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This work aimed to develop in a two-step strategy the deoxygenation of benzoic acid as a new probe reaction of the oxidation catalysts "at work". This choice was based on the experimental fact that the distribution of the potential main products, namely benzaldehyde, toluene and benzene depends on the presence and the mutual disposition of oxygen vacancies at the surface of the oxide catalysts. Indeed, it is claimed in the literature that single oxygen vacancies selectively produces benzaldehyde, twin oxygen vacancies (i.e. two oxygen vacancies separated by about 2Å) induce the formation of toluene while the benzene production does not need the presence of any oxygen vacancies. Two molybdenum based catalytic systems were chosen to test the new probe reaction : the molybdenum (sub)oxides and the metal molybdates. By the way of a new and original coupling between the probe reaction and the oxidation of propylene, we planned to correlate in real time the formation of the superficial oxygen vacancies monitored by the deoxygenation of benzoic acid and the activity in an oxidation reaction. Such an experimental coupling is a promising and a powerful tool which allows the fine characterization of the active catalytic site at work in an oxidation reaction.

Nitrous oxide is a greenhouse gas produced in large quantity by several industrial processes. Efficient means of eliminating N2O are therefore of interest. The denitrification enzyme nitrous oxide reductase (N2OR), which reduces N2O to N2 and water , has recently been shown to contain an unprecedented [Cu4-µ4S] active site. Multinuclear copper sulfide compounds are known but have not been studied in the context of modeling N2OR or as N2O reduction catalysts. The synthesis of new tetranuclear [Cu4-µ4S] compounds is proposed to model the N2OR active site.The purpose of our research is to synthesize [Cu2-µ2S] complex, which original compound of [Cu4-µ4S] complex. This can be groundwork for mimicking the copper protein active site.

The periplasmic nuclease of Vibrio vulnificus, Vvn, has been purified to homogeneity by a one step purification procedure using chromatography on a SP Sepharose column. The purified enzyme showed different mobilities on reducing and non-reducing SDS-PAGE, suggesting that disulfide bonds are involved in the maintenance of a stable tertiary conformation of the protein. Vvn randomly cleaved single and double stranded DNA and RNA, and possessed endonucleolytic activity. The enzyme exhibited an optimal activity between pH 8.0 and pH 10.0, and the optimal temperatures for the DNase and RNase activity were 40 oC ¡V 60 oC and 40 oC ¡V 50 oC, respectively. The enzymatic activity was inhibited by EDTA and EGTA, indicating that Vvn was a metalloenzyme. The DNase and RNase activity of Vvn had different requirements for divalent cations. Chemical modification studies on Vvn revealed the involvement of lysine, arginine, tryptophan and carboxylate residues in the catalytic activity of the enzyme. The extents of inactivation of the DNase and RNase activity of Vvn by modification of the carboxylate group with EDC were different. Substrate DNA and RNA protected the DNase and RNase activity of Vvn from inactivation by PLP, PGO, NBS and EDC which modified lysine, arginine, tryptophan and the carboxylate group. Mg2+ could not protect the DNase and RNase activity of Vvn against the inactivation by PLP and PGO. Whereas Mg2+ protection was observed in NBS- and EDC-mediated inactivation of the DNase but not the RNase activity of Vvn . From these results, it is postulate that there may be two distinct but overlapping active sites, for the DNase and RNase activity, respectively.

The active site of porcine kidney microsomal aminopeptidase was investigated using single, multiple and EDTA inactivation kinetic studies. Good inhibitors invariably contained a zinc-coordinating group such as the mercapto moiety, which proved to be the best ligand for aminopeptidase. Due to the potency of β -mercaptoethylamine, derivatives of this compound were examined for aminopeptidase inhibition. (S)-2-amino-4-methyl-l-pentanethiol (L-leucinthiol) exhibited the largest potency and specificity towards aminopeptidase when compared against carboxypeptidase A and thermolysin, two similar zinc-peptidases. The presence of a zinc-coordination subsite, two hydrophobic pocket subsites and a second amine-binding subsite (distinct from that responsible for substrate recognition) were discerned and the binding modes of amino acid hydroxamates and mercaptoamines compared using Yonetani-Theorell inhibition kinetics. Aminopeptidase does not show virtually any stereoselectivity between L-and D-leucine hydroxamate while greater than a 1,000-fold preference is seen for L-leucinthiol over the D isomer. Also, the amino group of mercaptoamines is crucial to the binding of these inhibitors whereas that of the hydroxamate compounds does not seen to contribute much to their binding. The differences in binding between hydroxamates and mercaptoamines are postulated to be a consequence of the product analogue nature of the former and transition state analogue character of the latter. L-leucine hydroxamate is proposed to bind in a backwards orientation while the D isomer binds in the normal substrate-like position. Similarly, L-leucinthiol is proposed to bind in the same fashion as substrate. Design of future inhibitors should endeavour to: (1) lower the pᵏₐ of the α-amino group, (2) include an extended chain structure capable of binding to additional hydrophobic pockets, (3) incorporate a second amine moiety into the structure to interact with the second amine-binding subsite and (4) replace the mercapto group with a more potent zinc ligand such as the selenol group. / Thesis / Master of Science (MSc)

Phosphotriesterase (PTE) from Pseudomonas diminuta is a zinc metalloenzyme found in soil bacteria capable of organophosphate hydrolysis at rates approaching the diffusion controlled limit. Interest in PTE for degradation of chemical warfare agents and disposal of pesticides supports the need to understand the mechanism by which it performs hydrolysis. For further mechanistic clarity, this work will provide direct confirmation of the solvent bridge identity and the protonated species resulting in loss of catalytic identity. Inhibitor and product binding to the metal center will also be addressed; as well as the evaluation of the catalytic activity of Fe(II)-substituted PTE. This work has determined that the Mn/Mn-PTE electron paramagnetic resonance (EPR) spectrum exhibits exchange coupling that is facilitated through a hydroxide bridge. Protonation of the bridging hydroxide results in the loss of the exchange coupling between the two divalent cations and the loss of catalytic activity. The reversible protonation of the bridging hydroxide has an apparent pKa of 7.3 based upon changes in the EPR spectrum of Mn/Mn-PTE with alterations in pH. The pH-rate profile for the hydrolysis of paraoxon by Mn/Mn-PTE shows the requirement of a single function group that must be unprotonated with a pKa of 7.1. The comparable pKa values are proposed to result from the protonation of the same ionizable species. The effects of inhibitor and product binding on the magnetic properties of the metal center and the hydroxyl bridge are investigated by accessing new EPR spectral features. This work concludes that the binding of inhibitor occurs at the metal center and results in an increase of non-bridged hydroxyl species. These results, in conjunction with kinetic and crystallographic data, suggest that substrate binding via the phosphoryl oxygen at the ?-metal weakens the hydroxyl bridge coordination to the ?-metal. This loss of coordination would increase the nucleophilic character of the bridge, and binding of the substrate to the metal center would result in a stronger nucleophile for hydrolysis. Lastly, Fe(II) binding and activation of apoenzyme is evaluated under anaerobic conditions. This work concludes Fe/Fe-PTE is not catalytically active, but can bind up to 2 equivalent Fe(II) ions per active site.

Recent improvements in structural genomics efforts have greatly increased the number of hypothetical proteins in the Protein Data Bank. Several computational methodologies have been developed to determine the function of these proteins but none of these methods have been able to account successfully for the diversity in the sequence and structural conformations observed in proteins that have the same function. An additional complication is the flexibility in both the protein active site and the ligand. In this dissertation, novel approaches to deal with both the ligand flexibility and the diversity in stereochemistry have been proposed. The active site analysis problem is formalized as a classification problem in which, for a given test protein, the goal is to predict the class of ligand most likely to bind the active site based on its stereochemical nature and thereby define its function. Traditional methods that have adapted a similar methodology have struggled to account for the flexibility observed in large ligands. Therefore, I propose a novel fragment-based approach to dealing with larger ligands. The advantage of the fragment-based methodology is that considering the protein-ligand interactions in a piecewise manner does not affect the active site patterns, and it also provides for a way to account for the problems associated with flexible ligands. I also propose two feature-based methodologies to account for the diversity observed in sequences and structural conformations among proteins with the same function. The feature-based methodologies provide detailed descriptions of the active site stereochemistry and are capable of identifying stereochemical patterns within the active site despite the diversity. Finally, I propose a Markov Random Field approach to combine the individual ligand fragment classifications (based on the stereochemical descriptors) into a single multi-fragment ligand class. This probabilistic framework combines the information provided by stereochemical features with the information regarding geometric constraints between ligand fragments to make a final ligand class prediction. The feature-based fragment identification methodology had an accuracy of 84% across a diverse set of ligand fragments and the mrf analysis was able to succesfully combine the various ligand fragments (identified by feature-based analysis) into one final ligand based on statistical models of ligand fragment distances. This novel approach to protein active site analysis was additionally tested on 3 proteins with very low sequence and structural similarity to other proteins in the PDB (a challenge for traditional methods) and in each of these cases, this approach successfully identified the cognate ligand. This approach addresses the two main issues that affect the accuracy of current automated methodologies in protein function assignment.

Carrageenans are sulfated polysaccharides found in the cell walls of red algae with 20 – 30 % of the dry weight coming from sulfate esters. The understanding of how heterotrophic bacteria desulfate and depolymerize carrageenan has become a rather arduous endeavor as there are 15 different classes of carrageenan distinguished by the degree of sulfation and the presence or absence of a unique galactose derivative, the 3,6-anhydro-D-galactose. The depolymerization of carrageenan requires the removal of the sulfate substituents, a role fulfilled by sulfatases, which hydrolyze sulfate esters playing a key role in the regulation of sulfation states that determine the function of sulfated biomolecules. Through structural, mechanistic, and sequence-based studies a highly conserved sulfate-binding motif has been identified among sulfatases; however, the molecular determinants for substrate specificity remain largely speculative. Additionally, the largest sulfatase family S1, requires a unique catalytic residue resulting from a post-translationally modified cysteine in order to be functional thus making them difficult to study in vitro. Using a strain of Pseudoalteromonas sp. PS47 isolated in the Boraston Lab I show that the depolymerization of carrageenan is dependent on the degree of sulfation and that recognition of the leaving group is the driving force behind S1 specificity. With little information on the recognition of sulfated biomolecules, the X-ray crystal structures of the three sulfatases from PS47; PsS1_19A, PsS1_19B, and PsS1_NC in complex with their biological substrates provides a deeper understanding of how carbohydrate specific sulfatases recognize their cognate substrate and how this recognition of the leaving group can be extended to other S1 sulfatase families. Furthermore, I show that an exo-acting glycoside hydrolase (PsGH42) requires desulfation of carrageenan oligosaccharides before it can hydrolyze the β-glycosidic linkage, a new specificity of family 42. This research demonstrates how carrageenan depolymerization is entirely dependent on the functionality and specificity of the sulfatases found within the carrageenan utilization locus. / Graduate / 2019-12-07

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