica e biologia molecular, foi verificada a importância de aminoácidos envolvidos na reatividade e em transições da estrutura terciária e quaternária. Por fim, foram realizados esforços para a determinação da estrutura cristalográfica de mutantes obtidos neste trabalho.
2-Cys Prx constitute a group of homodimeric antioxidant enzymes that act in the decomposition of hydroperoxides using a reactive cysteine (peroxidase cysteine - CysP). The high reactivity of the CysP is achieved by the participation of two vicinal amino acids: a threonine and an arginine, which constitute the catalytic triad. After the decomposition of hydroperoxide, the CysP forms an intermolecular disulfide with a second cysteine residue (resolving cysteine - CysR), which is reduced by the thioredoxin (Trx). During the redox cycle, these enzymes undergo to changes in the structure, but the molecular mechanisms involved in this process were poorly understood. In this study we have obtained the crystallographic structure of the 2-Cys Prx enzyme Tsa1 from Saccharomyces cerevisiae. By means of biochemical and molecular biology approaches, the importance of amino acids involved in reactivity and structural transitions were determined. Finally, efforts have been performed to the determination of the crystallographic structures of mutant proteins obtained in this study.

Proteína dissulfeto isomerase (PDI) é uma ditiol-dissulfeto óxido redutase ubíqua que é responsável por uma série de funções celulares, inclusive na sinalização celular e nas respostas a eventos que causam dano celular. Entretanto, a PDI pode se tornar disfuncional através das modificações pós-traducionais, incluindo as promovidas por oxidantes biológicos. Estes oxidantes são provavelmente os responsáveis pelas modificações oxidativas pós-traducionais da PDI que foram detectadas em várias condições associadas ao estresse oxidativo, levando à disfunção da proteína. Devido a falta de estudos cinéticos com a PDI nativa e a falta de caracterização dos produtos dessas reações, investigamos se a diminuição da fluorescência da PDI nativa pode ser empregada para estudos da cinética de oxidação com peróxido de hidrogênio. Posteriormente, investigamos a cinética e os produtos da reação entre PDI e peroxinitrito. Nossos experimentos mostraram que a oxidação por excesso de peróxido de hidrogênio levava a uma diminuição da fluorescência de forma dependente do tempo e da concentração do oxidante, permitindo a determinação da constante de velocidade de segunda ordem (k = (17,3±1,3) M-1 s-1, pH 7,4, 25 ºC). Relevantemente, mostramos que o processo era totalmente revertido por DDT, mostrando que o peróxido de hidrogênio oxida quase que exclusivamente os grupos ditióis da PDI (Cys53 e Cys56 e Cys397 e Cys400). Utilizando a mesma abordagem para estudar a oxidação da PDI por peroxinitrito, notamos que o decréscimo da fluorescência intrínseca da PDI nativa e a velocidade só era proporcional à concentrações sub-estequiométricas ou estequiométricas do oxidante em relação aos tióis reativos da PDI. Somente nessas condições o processo se mostrava reversível por DDT, indicando que os ditióis da PDI eram o alvo preferencial do peroxinitrito mas que a oxidação de outros resíduos também ocorria. A reação dos tióis reativos da PDI com peroxinitrito foi considerada relativamente rápida (6,9 ± 0,6 × 104 M-1 s-1, pH 7,4, 25 °C), e os resíduos de Cys reativos dos domínios a e a\' aparentam reagir com constantes de velocidade similares. Experimentos de proteólise limitada, simulações cinética e análises de MS e MS/MS confirmaram que o peroxinitrito oxida preferencialmente os tióis redox ativos da PDI para os ácidos sulfênicos correspondentes, que, subsequentemente, reagem com os tióis vizinhos, produzindo dissulfetos (Cys53- Cys56 e Cys397- Cys400). Entretanto, uma fração de peroxinitrito decai para radicais levando à hidroxilação e nitração de outros resíduos próximos ao sítio redox ativo (Trp52 Trp396 e Tyr393). Assim, investigamos também a oxidação da PDI por excesso de peroxinitrito em relação aos grupos tióis reativos por diferentes metodologias. Experimentos de SDS-PAGE, western-blot e atividade redutase mostraram que o peroxinitrito promove inativação, nitração e agregação da PDI de forma dependente da concentração de peroxinitrito. Análises de MS e MS/MS mostraram que, em excesso, o peroxinitrito promove nitração (Tyr43, Tyr49, Tyr196, Tyr393, Trp52, Trp396) e hidroxilação (Trp52, Trp396) da PDI. Em síntese, nossos estudos contribuem para melhor compreensão da oxidação da PDI por peroxinitrito e de suas possíveis consequências biológicas.
Protein disulfide isomerase (PDI) is a ubiquitous dithiol-disulfide oxidoreductase that performs an array of cellular functions, including in cellular signaling and responses to cell-damaging events. Nevertheless, PDI can become dysfunctional by post-translational modifications, including those promoted by biological oxidants. These oxidants are likely responsible for the oxidative post-translational modifications of PDI, which have detected under various conditions associated with oxidative stress, leading to protein dysfunction. However, the kinetics of the reactions of PDI with biological oxidants received limited studies and the products of these reactions were not characterized. Here, we examined whether the decrease in PDI fluorescence can be employed to follow the kinetics of the reaction of the full-length protein with biological oxidants. Also, we investigated the kinetics and products of the reaction between PDI and peroxynitrite. Our experiments showed that oxidation by excess hydrogen peroxide led to a decrease of PDI intrinsic fluorescence in a time- and concentration-dependent manner , permitting the determination of the second-order rate constant of the reaction (k = (17.3 ± 1.3 ) M1 s-1, pH 7.4, 25 ° C). The oxidation was reversed by DDT, indicating that hydrogen peroxide oxidizes mainly PDI dithiols (Cys53 and Cys56 and Cys397 and Cys400). Using the same approach to study PDI oxidation by peroxynitrite we noted that the decrease of the native PDI fluorescence was proportional to sub-stoichiometric or stoichiometric concentrations of the oxidant relative to that of PDI reactive thiols. Only under these conditions, PDI oxidation was reversed by DDT, indicating that PDI dithiols were the preferred target of peroxynitrite but that oxidation of other residues also occurred. The reaction of the active redox thiols of the PDI with peroxynitrite can be considered relatively fast (6.9 ± 0.6 × 104 M-1 s-1, pH 7.4, 25 ° C), and the reactive Cys residues of domains a and a\' were kinetically indistinguishable. Limited proteolysis experiments, kinetic simulations, and MS and MS/MS analyses confirmed that peroxynitrite preferentially oxidizes the redox-active Cys residues of PDI to the corresponding sulfenic acids, which subsequently react with the resolving thiols to produce disulfides (Cys53-Cys56 and Cys397-Cys400). However, a fraction of peroxynitrite decays to radicals leading to hydroxylation and nitration to other residues located close to the active site (Trp52 Trp396 and Tyr393). SDS-PAGE, western blotting and inhibition of the reductase activity experiments confirmed that excess peroxynitrite promotes further PDI oxidation, nitration, inactivation and aggregation in a concentration-dependent manner. MS and MS/MS analyzes showed that peroxynitrite in a ten times excess relative to PDI reactive thiols promote PDI nitration (Tyr43, Tyr49, Tyr196, Tyr393, Trp52, Trp396) and hydroxylation (Trp52, Trp396). In conclusion, our studies contribute to a better understanding of PDI oxidation by peroxynitrite and its possible biological consequences

L'oxydation des résidus cystéines est une modification biochimique très répandue survenant dans tous les compartiments des cellules eucaryotes. Ce phénomène sert le repliement oxydatif des protéines dans le réticulum endoplasmique (RE), l'importation de protéines dans l'espace intermembranaire de la mitochondrie (IMS). De plus, il a un rôle régulateur dans la matrice mitochondriale et dans le cytosol où il contrôle l’activité des enzymes et des protéines de signalisation et de régulation. Dans tous ces procédés, la réversibilité de l'oxydation des résidus Cys est une caractéristique essentielle. Deux systèmes oxydoréductase puissants existent : les voies de glutathion (GSH) et la thiorédoxine ; ils catalysent la réduction des ponts disulfure, et contrôlent la plupart des processus cellulaires thiol-redox dépendant. Cependant, en dépit d'énormes connaissances portant sur leur enzymologie, peu est connu sur les caractéristiques physiologiques de ces systèmes chez les eucaryotes. Pour déterminer l'importance physiologique de ces systèmes et indiquer lequel est à la base de l'exigence du GSH pour la viabilité, nous avons effectué une analyse complète des cellules de levure épuisée ou contenant des niveaux toxiques de GSH. Les deux conditions déclenchent une réponse « iron-starvation-like » et une altération de l'activité des enzymes d’assemblage des centres fer-soufre (Iron sulfure cluster : ISC) extra-mitochondriales. Cependant, elles n’ont pas d'impact sur l’entretien thiol redox, à l’exception des niveaux élevés de glutathion qui ont altéré le repliement oxydatif des protéines dans le reticulum endoplasmique. Alors que le fer sauve partiellement la maturation des ISC et les défauts de croissance des cellules appauvries eh GSH, des expériences génétiques ont indiqué que, contrairement à la thiorédoxine, le glutathion ne peut pas assurer par lui-même les fonctions thiol-redox de la cellule. Nous proposons que le glutathion soit essentiel par son exigence dans l’assemblage des centres fer-soufre, mais ne serve comme backup que pour maintenir l’état thiol-redox de la cellule. Des niveaux physiologiques élevés de GSH sont ainsi destinés à isoler sa fonction dans le métabolisme du fer des variations de sa concentration pendant le stress redox, ce qui constitue un modèle contestant la vision traditionnelle du GSH comme acteur primordial du contrôle thiol-redox cytosolique.Nos données préliminaires sur la distribution de GSH dans les cellules recueillies par lasurveillance de l'état redox de rxYFP ciblée pour différents compartiments cellulaires (RE,Matrice, cytosol et IMS) dans les cellules HGT1 indiquent un transport spécifique du GSH vers le RE et l'exportation de GSSG de ce compartiment. Nous avons pu caractériser deuxtransporteurs ABC dont la suppression modifie le RE plus oxydant et entraîne une accumulation de GSSG par rapport aux cellules sauvages. Ces données ont été confirmées par le suivi de l'état redox de PDI1 et ERO1 (WT et hyper active). Elles suggèrent un rôle de ces transporteurs dans l'exportation du GSSG du la RE, et que le flux de GSH entre les différents compartiments est très régulé
Cys residue oxidation is a widespread biochemical modification occurring in all eukaryotic cells compartments. It serves oxidative protein folding in the endoplasmic reticulum (ER), protein import in the intermembrane space of mitochondria (IMS), and it has a regulatory role in the mitochondrial matrix and in the cytosol where it controls enzymes and signaling regulatory proteins activity. In all these processes, reversibility of Cys residue oxidation is a crucial feature. Two potent oxidoreductase systems, the glutathione (GSH) and thioredoxin pathways, catalyze disulfide bond reduction, and presumably control most thiol-redox-dependent cellular processes. However, despite tremendous knowledge of their enzymology, little is known about the physiological features of these systems in eukaryotes. To determine the physiologic importance of these functions and sort out which of them accounts for the GSH requirement for viability, we performed a comprehensive analysis of yeast cells depleted of or containing toxic levels of GSH. Both conditions triggered an intense iron-starvation-like response and impaired the activity of extra-mitochondrial ISC enzymes, but did not impact thiol-redox maintenance, except high glutathione levels that altered oxidative protein folding in the endoplasmic reticulum. While iron partially rescued the ISC maturation and growth defects of GSH-depleted cells, genetic experiments indicated that unlike thioredoxin, glutathione could not support by itself the thiolredox duties of the cell. We propose that glutathione is essential by its requirement in ISC assembly but only serves as a thioredoxin back up in cytosolic thiol-redox maintenance. Glutathione high physiologic levels are thus meant to insulate its function in iron metabolism from variations of its concentration during redox stresses, a model challenging the traditional view of it as prime actor in cytosolic thiol-redox control.Our preliminary data on the distribution of GSH inside cells collected by monitoring the redox state of rxYFP targeted to different cell compartments (ER, Matrix, Cytosol and IMS) in HGT1 cells indicate a specific transport of GSH into the ER and export of GSSG out of it. We were able to characterize two ABC transporters on which their deletion modify the redox state of the ER to more oxidizing and result in accumulation of higher GSSG content compared to WT. These data were confirmed by looking to the redox state of the PDI1 and ERO1 (WT and hyper active), all together suggest a role of these transporters in GSSG export from the ER, and that GSH flux between the different compartments is highly regulated

This thesis concerns the development of surface ligation techniques for the preparation of carbohydrate biosensors. Several methodologies were developed based on efficient photochemical insertion reactions which quickly functionalize polymeric materials, with either carbohydrates or functional groups such as alkynes or alkenes. The alkyne/alkene surfaces were then treated with carbohydrate azides or thiols and reacted under chemoselective Cu-catalyzed azide-alkyne cycloaddition (CuAAC) or photo-radical thiol-ene/yne click chemistry, thus creating a range of carbohydrate biosensor surfaces under ambient conditions. The methodologies were evaluated by quartz crystal microbalance (QCM) and surface plasmon resonance (SPR) flow through instrumentations with recurring injections of a range of lectins, allowing for real-time analysis of the surface interactions. The developed methods were proven robust and versatile, and the generated carbohydrate biosensors showed high specificities and good capacities for lectin binding.  The methods were then used to investigate how varying the glycan linker length and/or a sulfur-linkage affect the subsequent protein binding. The survey was further explored by investigating the impact of sulfur in glycosidic linkages on protein binding, through competition assays with various O/S-linked disaccharides in solution interactions with lectins.
QC 20120309

A Xylella fastidiosa é uma bactéria gram-negativa, colonizadora do xilema e é o agente responsável por doenças em plantas cultivadas. No Brasil, a principal doença causada por esta bactéria é a CVC (Clorose Variegada dos Citros), a qual traz grandes prejuízos à produção de laranja dos estados de São Paulo e Minas Gerais. Apesar do atual controle da doença, ainda não se desenvolveu um método específico para o controle da bactéria. Durante a interação planta-patógeno ocorre uma geração exacerbada de oxidantes por parte do hospedeiro, na tentativa de eliminar o patógeno de seu organismo. Dessa forma, os patógenos são expostos a hidroperóxidos derivados de ácidos graxos, formados a partir da ação de lipoxigenases ou ainda pela reação direta de lipídeos com espécies oxidantes. Durante o processo evolutivo, foram selecionados mecanismos de defesa contra estas espécies oxidantes por parte dos patógenos. Dentre estes mecanismos, encontra-se a enzima Ohr (Organic Hydroperoxide Resistance protein), uma peroxidase baseada em resíduos de cisteínas, dependente de grupos lipoil e que possui alta atividade frente à hidroperóxidos orgânicos. Esta proteína provavelmente atua na proteção da célula bacteriana e possui algumas particularidades que fazem dela um alvo em potencial para o desenvolvimento de drogas. Os objetivos deste projeto foram caracterizar possíveis substratos fisiológicos de Ohr de X. fastidiosa, e ainda, buscar moléculas capazes de inibir a atividade peroxidásica desta enzima. Inicialmente demonstramos que Ohr é capaz de reduzir hidroperóxidos de ácido graxo com alta eficiência (kcat/KM ~ 106 M-1.s-1)e, além disso, estes hidroperóxidos são capazes de inativar Ohr em um processo dose dependente, provavelmente devido à alta afinidade entre estes e a enzima. Porém, a enzima não apresentou atividade frente à hidroperóxido de fosfolipídeo (fosfatidilcolina) e hidroperóxido de colesterol. Ademais, elucidamos a estrutura de Ohr na conformação oxidada (ponte dissulfeto), auxiliando no entendimento da dinâmica do ciclo catalítico da enzima. Por fim, selecionamos um composto capaz de inibir a atividade peroxidásica de Ohr in vitro, e temos indícios de que este é capaz de afetar o crescimento bacteriano em situação de estresse oxidativo.
Xylella fastidiosa is a gram-negative bacterium that colonizes the xylem and is the causative agent for several plant diseases. In Brazil, the main disease caused by this bacterium is the CVC (Citrus Variegated Chlorosis), which provokes large losses to the orange production in São Paulo and Minas Gerais states. Despite the current disease control, it has not been yet developed a specific method to eliminate the bacterium. During the plant-pathogen interactions, hosts produce an exacerbated amount of oxidants, in an attempt to eliminate the pathogen. Among them, fatty acids hydroperoxides are formed by the lipoxygenase action or even by the direct reaction between lipids and oxidant species. During the evolutionary process, pathogen defense mechanisms against oxidative species have evolved. Among them, Ohr (Organic Hydroperoxide Resistance protein) that is a Cys-based, lipoyl dependent peroxidase, displaying high activity towards organic hydroperoxides. This protein probably plays a central role in oxidative stress response and presnts some particularities, which make it a potential target for drug design. The objectives of this project were to characterize possible physiological substrates of Ohr from X. fastidiosa and search for molecules capable of inhibiting its peroxidase activity. Initially, we demonstrated that Ohr reduced fatty acid hydroperoxides with high efficiency (kcat/KM ~ 106 M-1.s-1). Moreover, these hydroperoxides inactivated Ohr in a dose-dependent manner, probably due to the high affinity between them and the enzyme. However, the enzyme did not display any activity towards phospholipids (posphatidilcholine) hydroperoxides and cholesterol hydroperoxide. Besides, we elucidated the structure of Ohr in the oxidized form (disulfide bond), which gave us insights on the dynamics of structural elements in the catalytic site. Ultimately, we identified a compound that was able to inhibit the peroxidase activity of Ohr in vitro, and we gained evidences that this compound can affect the bacterial growth under oxidative stress.

Almost all therapeutic proteins contain disulfide bonds to stabilize their native structure. Recombinant DNA technology enables many therapeutic proteins to be produced in bacteria, but the expression of native proteins is not always efficient due to the limited ability of bacteria to form disulfide bonds in vivo. It is often necessary to employ in vitro oxidative folding process to form the native disulfide bonds to obtain the native structure of disulfide-containing proteins. Aromatic disulfides are small molecules designed to match some of the physical properties of the active site of protein disulfide isomerase (PDI), which catalyzes the folding process of disulfide-containing proteins in eukaryotes. Three aromatic thiols with varying charges, PA, SA and QAS thiol, were used to fold reduced BPTI in vitro. Bovine pancreatic trypsin inhibitor (BPTI) is positively charged (pI = 10.5) at pH 7.3, and we hypothesized that mixed disulfide intermediates formed between BPTI and negatively charged small molecule thiols were more likely to precipitate due to their minimized net charge. Protein precipitation was observed during folding with negatively charged thiols, PA and SA, but not positively charged thiol QAS. At the folding pH of 7.3, almost 90% of native BPTI was produced in 2 h with the conditions of 0.25 mM QAS disulfide and 10 mM QAS thiol. Only 25% of native BPTI was produced in 2 h with the best conditions for glutathione and glutathione disulfide. Aromatic thiols with an elongated alkyl group on the aromatic ring, butyl, hexyl and octyl thiol, were hypothesized to increased interactions with the hydrophobic core of disulfide-containing proteins during folding, allowing more facile access to buried disulfide bonds. However, the longer the hydrocarbon chain, the more likely protein precipitation was to occur. About 90% native BPTI was formed in 1 h with 0.25 mM hexyl disulfide and 10 mM hexyl thiol. A method using capillary electrophoresis (CE) to analysis the oxidative folding process of reduced BPTI with small molecule thiols and disulfides was also developed. Folding of reduced BPTI with QAS disulfide was analyzed using CE in a shorter run time. The consumption of protein samples and solvent solutions was minimized.

A key component of the host’s ability to survive bacterial challenge consist in the innate ability of macrophages to ingest and destroy the invading organism via various mechanisms which the most thoroughly studied is oxidative burst (Hanna et al., 1994). In response pathogens have evolved different approaches to survive the severe oxidative stress generated by the host. Genome analysis have clustered more than 14000 sequences coding for putative rhodanese like proteins. These sequences contain domains structurally similar to those of the extensively studied bovine rhodanese, and were found in more than 2100 species homogeneously distributed in all life's phyla. Proteins belonging to the rhodanese like superfamily (PFAM accession number: PF00581) are characterized by having more than 140 different architectures of the rhodanese domain, that can be present mostly alone or in tandem with another rhodanese domain, or fused to other functional domains. Although only few amino acid residues are conserved among rhodanese-like proteins, their most distinctive structural feature is the active site configuration, that contains an electronegative residue (generally cysteine) surrounded by positively charged residues. This particular architecture allows rhodanese-like proteins to bear a low pKa catalytic residue that can be the clue to explain their biological activity (Bordo et al 2001). Although the in vitro reported sulfurtransferase activity for the few characterized rhodanese-like proteins is the transfer of sulfur atom from a sulfur donor (e.g. thiosulfate) to a thiophilic acceptor (e.g. cyanide) (E.C. 2.8.1.x), in the last two decades the scientific community has started to indicate biological roles different from cyanide detoxification for rhodanese like proteins. Proposed roles for rhodanese like proteins can be summarized in two different but complementary fields. Rhodanese-like proteins can function as source of bioactive sulfur equivalents by the formation of a persulfide sulfur on a cysteine residue (R-SSH) (Cartini et al 2011), or can be involved in maintaining redox homeostasis acting as a direct or indirect scavengers of reactive oxygen species (ROS). My PhD research project was devoted to unravel the biological roles of rhodanese-like proteins using two prokaryotic model systems: the Azotobacter vinelandii and the Bacillus subtilis system. A. vinelandii is a Gram negative bacterium of the Pseudomonadaceae family in which redox balance must be carefully controlled due to its ability to fix molecular nitrogen via the molybdenum-iron-sulfur cluster enzyme nitrogenase (Setubal et al., 2009). The A. vinelandii genome possesses 14 ORFs coding for rhodanese like proteins with the tandem domain rhodanese-like protein RhdA (Gene ID: 7759697) being responsible for more than 80% of the crude extract thiosulfate:cyanide sulfurtransferase (TST) activity (Cartini et al., 2011). RhdA was widely studied in our lab from both structural and functional point of views. Starting from the evidence that the rhdA null-mutant strain (MV474) showed altered sensitivity to oxidative events (Cereda et al., 2009), I investigated the nature of the endogenous oxidative stress induced in A. vinelandii by the absence of RhdA. I found that in MV474 strain the ratio GSH/GSSG was misregulated, and the levels of lipid hydroperoxides were significantly increased, although defensive activities against oxidative stress damage were activated (e.g. upregulation of the ahpC gene, coding for Alkylhydroperoxidase C, a member of the OxyR regulon). Furthermore, rhdA expression was highly induced in the A. vinelandii strain (UW136) when the oxidative stress was performed by the incubation with the superoxide generator phenazine methosulfate (PMS). These results demonstrated that RhdA has a role in protecting A. vinelandii from oxidative damage and were the subject of a publication (Remelli et al., 2010). Therefore I addressed my study to understand how RhdA could function in protecting redox homeostasis in A. vinelandii. I studied, in vitro, the oxidation behavior of the only cysteine residue (Cys230) present in RhdA. Site directed mutagenesis showed that the Cys230 residue is mandatory for RhdA TST activity (Cartini et al., 2011). Combining results of TST activity assays, and thiol quantification by the use of the fluorescence probe monobromobimane (mBBr), I found that, after incubation with PMS, Cys230 underwent irreversible oxidation, while underwent reversible oxidation if RhdA was preincubated with thiosulfate or reduced glutathione (GSH). This latter result was taken as an indication that productive interaction with GSH, the widespread redox buffer, could be a key point on understanding RhdA biological function in A. vinelandii. The RhdA/glutathione interaction was characterized using different approaches. The ability of RhdA to interact with different glutathione species of biological relevance was studied by measuring changes of the RhdA intrinsic fluorescence due to tryptophan residues surrounding the RhdA active site. In particular, RhdA is able to strongly interact with GSH (Kd = 1.5 µM), glutathione thiyl radical (GS•; Kd = 10.4 µM), a radical form of GSH, while interaction with disulfide glutathione (GSSG) is weak (Kd = 1.4 mM). According to the RhdA active site features and to the thiol chemistry, a covalent binding with GSH was excluded by mass spectroscopy analyses and by the finding that reducing agents were unable to break the RhdA/GSH complex. Moreover, the inability of RhdA to bind GSH in the presence of high ionic strength conditions suggests that RhdA/glutathione complex is stabilized by electrostatic interactions according to the in silico model produced by docking the interaction. The ability of RhdA to interact with glutathione (especially with GS•) as well as the results that GSH level was lower in the mutant than in the wild-type strain, were considered for discerning the biological functions of RhdA. Only a small number of proteins can manage GS•, among them human glutaredoxin 1 and 2 (hGrx1; hGrx2) can catalyze the reaction between GSH and GS• leading to the formation of GSSG and a superoxide radical (Starke et al., 2003). The ability of these proteins to catalyze the oxidation of glutathione is mainly due to the peculiar feature of their active site that bear a low pKa cysteine residue (Gallogly et al., 2008) . In vitro assays, using GS•-generating mix as a substrate, demonstrate the ability of RhdA to catalyze GSSG production with a turnover number 180-fold higher compared to human glutaredoxin 1, the glutaredoxin that present higher activity (RhdA kcat: 628 s-1). The lacking in the A. vinelandii genome of genes coding for hGrx1- and hGrx2-like glutaredoxins (while genes for other glutaredoxins are present), together with the absence of a complete ascorbic acid biosynthetic pathway, increases the biological relevance of the RhdA ability to scavenge GS•, preventing further oxidation of GS• to toxic and/or unrecoverable forms. Considering that GS• is mainly produced from GSH activity of, for example, detoxification of hydroxyl radicals (OH•) produced during cellular respiration (Lushchack, 2011), it is reasonable to believe that the RhdA function in protecting redox homeostasis must be related to the maintaining of the cellular respiration rate and has been further suggested by monitoring the oxygen consumption of UW136 and MV474 crude extracts. B. subtilis is a Gram positive bacterium that has been taken as a model prokaryotic system because of its close evolutional relationship with pathogen Gram positive bacteria like B. anthracis, (which causes anthrax), B. cereus (responsible of the foodborne illness), and B. thuringiensis that is an important insect pathogen. Analysis of the B. subtilis genome allowed the identification of 5 rhodanese like proteins; 3 (YtwF, YqhL, YbfQ) are single-domain protein and 2 (YrkF and YrkH) have the rhodanese domain fused to other functional domains. Noteworthy, rhodanese like proteins having the RhdA domain architecture (i.e. two rhodanese domains organized in tandem) are not present in the B. subtilis genome. B. subtilis rhodanese-like proteins share the structural features of the rhodanese catalytic domain: a putative catalytic cysteine residue surrounded by positively-charged amino acid residues. In silico analyses on transcription factor binding sites revealed that YbfQ, YhqL and YtwF are putatively controlled by FurR homologs, that in B. subtilis are the transcription factors that controls: the iron uptake (FurR), the zinc uptake (ZurR) and the peroxide response system (PerR). Furthermore yhqL transcription is also putatively controlled by NagC that is related to the expression of proteins involved in the N-acetil-glucosammine (GlcNac) transport. These informations suggest that B. subtilis rhodanese-like proteins, or at least some of them, could be involved in the oxidative stress response system. This idea have been recently supported by transcriptome analyses in which overexpression of ybfQ B. anthracis homolog has been shown after induction of the oxidative stress by treatment with hydrogen peroxide (Pohl et al., 2011). A preliminary characterization of biological function of rhodanese-like proteins in B. subtilis was performed analyzing phenotypic changes on the rhodanese-like quadruple null mutant J1235 strain (yrkF, yhqL, ybfQ, ytwF), kindly provided by professor T. Larson, compared to the isogenic wild type strain PS832. Whereas no visible growth differences were observed in rich medium (LB), a small, but significant, growth difference was observed in Spizizen minimal medium supplemented with 0.4% sucrose. Hydrogen peroxide challenging assays, using both sublethal and lethal stressor concentrations, indicated that J1235 strain was more prone to oxidative stress damage compared to the wild type PS832 strain. It suggests that the absence of rhodanese-like proteins caused a chronic endogenous oxidative stress condition enhanced by growths on the minimal media. These results were further confirmed by the ~40% decrease of the aconitase activity, an oxidative stress sensitive Fe-S cluster enzyme that is generally used as a marker to evaluate cellular oxidative stress conditions. Furthermore J1235 strain exhibited a ~50% increase of the intracellular lipid hydroperoxide content suggesting membrane oxidation. Differently from eukaryotes and most of the Gram negative bacteria, the majority of the Gram positive bacteria have evolved different strategies to maintain intracellular redox homeostasis that don't involve the synthesis of GSH (Fahey et al., 1978). The most thoroughly studied of these alternative compounds are mycothiol (MSH) and coenzyme A (CoA) (Rawat et al., 2007; del Cardayré et al., 1998). Recent studies on the redox-sensitive thiol proteins of B. subtilis, have uncovered an unknown low molecular mass thiol in association with the transcription factor Ohr (Nicely at al., 2007) that, in eukaryotic organisms, is regulated by glutathionylation (Hermansson et al., 1990). This new molecule, named bacillithiol (BSH), shares some structural characteristics with MSH (e.g. the GlcNac and cysteine mojeties) (Newton et al., 2009), and has proven to be the B. subtilis major low molecular weight thiol (Gaballa et al., 2010). Interestingly, a decrease of both total soluble BSH (~35%) and the BSH/BSSB ratio (~40%) were observed when the B. subtilis J1235 strain, where rhodanese-like proteins are not expressed, was compared with the wild-type strain. These and other phenotype features (i.e. differences of low-molecular weight thiol levels; increase of lipid oxidation), make the condition observed for the B. subtilis J1235 strain very similar to that observed for the A. vinelandii rhdA null mutant strain MV474, suggesting that at least one of the rhodanese-like protein shares the biological function of A. vinelandii RhdA. Structural differences between RhdA and B. subtilis rhodaneses could be explained by the structural differences between GSH and BSH, that requires a different active site architecture. For the cell localization and the presence of FurR and NagC control elements, among the B. subtilis rhodanese-like proteins, YhqL is supposed to be the primary candidate that could share the same biological function with RhdA. In preliminary experiments, the yhqL single mutant JD0206 and the rhodanese-like quadruple null mutant J1235 strains showed similar results about the BSH levels, further supporting the hypothesis that YhqL is the B. subtilis orthologous of RhdA. In conclusion, during my PhD research project, I gave solid indications of a direct involvement of members of the rhodanese-like protein superfamily in protecting the cell from endogenous oxidative stress that can arise, for example, from cellular respiration. The maintenance of the cellular respiration is equivalent to cell survival and became critic, for example, for pathogens bacteria when under attack of the host cell opening, among others, to future implications of the rhodanese-like protein superfamily as a potential drug target for pathogen eradication.

One advantage of higher life-forms over less developed organisms is their ability to respond to signals from their environment with motion. This requires highly specialized contractile cells and a whole locomotion apparatus. In vertebrates, the cells responsible for movement are the skeletal muscle cells. They receive signals from the autonomic nervous system in the form of an action potential, and they contract in an appropriate manner. Calcium is a vital intracellular passenger whose role in muscular function is to initiate contraction. It is released via specific channel proteins from an internal Ca++ store, the sarcoplasmic reticulum, and triggers muscular contraction, the actual interplay of actin and myosin filaments. The step that is still not fully understood is the coupling process between arrival of an action potential and the subsequent contraction, called excitation-contraction coupling. Several theories have been proposed to explain this process. Some years ago, our laboratory introduced the hypothesis that an oxidation-reduction reaction of critical sulfhydryls associated with the Ca+t channel protein are involved in the regulation of channel gating. In an effort to understand more about the Ca++ channel gating mechanism at the molecular level, this thesis focuses on the interaction between o-phthalaldehyde, a reagent which specifically forms an isoindole derivative with the amino acids cysteine and lysine, and the Ca++ release channel complex. In this thesis, the planar lipid bilayer technique was used to study the Ca++ release channel protein from skeletal muscle sarcoplasmic reticulum at the single channel level. Utilizing this experimental technique, the direct interaction between OP A and the channel was investigated. In this study, it was shown that the interaction of o-phthalaldehyde with the channel increases the channel's open probability as well as its mean open time. Furthermore, the covalent nature of o-phthalaldehyde binding to the calcium release channel complex is shown and its inhibiting effects on chloride channels are demonstrated.

Imidazolium trans-[tetrachloro (dimethyl sulfoxide)(imidazole)ruthenate(III)], NAMI-A, is an experimental metastasis inhibitor whose specific mechanism of activation and action remains to be elucidated. In the nucleophilic and reducing physiological environment; it is anticipated that the most relevant and available reductants upon introduction of NAMI-A as a therapeutic agent will be the biologically-relevant free thiols. The kinetics and mechanisms of interaction of NAMI-A with biologically-active thiols cysteamine, glutathione, cysteine and a popular chemoprotectant, 2-mercaptoethane sulfonate (MESNA) have been studied spectrophotometrically under physiologically-relevant conditions. The reactions are characterized by initial reduction of NAMI-A with simultaneous formation of dimeric thiol and subsequent ligand exchange with water to various degrees as evidenced by Electospray Ionization Mass Spectrometry. Stoichiometry of reactions shows that one molecule of NAMI-A reacted with one mole of thiol to form corresponding disulfide cystamine, dimeric MESNA, oxidized glutathione and cystine. Observed rate constants, ko, for the reaction of NAMI-A with cysteamine, MESNA, GSH and cysteine were deduced to be 6.85 + 0.3 x 10-1, 9.4 + 0.5 x 10-2 , 7.42 + 0.4 x 10-3 and 3.63 + 0.3 x 10-2 s-1 respectively. Activation parameters determined from Arrhenius plots are indicative of formation of associative intermediates prior to formation of products. A negative correlation was obtained from the Brønsted plot derived from observed rate constants and the pKa of the different thiols demonstrating significant contribution of thiolate species towards the rate. In conclusion, interactions of NAMI-A with biologically-active thiols are kinetically and thermodynamically favored and should play significant roles in in vivo metabolism of NAMI-A.

Orientador: Marcelo Ganzarolli de Oliveira
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Quimica
Made available in DSpace on 2018-08-15T02:21:46Z (GMT). No. of bitstreams: 1 Sassonia_RogerioCorte_D.pdf: 2947110 bytes, checksum: fc316c83bed9508d2e27063d89528d56 (MD5) Previous issue date: 2009
Resumo: Este trabalho apresenta os resultados da aplicação da titulação calorimétrica isotérmica na caracterização termodinâmica de reações de S-nitrosação de tióis e de interações proteínaproteína e proteína-íon. Foram estudadas as reações de S-nitrosação da N-acetil-L-cisteína (NAC), L-cisteína (CYS), L-glutationa (GLU) e do ácido mercaptosuccínico. Também foram avaliadas as interações entre a proteína sinalizadora Shc (Src homology collagen-like) e as proteínas glutationa S-transferase (GST) e a ciclofilina A (CypA) e a interação entre a região Cterminal da proteína humana EFHC1 (EFHC1-C) com íons Ca e Mg. Os valores da variação de entalpia revelaram que a S-nitrosação é um fenômeno exotérmico e ocorre com diminuição de entropia. Estes dados termodinâmicos revelam que as reações de S-nitrosação investigadas são entalpicamente dirigidas a 25 °C (1 atm) e possuem valores semelhantes de variações de entalpia, entropia e energia livre, apesar das diferenças entre as estruturas químicas dos tióis. Verificou-se que a proteína EFHC1C liga-se tanto a íons Ca quanto Mg numa estequiometria de 1:1, com afinidades definidas por diferentes contribuições entálpicas e entrópicas. Este dado confirmou a existência de um suposto domínio EF-hand ligante de Ca na porção C-terminal previsto pela seqüência primária da EFHC1C. Por outro lado, a EFHC1C perde sua capacidade de interação com íons Ca e Mg em solução sem 1,4-ditiotreitol (DTT), provavelmente, devido à formação de dímeros. A ausência de sinais térmicos de ITC mostrou que nem a proteína GST, nem a proteína CypA interagem com a proteína Shc nas condições experimentais usadas.
Abstract: This work presents the results of isothermal titration calorimetry application in the thermodynamic characterization of thiol nitrosation reactions, protein-protein and protein-ion interactions. The S-nitrosation reactions of N-acetyl-L-cysteine (NAC), L-cysteine (CYS), Lglutathione (GLU) and acid mercaptosuccinic were studied. The interactions of the signaling protein Shc (Src homology collagen-like) with glutathione S-transferase (GST) and ciclofilina A (CypA) and of the EF-hand motif from human EFHC1C with Caand Mg ions were also evaluated. Enthalpy change values revealed that the S-nitrosation reaction is an exothermic phenomenum associated to a decrease in entropy. These thermodynamic data show that the S-nitrosation reactions investigated are enthalpically driven at 25 °C (1 atm) and have similar enthalpic, entropic and free energy change values, despite the differences among the chemical structures of the thiols. It was verified that the EFHC1C protein binds to both Ca and Mg ions in a 1:1 stoichiometry with affinities defined by different enthalpic and entropic contributions. These data confirmed the presence of a putative EF-hand Ca-binding motif at the C-terminal portion as expected by the primary sequence of EFHC1C. On the other hand, EFHC1C losses its ability to interact with Ca and Mgions in solution without 1,4-ditiotreitol (DTT) likely due to protein dimerization. The absence of ITC thermal signals showed that neither GST nor CypA interact with the Shc protein in the experimental conditions used.
Doutorado
Físico-Química
Doutor em Ciências

Xylella fastidiosa é uma bactéria gram-negativa, colonizadora do xilema de plantas economicamente importantes, sendo responsável por diversas patogenias como a doença de Pierce em videiras e a clorose variegada dos citros (CVC). Plantas, ao serem infectadas por patógenos, dispõem de um maquinário de defesa que inclui a geração de espécies reativas de oxigênio (ROS). Peróxidos de lipídios podem ser formados pelo ataque de ROS à membrana bacteriana ou pela ação de lipoxigenases. O sistema da AhpR (alquil hidroperóxido redutase) foi inicialmente caracterizado como o principal responsável pela defesa contra hidroperóxidos orgânicos em bactéria. Recentemente, foi descrito um gene em muitas bactérias patógenas no qual a sua deleção conferia a célula uma maior susceptibilidade a hidroperóxidos orgânicos, mas não a H2O2 ou a geradores de superóxido (Mongkolsuk et al., 1998 e Ochsner et al., 2001). Por esta razão, este gene foi denominado ohr (organic hydroperoxide resistance gene). O objetivo desse trabalho foi caracterizar funcionalmente a proteína ohr de X. fastidiosa. Inicialmente, demonstramos que ohr possui atividade peroxidase dependente de tiól sendo que sua capacidade de reagir com hidroperóxidos é devida á presença de um par de cisteínas conservadas em seu sítio ativo. Também mostramos que ohr possui um enovelamento alfa/beta único, não observado nas estruturas de outras peroxidases dependentes de tiól como peroxirredoxinas e glutationa peroxidases. Análises do sítio ativo de ohr mostraram que seus prováveis substratos são moléculas hidrofóbicas e alongadas. Corroborando esta hipótese, demonstramos que enzimas lipoiladas, classicamente relacionadas com o metabolismo intermediário, interagem física e funcionalmente com ohr, enquanto que os sistemas tiorredoxina e glutationa, classicamente relacionados a tióis peroxidases, não sustentam a atividade peroxidásica de ohr. Este resultado representa a primeira descrição de uma peroxidase que é diretamente reduzida por grupos lipóicos de enzimas. Também fornecemos evidências que indicam que ohr atua na redução de hidroperóxidos derivados de ácidos graxos insaturados. De fato, análise cinética de estado estacionário por bi substrato mostra que ohr decompõem hidroperóxidos orgânicos com alta eficiência (kcat/KM ~ 106M-1.s1) através de um mecanismo ping-pong, sendo aproximadamente dez mil vezes mais eficiente do que na presença de H2O2. Esses dados em conjunto mostram que ohr é central na resposta bacteriana contra o estresse induzido por hidroperóxidos orgânicos, mas não por H2O2 e define uma nova classe de enzimas antioxidantes com propriedade únicas: peroxidases dependentes de grupos lipóicos. Outro objetivo desse trabalho foi estudar a via de regulação gênica de ohr em Xylella fastidiosa. Na maioria dos organismos, ohr é regulada por uma proteína repressora denominada ohrR (Sukchawalit et al., 2001), mas em algumas bactérias foi descrito que a expressão de ohr era regulada positivamente por um fator sigma alternativo (σE) de função extra citoplasmática (Gourion et al., 2008). Nossos resultados mostraram que ohr de X. fastidiosa não está sob controle de nenhuma dessas proteínas, sendo provavelmente expressa constitutivamente. Análises por northern blot não mostraram alterações nos níveis de ohr em células submetidas a estresse oxidativo ou etanólico. Esses resultados, ainda que preliminares, indicam que possivelmente o controle da expressão gênica de ohr em X. fastidiosa é distinto daqueles descritos até o momento na literatura para outras bactérias.
Xylella fastidiosa is a gram-negative bacterium, which colonizes the xylem from economically important plants, being responsible for several diseases such as Pierce disease (PD) in gravepines and citrus variegated clorosis (CVC). Plants, when infected by pathogens, are able to defend themselves through several mechanisms which include the generation of reactive oxygen species (ROS). Lipid hydroperoxides can be generated from the attack of ROS to the bacterial membrane or by the action of lipoxygenases. The alkyl hydroperoxide reductase system (AhpR) was initially characterized as the main responsible for the detoxification of organic hydroperoxides in bacteria. Recently, it was also characterized another gene in many pathogenic bacteria, whose deletion renders cells susceptibility to organic hydroperoxide treatments but not by H2O2 or by superoxide generators (Mongkolsuk et al., 1998 and Ochsner et al., 2001). For this reason, it was named ohr (organic hydroperoxide resistance gene). The goal of this work was to functionally characterize ohr, the product of ohr gene from Xylella fastidiosa. Initially, we demonstrated that ohr possesses Cys-based thiol-dependent peroxidase activity. Later, we showed that ohr possesses a unique alpha/beta fold not observed in the structures of other thiol peroxidases such as peroxiredoxins and glutathione peroxidases. Analyses of ohr active site showed that its likely substrates are elongated and hydrophobic molecules. Furthermore, we showed that lipoylated enzymes, classically related with the intermediary metabolism, interacts physically and functionally with ohr while classical thiol-dependent pathways, such as thioredoxin and glutathione, failed to support ohr activity. This finding represents the first evidence of a peroxidase that is directly reduced by lipoyl groups of enzymes. Also, we obtained evidences indicating that ohr acts in the detoxification of peroxides derived from unsaturated fatty acids. In fact, steady-state kinetics using bi-substrate analysis showed that ohr decomposes organic peroxides with high efficiency (kcat/KM ~ 106 M-1.s-1 through a ping-pong mechanism, at least ten thousand times more efficiently than hydrogen peroxide (H2O2). All these results together shows that ohr is central in the response of bacteria to the stress induced by organic hydroperoxides but not by H2O2 and defines a new class of antioxidant enzymes with unique properties such as lipoyl-dependent peroxidase activity. Another goal of this work was to study the regulation of ohr expression in Xylella fastidiosa. ohr expression is regulated in most bacteria by a repressor protein named ohrR (Sukchawalit et al., 2001) but, in some bacteria, ohr expression is positively regulated by an alternative sigma factor (σE) with extracitoplasmatic function (Gourion et al., 2008). Our results showed that ohr from X. fastidiosa was not under the control of none of these regulators, probably being constitutively expressed. Through northern blot analysis, we did not observed any changes in ohr levels in cells submitted to oxidative or ethanolic stress. These results, indicates that ohr expression probably differs from that previously described on literature for other bacteria.

Organic hydroperoxide resistance (Ohr) proteins are highly efficient thiol-based peroxidases that play central roles in bacterial response towards organic hydroperoxides. In Fungi, Ohr frequently presents a N-terminal extension, which is predicted to target them to mitochondria. The catalytic triad of Ohr comprises the peroxidatic Cys (Cp), the catalytic Arg (Rc) and a Glu (Ec) are fully conserved and interact among themselves by a salt bridge network in a reduced form of the enzyme (the so-called closed state). After getting oxidized to sulfenic acid (Cys-SOH), Cp condenses with the sulfhydryl group of resolution Cys (Cr) in a disulfide bond. The absence of negativity of the thiolate (RS-) in Cp facilitates the opening of the Arg-loop (containing the Rc) away from the active site, generating the so-called open state. However, the molecular events associated with the high reactivity of Ohr enzymes towards hydroperoxides and its specific reducibility by the dihydrolipoamide (DHL) or by lipoylated proteins were still elusive before this work. Additionally, several factors support the idea of Ohr as a target for drug development: (i) Ohr displays unique physicochemical properties; (ii) bacteria mutant for Ohr (Δ ohr) are highly sensitive to oxidative stress; (iii) the indications that Ohr might be involved in bacterial virulence; and (iv) its absence in mammals and vascularized plants. In this thesis, several aspects of Ohr enzymes were evaluated. In chapter 2, we biochemically characterized the Ohr homologs from the ascomycete fungus Mycosphaerella fijiensis Mf_1 (MfOhr), the causative agent of Black Sigatoka disease in banana plants, which presented extraordinary reactivity towards linoleic acid hydroperoxides (kobs = 3.18 (± 2.13) ×108 M-1.s-1). Furthermore, through subcellular fractionation of M fijiensis protoplast cells followed by western blot analysis, we confirmed the in silico prediction that MfOhr is a mitochondrial protein. In chapter 3 and 4, we described seven new crystallographic structures from two opportunistic pathogen, one from Xylella fastidiosa and six from Chromobacterium violaceum (including the first representative of the complex between Ohr and its biological reductant, DHL). Taken together these structures might represent new snapshots along the catalysis. Furthermore, several molecular modelling approaches, such as classical mechanics (MM), steered molecular dynamics (SMD), hybrid quantum mechanics (QM-MM) and together with enzymatic assays of point mutations, indicated that Ohr underwent unique structural switches to allow an intermittent opening (oxidized state) and returning to a more stable closed form (reduced state) of an Arg-loop along catalysis. Remarkably, dihydrolipoamide directly assisted the closing the Arg-loop and thereby the turnover of the enzyme. In chapter 5, we describe the identification of two compounds (C-31 & C-42) that could represent a framework for further studies attempting to find specific Ohr inhibitors, either through ab initio design of chemical compounds and virtual screening using pharmacophoric models. The IC50 calculated for C-31 and C-42 were 124.4-248.5 µM and 243.3-321.7 µM, respectively. Finally, this thesis highlights several new aspects related to Ohr function: 1 - evidence that eukaryotic Ohr are preferentially located in mitochondria and share several biochemical properties with the prokaryotic ones; 2 - the network of polar interactions among residues of the catalytic triad (Cp, Rc and E) strongly contributed to stabilize Ohr in the closed state, in an optimum configuration for hydroperoxide reduction; 3 - evidence that disulfide bond formation and the product release (alcohol derived from hydroperoxide reduction) facilitate the opening of the Rc loop to an intermediate state (probably not to the excessively open state presented in crystallographic structures); 4 - mapping the interactions between the biological reductant (DHL) and the Ohr active site; 5 - strong indications that DHL is not able to fit and react with Ohr in the close conformation; 6 - the first trials for search of molecules to specifically target Ohr proteins, although further assays must be performed to verify the specificity of the selected compounds to target Ohr. Therefore, we describe relevant new information for an antioxidant protein that displays highly efficient catalysis, comparable to other very important hydroperoxide removing enzymes, such as GSH peroxidase and peroxiredoxin
As proteínas Ohr (Organic hydroperoxide resistance) são peroxidases dependente de tiól extremamente eficientes e têm um papel central na resposta das bactérias contra peróxidos orgânicos. Em fungos, as proteínas Ohr apresentam uma extensão N-terminal, cujo predições in silico apontam estar associada ao direcionamento da proteína para a mitocôndria. A tríade catalítica é composta pela cisteína peroxidatic (Cp), a arginina (Rc) e o glutamato (Ec) catalíticos que são totalmente conservados e interagem entre eles por uma rede de interações de ponte salina, na forma reduzida da proteína (conformação fechada). Após se tornarem oxidadas em ácido sulfênico (Cis-SOH), a Cp condensa com o grupo sulfidrila da cisteína de resolução (Cr) numa ligação disulfeto. A ausência da carga negativa do tiolato (RS-) da Cp facilita a abertura da alça que contem a Rc para longe do centro ativo, gerando a conformação aberta. No entanto, os eventos moleculares associados a alta reatividade das enzimas Ohr contra hidroperóxidos e a sua redução pela dihydrolipoamida (presente em proteínas lipoiladas), ainda está descrita de forma bem superficial. Adicionalmente, vários fatores suportam a ideia de que a Ohr seria um potencial alvo para o desenvolvimento de drogas: (i) a Ohr exibe propriedade físico-químicas únicas; (ii) as bactérias mutantes para Ohr (Δohr) são fortemente sensíveis ao stress oxidativo; (iii) indicações de que a Ohr poderá está envolvida na virulência de várias bactérias; e (iv) a ausência de Ohr em mamíferos e plantas vascularizadas. Nesta tese, vários aspetos relacionados com as enzimas Ohr foram avaliados. No Capitulo 2, foi caracterizada bioquimicamente a proteína Ohr homologa de fungo ascomiceto, Mycosphaerella fijiensis Mf_1 (MfOhr), o agente causador da doença de bananas, Sigatoka-negra. A enzima apresentou eficiente atividade contra peroxido de ácido linoleico (kobs = 3.18 (± 2.13) ×108 M-1.s-1). Além disso, através do fracionamento sub celular de protoblasto de M fijiensis seguido de western blot, foram confirmadas as predições in silico de que a MfOhr é uma proteína mitocondrial. No capítulo 3 e 4, foram descritas sete estruturas cristalográficas oriundas de dois patógenos oportunistas, uma de Xylella fastidiosa e seis de Chromobacterium violaceum (incluindo o primeiro representante do complexo entre a Ohr e o seu redutor biológico, DHL). Estas estruturas poderão representar diferentes conformações ao longo do ciclo catalítico. Adicionalmente, várias abordagens de modelagem molecular, tais como mecânica clássica (MM), mecânica molecular direcionada (SMM) e mecânica quântica híbrida (QM-MM), juntamente com ensaios experimentais com mutações pontuais, indicaram que a Ohr sofre várias mudanças conformacionais para permitir uma abertura intermitente (estado oxidado) e o retorno para uma conformação fechada mais estável (estado reduzido) da alça da arginina ao longo da catálise. Notavelmente, a dihydrolipoamide assistiu diretamente o fechamento da alça da arginina e por consequência o turnover da enzima. No capítulo 5, foi descrita a identificação de dois compostos (C-31 e C-42) que representam estudos iniciais com a finalidade de encontrar inibidores específicos para a enzima Ohr. Estes compostos foram encontrados por ab initio design e por varrimento virtual com o uso de modelos farmacofóricos. Os IC50 calculados para o C-31 e C-42 foram de 124.4-248.5 µM e 243.3-321.7 µM, respectivamente. Finalmente, esta tese descreve vários aspetos relacionados com a função da Ohr: 1 - evidências que as Ohr de eucariotos estão preferencialmente localizadas na mitocôndria e partilham várias propriedades bioquímicas com as Ohr de bactéria; 2 - a rede de interações polares entre os resíduos da tríade catalítica (Cp, Rc e Ec) contribuem fortemente para a estabilização do estado fechado, a configuração ótima para a redução de hydroperoxidos; 3 - evidências de que a formação da ligação disulfeto e a liberação do produto (álcool derivado da redução do hydroperoxido) facilitam a abertura da alça da arginina até um estado intermediários (provavelmente não o estado totalmente exposto apresentado nas estruturas cristalográficas) 4 - o mapeamento das interações entre o redutor biológico no centro ativo da Ohr; 5 - fortes indicações de que a DHL não é capaz de interagir e reagir com a Ohr na conformação fechada; 6 - os primeiros ensaios para a procura por moléculas que especificamente interajam com a Ohr, apesar de que futuros ensaios terão de ser executados para verificar a especificidade dos compostos selecionados. Assim, nós descrevemos nova informação relevante sobre uma proteína antioxidante que exibe uma alta eficiência catalítica, comparável com outras importantes enzimas removedores de hydroperoxidos, tais como glutationa peroxidases e peroxiredoxinas