The glyoxalase pathway is widespread in both prokaryotic and eukaryotic organisms. This system utilizes two enzymes (glyoxalase I (GlxI) and glyoxalase II (GlxII)) to catalyze the formation of D-lactate from the substrates glutathione (GSH) and methylglyoxal (MG). The latter chemical is a harmful byproduct of glycolysis. This thesis gives detailed studies of the behavior of the GlxI enzyme as it pertains to its thiol co-substrate specificity, its structural similarity among its superfamily members (most particularly with the fosfomycin resistance protein (FosA)) and residue identification that would alter its metal selectivity. The thiol co-substrate GSH was thought to be the only thiol utilizied by the glyoxalase system. However, reports identified organisms that utilized the thiols trypanothione (T(SH)2) and glutahionylspermidine (GspdSH) as co-substrates. These organisms, known as the trypanosomes, are very well known in tropical environments to cause diseases. E. coli does not contain T(SH)2 but does contain GspdSH and manufactures the latter in increasing amounts under conditions of cell duress. Substrate specificity studies were conducted replacing GSH with GspdSH and T(SH)2. In addition to this, to ensure the thiols reacted in a true glyoxalase system, substrate specificity studies were also conducted on the second enzyme GlxII and verification of the product D-lactate was performed. To continue, structurally, the enzyme GlxI belongs to the βαβββ superfamily of proteins that are known to have very similar structure but to catalyze very different reactions. Comparing the active site of E. coli GlxI and FosA, there is one significant difference at one residue. Therefore an E56A mutation was performed on GlxI and the mutant bacterium were subjected to growth analysis in the presence of fosfomycin and MG. The mutant enzyme was also tested for its performance in the presence of MG and various divalent metals. Further, the Glx I enzyme from E. coli is known to be active in the presence of non-zinc bivalent metals, while the human counterpart is active in the presence of Zn2+. When one compares GlxI from E. coli with the human GlxI, there are many differences in the primary structure that could be viable areas that determine the metal specificity of the enzyme. Mutation analysis was performed on these areas to determine catalytic performance as well as metal specificity. These studies display how versatile the glyoxalase system is with regard to the use of its thiol co-substrates. These thiols participate in the detoxification pathway for MG in the cell especially under late log phase conditions. Structural studies can give some knowledge concerning the possible evolution of the enzyme among its family members, and is of monumental significance to the scientific community as it relates to enzyme metal selectivity and the development of enzymes over time.

The hydrogenation of aromatic sulfonyl chloride to produce aromatic thiol is an important industrial reaction. The aromatic thiol is a critical intermediate in the production of many pharmaceuticals as well as several agrochemicals. Density Functional Theory (DFT), a quantum mechanical method, was used to investigate the new aromatic thiol production technology at the molecular level in aspects including reaction species adsorption and transition state determination. Plant design methods and economic analysis were performed to determine the economic feasibility of the new technology in the current specialty chemicals market. The quantum mechanical calculations showed that the molecules adsorbed to three simulated (100) Pd catalyst surfaces will preferentially move to configurations that are favorable for reaction progression. The calculations also show that the proposed reaction sequence by DuPont is the most feasible option despite the investigation into an alternative sequence that arose from molecular observations during calculations. Predicted activation energies (Ea) were in the range of 6.88 ? 38.1 kcal/mol which is comparable to the 14.58 kcal/mol determined experimentally by DuPont, and the differences between experimental and simulated values are easily explained. Plant design calculations show that a semi-batch reactor plant can easily produce 2MM lb of thiol/year, giving the owner of the plant an immediate 18% market share in the worldwide market of benzenethiol. Economic analysis shows that a grassroots plant construction is not currently an economically feasible option for corporate investment unless a source of cheap, skilled labor can be found in addition to a means of a 25% discount on certain raw material feed stocks. However, if both of these requirements can be fulfilled then new plant construction will have a payback time of 3.71 years based on the price of benzenethiol in the summer of 2007, $2.27/lb thiol.

Advancements in the biomedical field are driven by the design of novel materials with controlled physical and bio-interactive properties. To develop such materials, researchers rely on the use of highly efficient reactions for the assembly of advanced polymeric scaffolds that meet the demands of a functional biomaterial. In this thesis two main strategies for such materials have been explored; these include the use of off-stoichiometric thiol-ene networks and dendritic polymer scaffolds. In the first case, the highly efficient UV-induced thiol-ene coupling (TEC) reaction was used to create crosslinked polymeric networks with a predetermined and tunable excess of thiol or ene functionality. These materials rely on the use of readily available commercial monomers. By adopting standard molding techniques and simple TEC surface modifications, patterned surfaces with tunable hydrophobicity could be obtained. Moreover, these materials are shown to have great potential for rapid prototyping of microfluidic devices. In the second case, dendritic polymer scaffolds were evaluated for their ability to increase surface interactions and produce functional 3D networks. More specifically, a self-assembled dendritic monolayer approach was explored for producing highly functional dendronized surfaces with specific interactions towards pathogenic E. coli bacteria. Furthermore, a library of heterofunctional dendritic scaffolds, with a controllable and exact number of dual-purpose azide and ene functional groups, has been synthesized. These scaffolds were explored for the production of cell interactive hydrogels and primers for bone adhesive implants. Dendritic hydrogels decorated with a selection of bio-relevant moieties and with Young’s moduli in the same range as several body tissues could be produced by facile UV-induced TEC crosslinking. These gels showed low cytotoxic response and relatively rapid rates of degradation when cultured with normal human dermal fibroblast cells. When used as primers for bone adhesive patches, heterofunctional dendrimers with high azide-group content led to a significant increase in the adhesion between a UV-cured hydrophobic matrix and the wet bone surface (compared to patches without primers). / <p>QC 20140116</p>

Monothiolate protected gold nanoclusters with near IR luminescence underwent a five-to-ten fold enhancement of quantum efficiency by heating in the presence of excess thiols. Two monothiolate nanoclusters, mercaptosuccinic acid and tiopronin, were shown to benefit from this procedure. Emission maximum around 700-900 nm is favorable for bioimaging applications due to reduction of background signal from autofluorescence. Dithiolate lipoic acid protected gold nanoclusters with higher near IR quantum efficiency present an interesting candidate for biological imaging due to the difference in hydrophobicity, resistance to quenching by divalent cations and cell growth media, and retained quantum efficiency when coupled to agents such as polyethylene glycol. Intracellular and nuclear internalization of mercaptosuccinic gold nanoclusters demonstrate a potential vector for delivery of nuclear targeting agents. The small size, chemical stability, high luminescence, and potential for targeting various intracellular domains make gold nanoclusters worthwhile for further studies as potential bioimaging probes.

Η ολοκληρωμένη εκτίμηση της θειολικής οξειδοαναγωγικής κατάστασης (ΘΟΚ) ενός οργανισμού ιστού ή κυττάρου είναι πολύ σημαντική καθώς οξειδοαναγωγικές αλλαγές των διαφόρων θειολικών μορίων συνδέονται με το οξειδωτικό στρες και με αρκετές ασθένειες. Η γενική ΘΟΚ (ΓΘΟΚ) χαρακτηρίζεται από τις συγκεντρώσεις ορισμένων συνόλων θειολικών μορίων στην αναγμένη και την οξειδωμένη μορφή τους (θειολικά οξειδοαναγωγικά ζεύγη). Αυτά τα ζεύγη μπορεί να είναι μη πρωτεϊνικά (non-protein ή NP) (όπως NPSH και NPSSNP με το NP να συμβολίζει οποιαδήποτε άλλη μη πρωτεϊνική θειόλη) ή πρωτεϊνικά (protein ή P) (όπως PSH, PSSP και PSSNP). Ειδικότερα, οι κυριότερες μη πρωτεϊνικές θειόλες γλουταθειόνη (GSH) και κυστεΐνη (CSH) μαζί με τα συμμετρικά, μεικτά δισουλφίδιά τους και τις οξειδωμένες τους μορφές (GSSG, PSSG, PSSC, NPGSHox, NPCSHox,) είναι τα οξειδοαναγωγικά ζεύγη τα οποία χαρακτηρίζουν την ειδική ΘΟΚ (ΕΘΟΚ), καθώς είναι εκείνα που απαντώνται σε υψηλότερη συγκέντρωση στους οργανισμούς. Στη διεθνή βιβλιογραφία δεν υπάρχει μεθοδολογία για την ταυτόχρονη ποσοτικοποίηση των θειολικών μορίων που χαρακτηρίζουν τη ΘΟΚ των οργανισμών. Συνεπώς, στόχος της παρούσας μελέτης είναι η ανάπτυξη μιας νέας μεθόδου ποσοτικοποίησης τόσο της ΓΘΟΚ όσο και της ΕΘΟΚ, που να είναι εφαρμόσιμη σε όλους τους οργανισμούς. Για το διαχωρισμό πρωτεϊνικών και μη πρωτεϊνικών μορίων χρησιμοποιήθηκε το τριχλωροακετικό οξύ που σε ορισμένη συγκέντρωση (>5%) καταβυθίζει αποτελεσματικά όλες τις πρωτεΐνες. Ο ποσοτικός προσδιορισμός των δισουλφιδικών μορίων και οξειδωμένων μορφών (NPSSNP, PSSP, PSSNP, GSSG, NPGSHox, NPCSHox, PSSG και PSSC) πραγματοποιήθηκε μετά από αναγωγή τους (με το αντιδραστήριο tributyl phosphine), ενώ ο ποσοτικός προσδιορισμός των ελεύθερων θειολών (PSH, NPSH, GSH και CSH) πραγματοποιήθηκε χωρίς την αναγωγή τους. Ειδικότερα, η ποσοτικοποίηση των αναγμένων διθειολικών ομάδων (δισουλφιδίων) και των ελεύθερων θειολών έγιναν με τα αντιδραστήρια 4,4-dithiodipyridine (για τις -SH ομάδες των αναγμένων δισουλφιδίων, καθώς και για τις ελεύθερες NPSH και PSH), o-phthalaldehyde (για την GSH, GSSG και NPGSHox) και νινυδρίνη (για την CSH και την NPCSHox), σε συνδυασμό με κατάλληλη μαθηματική επεξεργασία βασισμένη στη στοιχειομετρία των αντιδράσεων αναγωγής. Η υψηλή ευαισθησία της μεθόδου (στο επίπεδο του nmol) την καθιστά εφαρμόσιμη ακόμη και σε βιολογικά δείγματα χαμηλής περιεκτικότητας σε θειόλες (όπως πχ. το οφθαλμικό και το εγκεφαλονωτιαίο υγρό). / The thiol redox state (TRS) is an essential condition of prokaryotic and eukaryotic cells associated with all major biological processes. The general TRS (GTRS) part of it, is characterized by the levels of all thiol compounds of protein or non-protein origin in their reduced or oxidized form (thiol redox couples), while the specific TRS (STRS) by the levels of certain thiols, reduced and oxidized, free or membrane bound. The GTRS redox couples are composed of non-protein (NP) (such as NPSH and NPSSNP) or protein (P) (such as PSH, PSSP and PSSNP) thiols. On the other hand, the STRS redox couples are composed of the main non-protein thiol glutathione (GSH) and cysteine (CSH) together with their symmetric, mixed disulfides and oxidized forms (GSSG, PSSG, PSSC, NPGSHox, NPCSHox). In light of the fact that there is not available any appropriate method in literature for the simultaneous determination of the main thiol components that characterize TRS, a new method is developed for the purpose of this study for the quantification of GTRS and STRS, applicable to any organism. For the separation of protein from non protein thiols, trichloroacetic acid was chosen (at 5%) as the most effective protein precipitant. The determination of disulfides and oxidized forms (NPSSNP, PSSP, PSSNP, GSSG, PSSG, PSSC, NPGSHox and NPCSHox) was accomplished after their reduction with the tributyl phosphine (which, because of its hydrophobicity effectively reduces protein thiols as well), whereas the quantification of free thiols (PSH, NPSH, GSH and CSH) was accomplished without reduction. Reduced disulfides and free thiols were quantified by the more effective than DTNB 4,4-dithiodipyridine (for the determination of -SH groups of reduced disulfides as well as of free NPSH and PSH), o-phthalaldehyde (for the specific determination of GSH, GSSG and NPGSHox) and ninhydrin (for the specific determination of CSH and NPCSHox). The high sensitivity of the method (in the level of nmoles) makes it applicable even in biological samples of very low thiol concentration (such as ophthalmic or cerebrospinal fluid).

A família Tiol Peroxidases (TPxs - Peroxirredoxinas e Glutationa peroxidases) purificadas definitivamente reduzem peróxidos rapidamente (peroxinitrito, ONOOH/ONOO; peróxido de hidrogênio, H2O2), mas nenhuma evidência direta desta atividade foi demonstrada em células vivas. Isto é particularmente importante pois o ciclo catalítico da atividade peróxido redutase de TPxs depende de sucessivas reações de trocas de tióis que podem limitar a velocidade de redução do peróxido. Neste trabalho, esta questão foi investigada em Saccharomyces cerevisiae (Sc) por meio de cinética de competição com um indicador fluorescente que é específico para ONOO (ácido borônico de cumarina; CBA), com a expectativa de que quanto maior a atividade peroxinitrito redutase, menor a oxidação do indicador. Também foi investigado o papel de duas peroxirredoxinas (Prxs) específicas na remoção deste peróxido. O estudo mostrou que a oxidação do indicador CBA dependente de ONOO foi sempre significativamente maior em células de Saccharomyces cerevisiae deficientes em TPxs (cepa 8) relativo a cepa nativa (WT). Além disso, a transfecção do gene que codifica a Prx mais abundante em Saccharomyces cerevisiae (Tsa1) na cepa 8 diminui parcialmente a oxidação de CBA. Além disso, a oxidação de CBA foi maior na cepa deficiente apenas da peroxirredoxina Tsa1 (a mais abundante da família) relativo à cepa WT, mostrando a relevância desta isoforma especificamente. De forma adversa, a oxidação de CBA na cepa deficiente da peroxirredoxina Tsa2 foi semelhante à cepa WT. Também, foi constatado que o processo de remoção de ONOO é catalítico (e não estequiométrico) para crescentes fluxos de peroxinitrito em todas as cepas e condições utilizadas no estudo. Finalmente, o estudo sugere que células possuem sistemas catalíticos peroxinitrito redutase redundantes, já que a própria cepa 8 apresenta e pode modular esta atividade. Estes resultados confirmam a expectativa da relevância de TPxs na remoção de ONOO e por extensão de outros peróxidos biologicamente relevantes e são a primeira evidência direta e em tempo real da atividade peroxinitrito redutase de TPxs em células. / The purified Thiol Peroxidases family (TPxs - Peroxiredoxins and Glutathione peroxidases) rapidly reduces peroxides (peroxynitrite, ONOOH/ONOO-, hydrogen peroxide, H2O2), but no direct evidence of this activity has been demonstrated in living cells. This is particularly important since the catalytic cycle of the TPxs peroxide reductase activity depends on successive thiol exchange reactions, which may limit the rate of peroxide reduction. In this work, this question was investigated in Saccharomyces cerevisiae (Sc) by competition kinetics using a fluorescent indicator that is specific for ONOO- (coumarin boronic acid; CBA). It is expected that the higher the peroxynitrite reductase activity, the lower the oxidation of the indicator. The role of two specific peroxiredoxins (Prxs) in the removal of this peroxide has also been investigated. The study showed that the oxidation of ONOO- dependent CBA indicator was always significantly higher in TPxs-deficient Saccharomyces cerevisiae cells (strain 8) compared to the native strain (WT). In addition, the transfection of the gene encoding the most abundant Prx into Saccharomyces cerevisiae (Tsa1) in the 8 strain partially diminishes CBA oxidation. Besides that, CBA oxidation was greater in the deficient strain only of the peroxiredoxin Tsa1 (the most abundant in the family) compared to the WT strain, showing the relevance of this isoform specifically. On the other hand, CBA oxidation in the deficient strain of the Tsa2 peroxiredoxin was similar to the WT strain. Also, it was found that the ONOO- removal process is catalytic (and not stoichiometric) for increasing peroxynitrite fluxes in all strains and conditions used in the study. Finally, the study suggests that cells have redundant peroxynitrite reductase catalytic systems, since the 8 strain itself presents and can modulate this activity. These results confirm the expectation of the relevance of TPxs in the removal of ONOO- and by extension of other biologically relevant peroxides and are the first direct and real-time evidence of peroxynitrite reductase activity of TPxs in cells.

京都大学 / 新制・課程博士 / 博士(工学) / 甲第23215号 / 工博第4859号 / 新制||工||1758(附属図書館) / 京都大学大学院工学研究科物質エネルギー化学専攻 / (主査)教授 大江 浩一, 教授 近藤 輝幸, 教授 深澤 愛子 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

Indiana University-Purdue University Indianapolis (IUPUI) / The extracellular matrix (ECM) governs many cellular processes through biochemical and mechanical cues. Particularly, the effect ECM mechanical properties on cells fate has been well established over the years. Many hydrogel systems have been used to mimic the dynamic stiffening processes occurring in ECM. However, changes in ECM stiffness does not fully recapitulate the mechanics of native ECM, as viscoelasticity is also a major factor contributing to ECM dynamic property. This thesis describes the design and characterization of an enzyme-crosslinked hydrogel system that is not only capable of being stiffened on demand, but also can be tuned to obtain viscoelasticity. The first objective of this thesis was to utilize horseradish peroxidase (HRP) to crosslink thiol-norbornene hydrogel and use mushroom tyrosinase (MT) to create secondary DOPA-dimer crosslinks that stiffened the hydrogel. The cytocompatibility of HRP-mediated thiol-norbornene gelation and the effect of stiffening on cell fate was evaluated. The second objective of this thesis represented the first step towards developing a hydrogel system whose viscoelasticity could be dynamically tuned. Thiol-norbornene hydrogel was designed to yield dynamically adaptable boronic ester bonds via partial enzymatic reaction. Thiol-norborne hydrogel was made to contain hydroxyl phenol as well as boronic acid residues within its network. MT, in this case was used to oxidize the hydroxy phenol moieties into DOPA, which then complexed with boronic acid, created dynamic bonds, introducing viscoelasticity to an initial elastic hydrogel.

Targeted covalent inhibitors (TCIs) are irreversible enzyme inhibitors that are designed to first bind to a targeted enzyme’s active site reversibly using non-covalent interactions between the molecular scaffold of the inhibitor and the surrounding amino acid residues of the enzyme’s binding site. They then form a covalent bond between the inhibitor’s electrophilic warhead and a nucleophilic amino acid residue located inside of the binding pocket. Cysteine (Cys), a redox-sensitive thiol, is found in many enzyme active sites and is used as the target for many current TCIs in clinical application. Electrophilic warheads such as acrylamides and chloroacetamides are known to readily undergo thiol-addition, and although they are commonly used in the development of enzyme inhibitors, few previous studies have explored the mechanism of thiol-addition and the intrinsic reactivities of these moieties. In this work, a robust kinetic assay was developed to perform mechanistic studies of thiol-addition to the electrophilic warhead derivatives N-phenylacrylamide (NPA), N-acryloylpiperidine (AcrPip), and N-phenylchloroacetamide (NPC). By reacting these warhead derivatives with thiol nucleophiles having various pKa values, we were able to construct Brønsted-type plots, resulting in shallow positive βNucRS- values for NPA, AcrPip and NPC (βNucRS- = 0.07 ± 0.04, 0.11 ± 0.03, and 0.21 ± 0.07, respectively), meaning that these electrophiles are relatively insensitive to thiolate nucleophilicity. However, while the trend in their reactivity across thiolate nucleophilicity is similar, their intrinsic reactivity was found to be vastly different. In conjunction with the Brønsted-type plot, temperature, ionic strength, and kinetic isotope effects were studied to afford information about the rate-limiting transition state and elucidate the mechanism of thiol-addition. NPA and AcrPip were found to undergo very similar thiol-additions, consistent with the microscopic reverse of the E1cbrev elimination, whereas NPC follows an SN2 type addition, consistent with the intuitive mechanism of addition to a haloacetamide.

No description available.