Cells are constantly exposed to different stresses – one being redox stress, which is induced by metal, reactive oxygen species and reactive nitrogen species. S-nitrosoglutathione reductase (GSNOR) helps modulate redox stress by two different mechanisms – either by reducing S-nitrosoglutathione (GSNO) to oxidized glutathione (GSSG) or by oxidizing hydroxymethyl glutathione (HMGSH), a biproduct of glutathione and formaldehyde, to formic acid. GSNO has the potential to posttranslational modify proteins in two different manners, either by S-nitrosation or by S-glutathionylation. Interestingly, GSNOR can be modified by its substrate GSNO, either by S-nitrosation, which has previously been reported, or, as discussed in this thesis, by S-glutathionylation. As S-glutathionylation has been reported to occur through intermediate species, the S-glutathionylation of GSNOR appears to occur though the S-nitrosated intermediate, instead of the most common route of an oxidation pathway. It is hypothesized that the S-glutathionylation, and the overall presence of glutathione, can act as a buffer to regulate the amount of nitrosation that GSNOR experiences, and thus the enzymatic activity. It is has reported that the S-nitrosation occurs on three different non-structural, non-catalytic, solvent-accessible cysteine residues. Experimentation was conducted using Saccharomyces cerevisiae as a model organism to determine how those three cysteine residues of the GSNOR homolog Sensitive to Formaldehyde 1 (SFA1) participate in the indirect detoxification of formaldehyde, through the hydroxymethyl glutathione pathway. It has been determined that cysteine 370 is not as important as previously thought, but the other one or two cysteines (either cysteine 10 or 271) do indeed play a role in the detoxification, but further analysis needs to be conducted.

While the cardiotoxicity of doxorubicin (DOX) is known to be partly mediated through the generation of reactive oxygen species (ROS), the biochemical mechanisms by which ROS damage cardiomyocytes remain to be determined. This study investigates whether S-glutathionylation of mitochondrial proteins plays a role in DOX-induced myocardial injury using a line of transgenic mice expressing the human mitochondrial glutaredoxin 2 (Glrx2), a thiotransferase catalyzing the reduction as well as formation of protein-glutathione mixed disulfides, in cardiomyocytes. The total glutaredoxin (Glrx) activity was increased by 76% and 53 fold in homogenates of whole heart and isolated heart mitochondria of Glrx2 transgenic mice, respectively, compared to those of nontransgenic mice. The expression of other antioxidant enzymes, with the exception of glutaredoxin 1, was unaltered. Overexpression of Glrx2 completely prevents DOX-induced decreases in NAD- and FAD-linked state 3 respiration and respiratory control ratio (RCR) in heart mitochondria at days 1 and 5 of treatment. The extent of DOX-induced decline in left ventricular function and release of creatine kinase into circulation at day 5 of treatment was also greatly attenuated in Glrx2 transgenic mice. Further studies revealed that heart mitochondria overexpressing Glrx2 released less cytochrome c than did controls in response to treatment with tBid or a peptide encompassing the BH3 domain of Bid. Development of tolerance to DOX toxicity in transgenic mice is also associated with an increase in protein S-glutathionylation in heart mitochondria. Taken together, these results imply that S-glutathionylation of heart mitochondrial proteins plays a role in preventing DOX-induced cardiac injury.

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Acteurs des mécanismes moléculaires de signalisation cellulaire, les espèces réactives de l'oxygène (ROS) et les espèces réactives de l'azote (RNS) agissent comme des molécules signal transférant des informations extracellulaires ou intracellulaires et induisant des réponses spécifiques. Les ROS/RNS agissent principalement via un ensemble de modifications post-traductionnelles réversibles des résidus thiols sur les protéines parmi lesquelles la nitrosylation et la glutathionylation apparaissent comme des éléments jouant un rôle important dans de nombreux processus cellulaires fondamentaux et impliqués dans nombre de maladies humaines. Bien que présents chez les organismes photosynthétiques, ces modifications ont été moins étudiées. Mon projet était d'étudier, in vivo, chez l'algue Chlamydomonas reinhardtii, la dynamique de la nitrosylation et de la glutathionylation, en utilisant une combinaison d'approches multidisciplinaires incluant protéomique, biochimie et biologie moléculaire. En réponse au stress nitrosatif, 492 protéines S-nitrosylées in vivo et 392 sites de nitrosylation ont été identifiés par spectrométrie de masse. Ces protéines participent à un large éventail de processus biologiques tels que la photosynthèse et la réponse au stress. Avec une stratégie similaire, l’analyse de la glutathionylation en réponse à des stresses physiologiques de forte lumière et de choc thermique, a révélé des voies spécifiques de réponse au stress. En parallèle, la dépendance redox des mécanismes moléculaires sous-jacents a été examinée pour la GAPDH cytoplasmique et l’isocitrate lyase, mais aussi la triosephosphate isomérase et la phosphoglycérate kinase chloroplastiques. / Actors of the molecular mechanism of cell signaling, reactive oxygen species (ROS) and reactive nitrogen species (RNS) act as signaling molecules to transfer extracellular or intracellular information and elicit specific responses. ROS/RNS mainly act through a set of reversible post-translational modifications of thiol residues on proteins among which nitrosylation and glutathionylation have emerged as key elements playing a major role in numerous fundamental cell processes and implicated in a broad spectrum of human diseases. Despite ROS and RNS are present in photosynthetic organisms, such modifications have been less studied. My project was to investigate in the green algae Chlamydomonas reinhardtii, the in vivo dynamics of nitrosylation and glutathionylation, using a combination of multidisciplinary approaches including proteomic, biochemistry and molecular biology. In response to nitrosative stress, 492 in vivo s-nitrosylated proteins and 392 sites of nitrosylation were identified by mass spectrometry. These proteins were found to participate in a wide range of biological processes and pathway such as photosynthesis, stress response and carbohydrate metabolism. Employing a similar strategy, analysis of glutathionylation in response to physiological stresses, specifically high light and heat stress revealed specific stress dependent targeted pathways. In a second part, the redox dependence of the underlying molecular mechanisms was examined for the cytoplasmic GAPDH and ICL, but also the chloroplastic TPI and PGK. This work has highlighted the existence of a strong interplay between these redox modifications. a complex redox network

The KATP channels play an important role in the membrane excitability and vascular tone regulation. Previous studies indicate that the function of KATP channels is disrupted in oxidative stress seen in a variety of cardiovascular diseases, while the underlying mechanism remains unclear. Here, we demonstrate S-glutathionylation to be a modulation mechanism underlying the oxidant-mediated vascular KATP channel inhibition, the molecular basis for the channel inhibition and the alleviation of the channel inhibition by vasoactive intestinal peptide (VIP). We found that an exposure of isolated mesenteric rings to H2O2 impaired the KATP channel-mediated vascular dilation. In whole-cell recordings and inside-out patches, micromolar H2O2 or diamide caused a strong inhibition of the vascular KATP channel (Kir6.1/SUR2B) in the presence, but not in the absence, of glutathione (GSH), indicating S-glutathionylation. By co-expressions of Kir6.1 or Kir6.2 with SUR2B subunits, we found that the oxidant sensitivity of the KATP channel relied on the Kir6.1 subunit. Systematic mutational analysis revealed three cysteine residues (Cys43, Cys120 and Cys176) to be important. Among them, Cys176 was prominent, contributing to >80% oxidant sensitivity. Biochemical pull-down assay with biotinylated glutathione ethyl ester (BioGEE) showed that mutations of Cys176 impaired the oxidant-induced incorporation of GSH to the Kir6.1 subunit. Simulation modeling of Kir6.1 S-glutathionylation revealed that after incorporation to residue 176, the GSH moiety occupied a space between slide helix and two transmembrane helices. This prevented the necessary conformational change of the inner helix for channel gating, and retained the channel in its closed state. VIP is a potent vasodilator, and is shown to have protective role against oxidative stress. We found that the channel was strongly augmented by VIP and the channel activation relied on PKA phosphorylation. These results therefore indicate that 1) the vascular KATP channel is strongly inhibited in oxidative stress, 2) S-glutathionylation underlies the oxidant-mediated KATP channel inhibition, 3) Cys176 in the Kir6.1 subunit is the major site for S-glutathionylation, and 4) the Kir6.1/SUR2B channel is activated in a PKA-dependent manner by VIP that has been previously shown to alleviate oxidative stress.

To unravel the mysteries of complex biological processes carried out by biomolecules it is necessary to adopt a multifaceted approach, which involves employing a wide variety of tools both computational and experimental. In order to gain a clear understanding of the function of biomolecules their three dimensional structure is required. X-ray crystallography and Nuclear Magnetic Resonance (NMR) spectroscopy are the only two methods capable of providing high-resolution three-dimensional structure of biomolecules. NMR has the advantage of allowing the study of structure of biomolecules in solution and is better equipped to characterize the dynamics of the protein. Protein structure determination by NMR spectroscopy consists of recombinant expression of isotopically labeled proteins, purification, data collection, data processing, resonance assignment, distance restraint and angular restraint generation, structure calculation and structure validation. Apart from 3D structure determination of biomolecules NMR has become the method of choice for studying transient protein-protein interactions, which are notoriously difficult to study at higher resolution by other methods. Mass spectrometry plays an important role in enabling rapid identification of biomolecules and their modifications. The high sensitivity and resolution mass spectrometry offers makes it the method of choice for studying post-transitional modification of proteins. Use of computers in biology has played an essential role in elucidating those structure function relationships in biomolecules that are not possible to study by experimental techniques. The first chapter of this thesis deals with the introduction of methods used in this study. A brief introduction about the theory of Nuclear Magnetic Resonance (NMR) spectroscopy is given. Protein NMR methods used for structure determination of medium sized proteins are discussed. A part of this chapter discusses about the application of mass spectrometry in biochemistry and the use of tandem MS/MS experiments in identification of proteins and peptide fragments. Finally, the last part of this chapter gives an introduction about the theory of molecular dynamics and techniques used in the post processing of MD trajectories to elucidate the dynamics of proteins. The second chapter of this thesis is concerned with NMR characterization of a novel protein-protein interaction between the glycolytic enzyme Triosephosphate isomerase and the redox protein Thioredoxin. Chemical shift perturbation studies have been done to map the binding interfaces of these proteins. The structure of the complex was then modeled using NMR restraints based docking using the known 3D structure of these proteins. The docked complex reveals crucial insights into the glutathione mediated redox regulation of Triosephosphate isomerase and the role of thioredoxin as a deglutathionylating agent. Enzyme activity assays of Triosephosphate isomerase were done to show the inhibitory effects of s-glutathionylation of Cys217 and the role of thioredoxin as a deglutathionylating agent. The third chapter of the thesis is aimed to address some important issues related to the inhibition of Plasmodium falciparum Triosephosphate isomerase by S-glutathionylation. Oxidative stress induces protein glutathionylation which is a reversible post translational modification consisting of the formation of a mixed disulfide between protein cysteines and glutathione. Mass spectrometric analysis of the kilnetics of glutathionylation along with enzyme activity assays clearly show that gluthionylation of either Cys-13 (situated in the dimmer interface) or Cys-217 (situated in Helix G) can render the enzyme inactive. Molecular dynamics simulations provide a mechanistic basis of inhibition and predict that glutathionylation at Cys217 allosterically induces loop 6 disorder. The fourth chapter of this thesis addresses the stabilizing effect of introduction of a cross-strand disulfide bond across a non-hydrogen bonded position of an antiparallel beta sheet. Multidimensional heteronuclear NMR experiments have been used to get the backbone and side-chain resonance assignments, distance and angular restraints. In addition RDC based restraints have been used to calculate the structure of oxidixed form of L79C, T89C thiroedoxin. The observation of predominantly –RH staple conformation among the NMR ensemble in typical of cross-strand disulfides. The fifth chapter of this thesis deals with the dynamics of thioredoxin using computational methods.In this chapter analysis of known complexes of thiroedoxin was done to determine binding hot spot residues using free energy calculations. The physicochemical basis for the multispecificity of thioredoxin is probed using molecular dynamics simulations. In this chapter it has been shown that conformational selection plays a very important role in thioredoxin target recognition.

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