Ο ρόλος του χαλκού είναι πολύ σημαντικός για τη σωστή λειτουργία της κυτοχρωμικής c οξειδάσης (CcO), και συνεπώς για την κυτταρική αναπνοή στους ευκαρυωτικούς και προκαρυωτικούς οργανισμούς. Η συγκρότηση της CcO στον ενδομεμβρανικό μιτοχονδριακό χώρο είναι μια πολύπλοκη διαδικασία, εξαρτώμενη από πλήθος συνεργών πρωτεϊνών, υπεύθυνων για τη λειτουργική αναδίπλωση των υπομονάδων του ενζύμου και τη μεταφορά αίμης και ιόντων Cu σε αυτές. Ενώ οι πρωτεΐνες που ενέχονται στη διαδικασία είναι μάλλον γνωστές, οι μηχανισμοί μεταφοράς και ενσωμάτωσης των μεταλλικών ιόντων στα δυο ενεργά κέντρα της CcO, CuA και CuB, παραμένουν ανεξερεύνητοι. Το CuA κέντρο είναι ένα διπυρηνικό κέντρο χαλκού, του οποίου ο ρόλος εντοπίζεται στη μεταφορά e- από το κυτόχρωμα c στο καταλυτικό κέντρο CuB της CcO. Η σωστή συγκρότηση του CuA κέντρου είναι κρίσιμης σημασίας για την καταλυτική δράση του ενζύμου. Αρκετές πρωτεΐνες έχουν χαρακτηριστεί σαν ενεργοί παράγοντες στη μεταφορά ιόντων Cu στο CuA κέντρο, ο ακριβής, ωστόσο, μοριακός μηχανισμός και ρόλος της κάθε πρωτεΐνης είναι άγνωστος. Στους προκαρυωτικούς οργανισμούς, δυο οικογένειες πρωτεϊνών έχουν προταθεί για την εμπλοκή τους στη συγκρότηση του CuA. Η πρώτη περιλαμβάνει πρωτεΐνες που δεσμεύουν ιόντα Cu1+ με ένα συντηρημένο μοτίβο δέσμευσης H(M)x10Mx21HxM (υποθετικές πρωτεΐνες Hyp1) ενώ η δεύτερη περιλαμβάνει τις πρωτεΐνες της οικογένειας Sco, των οποίων ο ρόλος στον μηχανισμό του CuA κέντρου σαν θειορεδοξίνες ή χαλκομεταφορείς, παραμένει ασαφής. Στην παρούσα εργασία αποδείχθηκε ότι μια νέα περιπλασματική πρωτεΐνη (TtHyp1 ή PCuAC) εισάγει επιλεκτικά ιόντα Cu1+ στην Cox2 υπομονάδα της ba3-CcO του Thermus thermophilus προς σχηματισμό του φυσιολογικού διπυρηνικού TtCuA κέντρου, καθώς και ότι η Sco πρωτεΐνη του συγκεκριμένου οργανισμού (TtSco1) δεν μεταφέρει μεταλλικά ιόντα στο CuA, αλλά δρα σαν θειο-δισουλφιδική αναγωγάση ρυθμίζοντας τη σωστή οξειδωτική κατάσταση των κυστεϊνικών καταλοίπων του CuA. Οι πρωτεΐνες PCuAC, TtSco1 και TtCuA εκφράστηκαν, απομονώθηκαν και μελετήθηκαν τα βιοχημικά χαρακτηριστικά τους, η ικανότητα δέσμευσης μεταλλικών ιόντων και οι μεταξύ τους αλληλεπιδράσεις. Επιπλέον η PCuAC χαρακτηρίστηκε δομικά με φασματοσκοπία NMR στην απο και Cu(I) μορφή της. Ο ρόλος των προκαρυωτικών Sco διερευνήθηκε περαιτέρω με μελέτες γονιδιακής ανάλυσης και την έκφραση και τον προκαταρκτικό χαρακτηρισμό μιας νέας πρωτεΐνης, PpSco1/cytc της Pseudomonas putida, πρωτεΐνης αποτελούμενης από δυο επικράτειες, Sco1 και cytc, συνδέοντας το ρόλο των Sco πρωτεϊνών με τη θεωρια περί θειρεδοξινικής τους δράσης. Καινοτομία στην παρούσα εργασία αποτέλεσε η μεθοδολογική προσέγγιση της πολλαπλής κλωνοποίησης των γονιδίων-στόχων με μια νέα τεχνολογία κλωνοποίησης (Gateway) συνδυασμένης με τοποειδική ένθεση σε πολλαπλούς πλασμιδιακούς φορείς και η ανάπτυξη high throughput τεχνικών για πολλαπλές δοκιμές έκφρασης – απομόνωσης. Η συγκεκριμένη μελέτη παρέχει νέα δεδομένα για το μηχανισμό τη συγκρότησης του CuA κέντρου της προκαρυωτικής CcO, υποστηρίζοντας ένα νέο μοντέλο για τη συγκεκριμένη διαδικασία και παράλληλα συνδράμει στην αποκρυπτογράφηση του πολύπλοκου ρόλου των Sco πρωτεϊνών. / Copper is essential for the correct assembly and function of the cytochrome c oxidase (CcO), thus for the efficient cellular respiration in both eukaryotes and prokaryotes. CcO assembly in the inner mitochondrial membrane space is a multi complicated procedure, depended on a number of co-factors and their synergic action. These co-factors are proteins commissioned with the correct folding of the enzyme subunits and the transport/incorporation of heme moieties and Cu ions to them. While the proteins involved in this multistep procedure are rather known, the mechanisms of metal ion delivery and incorporation within the two active centers of CcO, CuA and CuB, still remain uncharted. The CuA center is a binuclear copper center, whose part in the respiratory chain is spoted in electron transport from the active cytochrome c to the catalytic CuB center of CcO. Efficient CuA assembly is crucial for the catalytic action of the entire enzyme. Several proteins have been characterized as essential factors for the transport of Cu ions to the CuA center; however their exact molecular mechanism of action still remains obscure. In prokaryotes, two protein families have been suggested to be involved in the CuA assembly. The first includes proteins that bind Cu1+ ions through a potential conserved motif H(M)x10Mx21HxM (hypothetical proteins, Hyp1), while the second includes proteins of the Sco family, whose exact role in CuA assembly as thioredoxins or copper chaperones is widely debated. In this work, it is propesed that a new periplasmic protein (TtHyp1 or PCuAC) selectively inserts Cu1+ ions in the Cox2 subunit of the ba3-CcO of Thermus thermophilus resulting the formation of the physiological binuclear TtCuA center, as well as that the Sco protein of the organism (TtSco1) is not able to transfer metal ions to the CuA center; instead it acts rather like a thio-disulfide reductase adjusting the proper redox state of the CuA cysteine residues. Proteins PCuAC, TtSco1 and TtCuA were over-expressed, purified and subjected to biochemical characterization, while their Cu binding capability and their inter se interactions were studied through NMR and UV spectroscopy. In addition, PCuAC was structurally characterized through NMR in its apo and Cu(I) form. The role of Sco proteins was further investigated through genome based analysis and the expression and biochemical characterization of a new protein, PpSco1/cytc from Pseudomonas putida, a unique bacterial protein consisted on two domains, a Sco1 and a cytc domain, presumptively connecting the role of Sco proteins with the suggested theory of thioredoxin action. A novelty in this work was the methodological aspect of the multiple cloning of the target genes with a new cloning technology (Gateway) combined with site specific recombination into multiple expression plasmid vectors and the development of a high throughput technique for parallel expression/purification tests. The infra work provides new insights to the CuA center assembly molecular mechanism of the prokaryotic CcO, supporting a new model for the particular procedure and also subscripts for the decipherment of the complicated role of Sco proteins.

The thesis summarizes data gathered on various components of respiratory chain of Trypanosoma brucei. Namely, NADH:ubiquinone oxidoreductase (complex I), alternative NADH:ubiquinone oxidoreductase (NDH2) and mitochondrial glycerol-3-phosphate dehydrogenase are discussed themselves and in broader context of energy metabolism. Also, a work done using RNA interference library is described.

Neste trabalho estão apresentadas novas estratégias para funcionalizar superfícies de ouro baseadas na sustentação de bicamadas lipídicas em superfícies de sensores de imagem por Ressonância de Plasmons de Superfície (SPRi) e a construção de um biosensor para detecção de citocromo c. SPRi é uma técnica ótica de gravimetria em tempo real. Por meio de medidas de variações de índice de refração (n) próximas a uma interface, a adsorção e desorção de moléculas podem ser mensuradas. Inicialmente testamos várias estratégias para encontrar um suporte adequado que se ligasse na superfície de ouro e que oferecesse sustentação e estabilidade para a bicamada de fosfolipídeo biotinilado. Estudos de FT-IR e MEV mostraram que a quitosana facilita a formação de uma bicamada íntegra de fosfolipídeos, de tal modo, que a mesma alcança valores de espessura próximos àqueles previstos, ~ 34,5 Å. Além disso, mostramos que esse sistema apresenta vantagens perante outros modelos, tais como, (poli-lisina/fosfolipídeos) e (tiol hidrofóbico/fosfolipídeo). Utilizando-se o complexo químico biotina/estreptoavidina conseguimos imobilizar o anticorpo anti cit c na bicamada, mantendo-o afastado da superfície de ouro. A construção do biosensor foi acompanhada com experimentos de SPRi. O limite de detecção de citocromo c atingido foi de 10-11mol/L. Um sensor construído somente com BSA e anticorpo anti cit c apresentou sensibilidade semelhante. Esta sensibilidade é em torno de três ordens de grandeza superior aos experimentos de imunoblotting usualmente utilizados para detecção de cit c. A principal limitação deste biosensor, tal como de outros imunoensaios, está intimamente ligada às vantagens e desvantagens dos anticorpos como ferramentas analíticas. / In this work we developed new strategies to functionalize gold surfaces based on the support of lipid bilayers on the surfaces of surface plasmon resonance imaging sensors (SPRi) and the construction of a biosensor for detection of cytochrome c. SPRi is an optical gravimetric real time technique. Through measurements of changes in refractive index (n) in close proximity to an interface, the adsorption and desorption of molecules can be measured. Initially we tested several strategies for finding a suitable medium that would adsorb on the gold surface and also support and stabilize a biotinylated phospholipid bilayer. Studies of FT-IR and SEM showed that chitosan induces the formation of an intact phospholipid bilayer, so that it reaches thickness values close to those expected, ~ 34.5 Å. Furthermore, we showed that this system has advantages in relation to other models, such as (poli-lisine/phospholipids) and (thiol hydrophobic / phospholipid). Using the chemical complex biotin/streptavidin anti cyt c antibody could be immobilized in the bilayer, keeping it away from the gold surface. The construction of the biosensor was accompanied with SPRi experiments. The limit of detection of cytochrome c was achieved from 10-11mol / L. A sensor built only with BSA and anti cyt c showed similar sensitivity. This sensitivity is about three orders of magnitude higher than the immunoblotting experiments commonly used for detection of cyt c. The main limitation of this biosensor, like in other immunoassays, is linked to the advantages and disadvantages of antibodies as analytical tools.

COX deficiency in human presents a plethora of phenotypes which is not surprising given the complexity of the enzyme structure and the multiple factors and many steps required for its assembly. A functional COX requires three mitochondrially encoded subunits (Cox1p, Cox2p and Cox3p), at least 10 nuclearly encoded subunits, some of which are tissue specific, and a yet unknown number of assembly factors. Mutations in four of these factors, hSco1p, hSco2p, hCox10p and hSurf1p, have been associated with lethal COX deficiency in patients. Sco proteins, conserved from prokaryotes to eukaryotes, are probably involved in the insertion of copper in COX. The role of hSco1p and hSco2p in this process was investigated in this work. Moreover the importance of some hSco mutations found in patients was analysed. Both in vitro and in vivo analyses show that the hSco proteins are localised in the mitochondria. Both proteins are per se unable to substitute for ySco1p. However, a chimeric construct consisting of the N-terminal portion, the TM and a part of the C-terminal portion of ySco1p and the remaining C-terminal part derived from hSco1p was able to complement a ysco1 null mutant strain. This construct was used to define the role of a point mutation (P174L) found in the hSCO1 gene of infants suffering from ketoacidotic coma. These mutation was shown to affect the COX activity and the levels of Cox1p and Cox2p. The fact that copper was able to suppress this mutation, strongly outlined the importance of Sco proteins in the copper insertion in COX. The C-terminal portions of recombinant hSco1p and hSco2p were purified from E. coli by affinity chromatography. The purified proteins were subjected to atomic emission and absorption analyses and were shown to specifically bind copper. A stoichiometry of 1:1 for hSco2p and of 0,6:1 for hSco1p was determined. To identify the Aa residues involved in copper binding, in vitro mutagenesis was performed. hSco1p and hSco2p, lacking the cysteines of the predicted metal binding site CxxxC, show a dramatic decrease in the ability to bind copper. A model for the structure of the metal binding site in hSco proteins is proposed. hSco proteins could bind copper with trigonal coordination, involving the two cysteines of the CxxxC motif and a conserved histidine. The purified recombinant proteins were also used in an enzymatic assay to test their ability to reduce disulfide bridges, similar to thioredoxin-like proteins involved in the assembly of bacterial COX. Both hSco proteins were not able to act as thioredoxins suggesting a role for the hSco proteins as copper chaperones. To define the pathway of the copper transfer to COX, hSco proteins were tested for their ability to interact with hCox17p, a mitochondrial copper chaperone, and with Cox2p, which contains two copper ions. An interaction between hSco1p and Cox2p was detected. Both hSco proteins were shown to homomerise and to form heterodimers one with each other. Two mutations found in hSCO2 patients suffering from hypertrophic cardiomyopathy, (E140K and S225F) were shown not to affect the copper binding properties, the intracellular localisation and the ability to form homomers. In accordance to these data, a model is proposed in which hSco2p dimers transfer copper to hSco1p dimers. hSco1p dimers interact with COX and insert copper in the binuclear centre of Cox2p.

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Many bacteria use inorganic nitrogen and sulfur compounds for energy metabolism. These compounds are often toxic and so bacteria must adapt to survive their deleterious effects. Bacteria use specific proteins in order to metabolise, sense and detoxify these compounds. In this thesis protein interactions with inorganic nitrogen and sulfur compounds are examined at the mechanistic level. Intermediates in the Sox sulfur oxidation pathway are covalently attached to a cysteine on the swinging arm of the substrate carrier protein SoxYZ. An interaction between the Sox pathway enzyme SoxB and the carrier protein SoxYZ is demonstrated. A crystal structure of a trapped SoxB-SoxYZ complex at 3.3 Å resolution identifies two sites of interaction, one between the SoxYZ carrier arm and the SoxB active site channel and the other at a patch distal to the active site. The presence of a distal interaction site suggests a mechanism for promiscuous specificity in the protein-protein interactions of the Sox pathway. Using biophysical methods it is shown that SoxB distinguishes between the substrate and product forms of the carrier protein through differences in interaction kinetics and that the carrier arm-bound substrate group is able to out-compete the adjacent C-terminal carboxylate for binding to the SoxB active site. The thiosulfate dehydrogenase TsdA has an unusual His/Cys coordinated heme. TsdA catalyses oxidative conjugation of two thiosulfate molecules to form tetrathionate. Mass spectrometry and UV/visible spectroscopy are used to identify an S-thiosulfonate reaction intermediate which is covalently attached to the cysteine heme ligand. A catalytic mechanism for TsdA is proposed using a crystal structure of TsdA at 1.3 Å resolution alongside site-directed mutagenesis of active site residues. Nitric oxide is produced by the mammalian immune response to kill bacterial pathogens. Part of the killing mechanism occurs through the reaction of nitric oxide with protein-bound iron-sulfur clusters. However, the same type of reaction is also exploited by nitric oxide-sensing bacterial proteins. An infrared spectroscopy approach is developed to detect the products of iron-sulfur protein nitrosylation. Using this methodology it is shown that the presence of trace O2 strongly impacts which products are formed in these nitrosylation reactions. These observations are of physiological relevance because bacteria are often exposed to NO under aerobic conditions during an immune response.

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